diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..439d833 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,12 @@ +^treescan_project$ +^.*\.docx$ +^README\.qmd$ +^\.claude$ +^.*\.Rproj$ +^\.Rproj\.user$ +^\.quarto$ +^data-raw$ +^README_files$ +^\.devcontainer$ +^\.github$ +^r-package-port\.md$ diff --git a/.devcontainer/Containerfile b/.devcontainer/Containerfile new file mode 100644 index 0000000..2f6675a --- /dev/null +++ b/.devcontainer/Containerfile @@ -0,0 +1,34 @@ +# Development / CI image for treescanr: rocker devcontainer + Quarto + TreeScan. +# +# TreeScan(TM) cannot be downloaded without an account, so the binary is NOT +# in the repository. Build with .devcontainer/build.sh, which copies the Linux +# tarball (treescan.X.Y.Z.tar.gz, from https://www.treescan.org) into the +# build context. The resulting image must stay PRIVATE: users of TreeScan(TM) +# must read and agree to its license (/opt/treescan/documents/eula). +FROM ghcr.io/rocker-org/devcontainer/r-ver:4.6 + +LABEL org.opencontainers.image.source="https://github.com/EpiForeSITE/TreeScan" \ + org.opencontainers.image.description="treescanr development image (includes TreeScan(TM), private)" + +# Architecture-specific variable (the TreeScan Linux binary is amd64 only) +ARG TARGETARCH + +# Install quarto-cli +RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.9.35/quarto-1.9.35-linux-${TARGETARCH}.deb && \ + dpkg -i quarto-1.9.35-linux-${TARGETARCH}.deb && \ + rm quarto-1.9.35-linux-${TARGETARCH}.deb + +# Adding R packages +RUN install2.r --error data.table tinytest roxygen2 quarto knitr rmarkdown + +# TreeScan(TM) command-line binary +COPY treescan.tar.gz /tmp/treescan.tar.gz +RUN mkdir -p /opt/treescan && \ + tar xzf /tmp/treescan.tar.gz -C /opt/treescan && \ + rm /tmp/treescan.tar.gz && \ + chmod 0755 /opt/treescan/treescan64 && \ + ln -s /opt/treescan/treescan64 /usr/local/bin/treescan64 + +ENV TREESCAN_BIN=/opt/treescan/treescan64 + +CMD ["bash"] diff --git a/.devcontainer/build.sh b/.devcontainer/build.sh new file mode 100755 index 0000000..fb4bbf7 --- /dev/null +++ b/.devcontainer/build.sh @@ -0,0 +1,25 @@ +#!/bin/sh +# Build and push the private treescanr dev image to ghcr.io. +# +# Usage: .devcontainer/build.sh [tag] +# +# Requires docker or podman, and a login to ghcr.io with a token that has the +# write:packages scope, e.g.: +# gh auth refresh -s write:packages,read:packages +# gh auth token | podman login ghcr.io -u --password-stdin +set -eu + +TARBALL=${1:?"path to the TreeScan Linux tarball"} +TAG=${2:-latest} +IMAGE=ghcr.io/epiforesite/treescanr-dev +ENGINE=$(command -v docker || command -v podman) +DIR=$(cd "$(dirname "$0")" && pwd) + +cp "$TARBALL" "$DIR/treescan.tar.gz" +trap 'rm -f "$DIR/treescan.tar.gz"' EXIT + +# The TreeScan Linux binary is x86-64 only +"$ENGINE" build --platform linux/amd64 -f "$DIR/Containerfile" \ + -t "$IMAGE:$TAG" "$DIR" + +"$ENGINE" push "$IMAGE:$TAG" diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..4ee242e --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,19 @@ +// Private image built from .devcontainer/Containerfile with .devcontainer/build.sh +// (it bundles TreeScan, which cannot be downloaded anonymously). +{ + "name": "treescanr", + "image": "ghcr.io/epiforesite/treescanr-dev:latest", + "runArgs": ["--platform=linux/amd64"], + "customizations": { + "vscode": { + "extensions": [ + "reditorsupport.r", + "rdebugger.r-debugger", + "quarto.quarto", + "github.vscode-github-actions" + ] + } + }, + "postCreateCommand": "R CMD INSTALL .", + "remoteUser": "root" +} diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..f4cfc55 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,43 @@ +# R CMD check inside the private dev image, which includes TreeScan(TM) so the +# full pipeline test (ts_run) is exercised. Pull requests from forks cannot +# pull the private image. +name: R-CMD-check + +on: + push: + branches: [main] + pull_request: + workflow_dispatch: + +permissions: + contents: read + packages: read + +jobs: + R-CMD-check: + runs-on: ubuntu-latest + container: + image: ghcr.io/epiforesite/treescanr-dev:latest + credentials: + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - name: Build + run: R CMD build . + + - name: Check + env: + _R_CHECK_CRAN_INCOMING_: false + run: R CMD check --no-manual --as-cran treescanr_*.tar.gz + + - name: Show test output + if: always() + run: find treescanr.Rcheck -name '*.Rout*' -exec cat {} \; + + - uses: actions/upload-artifact@v4 + if: failure() + with: + name: R-CMD-check-results + path: treescanr.Rcheck diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b6a4f5a --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +*.Rcheck/ +treescanr_*.tar.gz +README_files/ +.Rproj.user/ +.quarto/ +.devcontainer/*.tar.gz +.devcontainer/*.bz2 diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..e5c8bf7 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,23 @@ +Package: treescanr +Title: Tree-Based Scan Statistics for Syndromic Surveillance with 'TreeScan' +Version: 0.0.1 +Authors@R: + person("George G.", "Vega Yon", , "g.vegayon@gmail.com", role = c("aut", "cre")) +Description: A lightweight pipeline to prepare emergency department visit data, + build incident-diagnosis count files, write parameter files, and run the + 'TreeScan' command-line software on ICD-10-CM trees. Ported from the + epiENGAGE TreeScan implementation scripts. +License: MIT + file LICENSE +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +Depends: R (>= 4.1.0) +Imports: + data.table, + utils +Suggests: + tinytest, + quarto +VignetteBuilder: quarto +SystemRequirements: TreeScan (>= 2.4.1) command-line binary + (https://www.treescan.org), Quarto (for vignettes) +Config/roxygen2/version: 8.0.0 diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..77f56e0 --- /dev/null +++ b/LICENSE @@ -0,0 +1,2 @@ +YEAR: 2026 +COPYRIGHT HOLDER: treescanr authors diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..7f96c3d --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,17 @@ +# Generated by roxygen2: do not edit by hand + +S3method(print,ts_prm) +S3method(print,ts_result) +export(ts_binary) +export(ts_counts) +export(ts_ineligible_pattern) +export(ts_prm_get) +export(ts_prm_read) +export(ts_prm_set) +export(ts_prm_template) +export(ts_prm_write) +export(ts_results) +export(ts_run) +export(ts_visits) +export(ts_visits_nssp) +import(data.table) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..fb91458 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,8 @@ +# treescanr 0.0.1 + +* Initial MVP: `ts_visits()`, `ts_visits_nssp()`, `ts_counts()`, `ts_prm_*()`, + `ts_binary()`, `ts_run()`, and `ts_results()`, ported from the scripts in + `treescan_project/code/` (steps 2 to 5). + +* Private devcontainer image (`ghcr.io/epiforesite/treescanr-dev`) with + TreeScan 2.4.1, used by the `R-CMD-check` GitHub Action. diff --git a/R/binary.R b/R/binary.R new file mode 100644 index 0000000..3f26c5c --- /dev/null +++ b/R/binary.R @@ -0,0 +1,36 @@ +#' Locate the TreeScan command-line binary +#' +#' Checks that the TreeScan binary exists and is executable. The non-graphical +#' (command-line) version of TreeScan can be downloaded from +#' . +#' +#' @param path Path to the binary (e.g., `treescan64` or `treescan64.exe`). +#' Defaults to the `treescanr.binary` option, then the `TREESCAN_BIN` +#' environment variable, then `treescan64` on the `PATH`. +#' @return The normalized path to the binary. +#' @export +#' @examples +#' \dontrun{ +#' options(treescanr.binary = "~/TreeScan/treescan64") +#' ts_binary() +#' } +ts_binary <- function( + path = getOption("treescanr.binary", Sys.getenv("TREESCAN_BIN")) +) { + if (is.null(path) || !nzchar(path)) + path <- Sys.which(c("treescan64", "treescan64.exe"))[1L] + + if (is.na(path) || !nzchar(path) || !file.exists(path)) + stop( + "TreeScan binary not found. Download the command-line version from ", + "https://www.treescan.org/download_treescan.html and set ", + "`options(treescanr.binary = )` or the TREESCAN_BIN environment ", + "variable.", call. = FALSE + ) + + path <- normalizePath(path, winslash = "/", mustWork = TRUE) + if (.Platform$OS.type == "unix" && file.access(path, 1L) != 0L) + Sys.chmod(path, mode = "0755") + + path +} diff --git a/R/counts.R b/R/counts.R new file mode 100644 index 0000000..b3f6a2f --- /dev/null +++ b/R/counts.R @@ -0,0 +1,257 @@ +#' Build a TreeScan count file of incident diagnoses +#' +#' Port of the epiENGAGE count-file algorithm (Ramona Lall and Alison +#' Levin-Rector, NYC DOHMH). Starting from visit-level data it: +#' +#' 1. splits diagnosis codes and removes ineligible ones (`ineligible`); +#' 2. keeps codes present in the tree and looks up their level-3 parent; +#' 3. keeps only **incident** diagnoses: a level-3 group seen for the same +#' patient within `lookback_days` is dropped, with special handling of +#' admissions; +#' 4. restricts to the `study_days` ending on `end_date`; +#' 5. keeps the rarest code per level-3 group within a visit (random +#' tie-break, see `seed`); +#' 6. aggregates counts by node (`0-` = not admitted, `1-` = admitted) and day. +#' +#' `visits` should cover `study_days + lookback_days` so every day in the study +#' period has a full lookback. +#' +#' @param visits Output of [ts_visits()]. +#' @param end_date Last day of the study period (e.g., `Sys.Date() - lag`). +#' @param tree_wide Wide-format tree (path or `data.frame`) with columns +#' `Name1` (code without dot), `Level2`, and `Level3`. +#' @param study_days Length of the study period in days. +#' @param lookback_days Window used to define incident diagnoses. +#' @param ineligible Regular expression of codes to exclude. +#' @param seed Optional seed for the tie-break. The global RNG state is +#' restored on exit. +#' @return A `data.table` with columns `code`, `date` (`yyyy/mm/dd`), and `n`, +#' with attributes `end_date`, `study_days`, and `incident` (the incident +#' visit-code table, one row per `date`, `key`, `dispo`, `code`). +#' @export +#' @examples +#' ex <- function(f) system.file("extdata", f, package = "treescanr") +#' counts <- read.csv(ex("toy_visits.csv")) |> +#' ts_visits() |> +#' ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) +#' head(counts) +ts_counts <- function( + visits, + end_date, + tree_wide, + study_days = 90L, + lookback_days = 365L, + ineligible = ts_ineligible_pattern(), + seed = NULL +) { + if (!is.null(seed)) { + old_seed <- get0(".Random.seed", envir = globalenv(), inherits = FALSE) + on.exit( + if (is.null(old_seed)) rm(".Random.seed", envir = globalenv()) + else assign(".Random.seed", old_seed, envir = globalenv()) + ) + set.seed(seed) + } + + end_date <- as.Date(end_date) + visits <- as.data.table(visits)[, list(key, date, diagnosis_codes, severity)] + visits[, `:=`( + date = as.Date(date), + diagnosis_codes = trimws(gsub("\\s+", " ", diagnosis_codes)) + )] + + if (!is.data.frame(tree_wide)) + tree_wide <- fread(tree_wide, select = c("Name1", "Level2", "Level3")) + tree_wide <- as.data.table(tree_wide)[ + !is.na(Level2) & !is.na(Level3), list(Name1, Level2, Level3) + ] + + # One row per visit-code, most severe outcome per patient-day + long <- .explode(visits, "diagnosis_codes", " ") + long[, code := gsub(".", "", gsub("\\s+", "", code), fixed = TRUE)] + long <- long[!is.na(code) & code != "" & !grepl("^[0-9]", code) & + grepl("\\d", code)] + long[, severity := if ("A" %in% severity) "A" else "V", by = list(date, key)] + long <- unique(long) + long <- long[!grepl(ineligible, code)] + long <- merge(long, tree_wide[, list(Name1, Level2, Level3)], + by.x = "code", by.y = "Name1", sort = TRUE) + + # One row per visit + all_visits <- long[, list( + Level3 = paste(Level3, collapse = ","), + code = paste(code, collapse = ",") + ), by = list(date, key, severity)] + all_visits[, Level3 := gsub("-", "_", Level3, fixed = TRUE)] + all_visits[, visit_count := .N, by = key] + + single <- all_visits[visit_count == 1, list(date, key, severity, code)] + multiple <- all_visits[visit_count >= 2, list(date, key, severity, code, Level3)] + multiple <- multiple[, .incident(.SD, lookback_days), by = key] + + # Replace non-incident codes by REMOVE + multiple[, Level3 := mapply(function(l3, s) gsub(s, "REMOVE", l3), + Level3, searchf, USE.NAMES = FALSE)] + multiple[, code := mapply(function(cd, l3) { + cd <- strsplit(cd, ",", fixed = TRUE)[[1L]] + cd[strsplit(l3, ",", fixed = TRUE)[[1L]] == "REMOVE"] <- "REMOVE" + paste0(cd, collapse = ",") + }, code, Level3, USE.NAMES = FALSE)] + + cohort <- rbindlist(list(single, multiple[, list(date, key, severity, code)])) + study <- cohort[date >= end_date - study_days + 1 & date <= end_date] + study <- .explode(study, "code", ",")[code != "REMOVE"] + + # Keep the rarest code per level-3 group within a visit + all_codes <- unlist(strsplit(visits$diagnosis_codes, " ", fixed = TRUE), + use.names = FALSE) + all_codes <- gsub(".", "", all_codes[all_codes != ""], fixed = TRUE) + freq <- as.data.table(table(all_codes)) + setnames(freq, c("code", "Freq")) + + study <- merge(study, freq, by = "code", all.x = TRUE, sort = FALSE) + study <- merge(study, tree_wide[, list(Name1, Level3)], by.x = "code", + by.y = "Name1", all.x = TRUE, sort = FALSE) + study <- .keep_rarest(study) + + incident <- study[, list(date = as.Date(date), key = as.character(key), + dispo = severity, code)] + + counts <- study[, list(n = sum(n)), by = list(code, severity, date)] + counts[nchar(code) >= 4L, + code := paste0(substr(code, 1L, 3L), ".", substr(code, 4L, nchar(code)))] + counts[, code := paste0(fifelse(severity == "V", "0-", "1-"), trimws(code))] + counts <- counts[, list( + code, date = format(as.Date(date), "%Y/%m/%d"), n = as.integer(n) + )] + + setattr(counts, "end_date", end_date) + setattr(counts, "study_days", as.integer(study_days)) + setattr(counts, "incident", incident) + counts[] +} + +#' @rdname ts_counts +#' @details `ts_ineligible_pattern()` returns the default exclusions: COVID-19, +#' influenza, allergic rhinitis, asthma, anaphylaxis, most Z codes, neoplasms, +#' and congenital malformations. +#' @export +ts_ineligible_pattern <- function() { + paste( + "U071|J09|J10|J11|\\bJ301\\b|\\bJ302\\b|\\bJ3089\\b|\\bJ309\\b|J45|T7840", + "Z0|Z10|Z1152|Z12|Z13|Z14|Z15|Z17|Z18|Z19|Z21|Z28|Z30|Z3|Z4|Z50|Z51|Z52|Z53|Z55|Z56|Z62|Z63|Z64|Z66|Z67|Z68|Z76|Z78|Z8|Z90|Z91|Z92|Z93|Z94|Z95|Z96|Z97|Z98", + "\\bC|\\bD0|\\bD1|\\bD2|\\bD3|\\bD4|\\bQ", + sep = "|" + ) +} + +# Split a delimited column into one row per element +.explode <- function(dt, col, split) { + parts <- strsplit(dt[[col]], split, fixed = TRUE) + out <- dt[rep.int(seq_len(.N), lengths(parts))] + out[, (col) := NULL] + out[, code := unlist(parts, use.names = FALSE)] + out +} + +# Search strings of non-incident level-3 codes for one patient (rows as +# ordered in the data). Port of `process_patient_faster()`. +.incident <- function(patient_data, lookback_days = 365) { + n <- nrow(patient_data) + dates_num <- as.numeric(patient_data$date) + severity <- patient_data$severity + level3 <- patient_data$Level3 + + search <- search2 <- search3 <- searchf <- rep(NA_character_, n) + level3_split_space <- strsplit(gsub(",", " ", level3, fixed = TRUE), " ", fixed = TRUE) + level3_split_comma <- strsplit(level3, ",", fixed = TRUE) + + # search: level-3 codes from prior rows within the lookback + for (i in seq_len(n)) { + prior_idx <- which(seq_len(n) < i & abs(dates_num - dates_num[i]) <= lookback_days) + if (!length(prior_idx)) { + search[i] <- "NONE" + } else { + prior_codes <- unlist(level3_split_space[prior_idx], use.names = FALSE) + search[i] <- paste0(unique(prior_codes[!is.na(prior_codes)]), collapse = "|") + } + } + + admit_idx <- which(severity == "A") + n_admit <- length(admit_idx) + + if (n_admit >= 1L) { + admit_dates <- dates_num[admit_idx] + + # search2: admit codes propagated to visits in the preceding lookback + for (i in seq_len(n_admit)) { + this_row <- admit_idx[i] + this_date <- dates_num[this_row] + + if (!any(seq_len(n_admit) < i & abs(admit_dates - admit_dates[i]) <= lookback_days)) + search2[this_row] <- "NONE" + + prior_visit_idx <- which(dates_num - this_date < 0 & + dates_num - this_date >= -lookback_days & + severity == "V") + if (length(prior_visit_idx)) { + # NOTE: indexes search2 by `i` (not `this_row`), as in the original + existing <- unlist(strsplit(search2[i], "\\|"), use.names = FALSE) + new_codes <- level3_split_comma[[this_row]] + search2[prior_visit_idx] <- paste0( + unique(c(existing[!is.na(existing)], new_codes[!is.na(new_codes)])), + collapse = "|" + ) + } + } + + # search3: admit codes not seen in prior admits within the lookback + if (n_admit >= 2L) { + for (i in 2:n_admit) { + this_row <- admit_idx[i] + prior_rows <- admit_idx[admit_dates - dates_num[this_row] < 0 & + admit_dates - dates_num[this_row] >= -lookback_days] + prior_codes <- unlist(strsplit(paste0(level3[prior_rows], collapse = ","), + ",", fixed = TRUE), use.names = FALSE) + search3[this_row] <- paste0(setdiff(level3_split_comma[[this_row]], prior_codes), + collapse = "|") + } + } + } + + for (i in seq_len(n)) { + if (!is.na(search3[i])) + search[i] <- gsub(search3[i], "", search[i]) + + searchf[i] <- if (is.na(search2[i])) { + search[i] + } else if (search2[i] != "NONE" && search[i] == "NONE") { + search2[i] + } else if (search2[i] == "NONE") { + "NONE" + } else { + paste0(c(search[i], search2[i]), collapse = "|") + } + } + + patient_data$searchf <- searchf + patient_data +} + +# One code per (key, date, Level3): the least frequent, ties broken at random +.keep_rarest <- function(study) { + setorder(study, key, date, Level3, Freq) + study[, n := seq_len(.N), by = list(key, date, Level3)] + + ties <- study[, .SD[.N >= 2L & Freq == Freq[1L]], by = list(key, date, Level3)] + ties <- ties[, { + tmp <- copy(.SD) + tmp[, n := sample(seq_along(Freq), size = .N, replace = FALSE)] + tmp[n == 1L] + }, by = list(key, date, Level3)] + + singles <- study[, .SD[!(.N >= 2L & Freq == Freq[1L]) & n == 1L], + by = list(key, date, Level3)] + + rbindlist(list(singles, ties), use.names = TRUE, fill = TRUE) +} diff --git a/R/prm.R b/R/prm.R new file mode 100644 index 0000000..4882ef5 --- /dev/null +++ b/R/prm.R @@ -0,0 +1,95 @@ +#' TreeScan parameter files +#' +#' A parameter file (`.prm`) is stored as its raw lines (comments included) +#' with class `ts_prm`. Values are set by key name, without needing to know +#' the `[Section]` they belong to. +#' +#' @param path Path to a `.prm` file. +#' @param prm A `ts_prm` object. +#' @param ... Named values to set, e.g. `"monte-carlo-replications" = 999`. +#' Dates are formatted as `yyyy/mm/dd`, logicals as `y`/`n`. +#' @return `ts_prm_read()`, `ts_prm_template()`, and `ts_prm_set()` return a +#' `ts_prm` object. `ts_prm_get()` returns a character value. +#' `ts_prm_write()` returns `path` invisibly. +#' @name ts_prm +#' @examples +#' prm <- ts_prm_template() |> +#' ts_prm_set("monte-carlo-replications" = 999) +#' ts_prm_get(prm, "monte-carlo-replications") +#' ts_prm_write(prm, tempfile(fileext = ".prm")) +NULL + +#' @rdname ts_prm +#' @export +ts_prm_read <- function(path) { + structure(readLines(path, warn = FALSE), class = "ts_prm") +} + +#' @rdname ts_prm +#' @details `ts_prm_template()` returns the template bundled with the package +#' (TreeScan v2.4.1, tree-temporal Poisson scan, 9,999 replications). +#' @export +ts_prm_template <- function() { + ts_prm_read(system.file("extdata", "Parameter_File_template.prm", + package = "treescanr")) +} + +#' @rdname ts_prm +#' @export +ts_prm_set <- function(prm, ...) { + values <- list(...) + if (length(values) && (is.null(names(values)) || any(!nzchar(names(values))))) + stop("All values passed to `ts_prm_set()` must be named.", call. = FALSE) + + for (key in names(values)) { + pattern <- paste0("^", key, "=") + idx <- grep(pattern, prm) + if (!length(idx)) + stop("Unknown TreeScan parameter: '", key, "'.", call. = FALSE) + prm[idx] <- paste0(key, "=", .prm_value(values[[key]])) + } + + prm +} + +#' @rdname ts_prm +#' @param key Parameter name. +#' @export +ts_prm_get <- function(prm, key) { + line <- grep(paste0("^", key, "="), prm, value = TRUE) + if (!length(line)) + stop("Unknown TreeScan parameter: '", key, "'.", call. = FALSE) + sub("^[^=]*=", "", line[1L]) +} + +#' @rdname ts_prm +#' @export +ts_prm_write <- function(prm, path) { + writeLines(unclass(prm), path) + invisible(path) +} + +#' @export +print.ts_prm <- function(x, ...) { + x <- unclass(x) + cat(x[!grepl("^\\s*;", x) & nzchar(trimws(x))], sep = "\n") + invisible(x) +} + +.prm_value <- function(x) { + if (inherits(x, "Date")) + return(format(x, "%Y/%m/%d")) + if (is.logical(x)) + return(ifelse(x, "y", "n")) + paste(x, collapse = ",") +} + +.prm_range <- function(from, to) { + paste0("[", .prm_value(as.Date(from)), ",", .prm_value(as.Date(to)), "]") +} + +# TreeScan wants forward slashes; keep leading "//" for UNC paths +.prm_path <- function(path) { + path <- normalizePath(path, winslash = "/", mustWork = FALSE) + if (grepl("^//", path)) sub("^/+", "//", path) else path +} diff --git a/R/results.R b/R/results.R new file mode 100644 index 0000000..3216661 --- /dev/null +++ b/R/results.R @@ -0,0 +1,54 @@ +#' Read TreeScan results +#' +#' Reads the CSV results written by TreeScan, e.g., from a previous +#' [ts_run()] stored in a persistent directory. +#' +#' @param path A directory created by [ts_run()] or a TreeScan results `.csv`. +#' @return A `ts_result` object: a list with `results` (a `data.frame`, one row +#' per cut, as written by TreeScan), `dir`, `files`, and `prm` (the +#' parameter file used, if found). +#' @export +#' @examples +#' \dontrun{ +#' dir <- tools::R_user_dir("treescanr", "data") +#' ts_results(file.path(dir, "2026-09-23", "lag1")) +#' } +ts_results <- function(path) { + if (dir.exists(path)) { + dir <- path + csv <- file.path(dir, "results.csv") + } else { + dir <- dirname(path) + csv <- path + } + if (!file.exists(csv)) + stop("TreeScan results not found: ", csv, call. = FALSE) + + prm_file <- file.path(dir, "parameters.prm") + structure( + list( + results = utils::read.csv(csv, check.names = TRUE), + dir = normalizePath(dir, winslash = "/"), + files = list.files(dir, full.names = TRUE), + prm = if (file.exists(prm_file)) ts_prm_read(prm_file) + ), + class = "ts_result" + ) +} + +#' @export +print.ts_result <- function(x, n = 10L, ...) { + res <- x$results + cat("TreeScan results:", nrow(res), "cuts\n") + cat("Directory:", x$dir, "\n") + if (nrow(res)) { + if ("P.value" %in% names(res)) + res <- res[order(res$P.value), , drop = FALSE] + cols <- intersect(c("Node.Identifier", "Time.Window.Start", "Time.Window.End", + "Cases.in.Window", "Expected.Cases", "P.value", + "Recurrence.Interval"), names(res)) + if (length(cols)) res <- res[, cols, drop = FALSE] + print(utils::head(res, n), row.names = FALSE) + } + invisible(x) +} diff --git a/R/run.R b/R/run.R new file mode 100644 index 0000000..82d5910 --- /dev/null +++ b/R/run.R @@ -0,0 +1,85 @@ +#' Run TreeScan on a count file +#' +#' Writes the count file and a parameter file into `dir`, runs the TreeScan +#' binary, and reads the results. The data time range and temporal windows +#' are set from the `end_date` and `study_days` stored in `counts`. +#' +#' @param counts Output of [ts_counts()]. +#' @param tree Path to the TreeScan tree file (long format, e.g. +#' `Tree_File_2027.csv`). +#' @param dir Output directory. Defaults to a temporary directory; for routine +#' use pass a persistent location such as +#' `file.path(tools::R_user_dir("treescanr", "data"), Sys.Date(), "lag1")`. +#' @param prm A `ts_prm` object used as template (see [ts_prm_template()]). +#' @param not_evaluated Optional path to a file of nodes not to evaluate +#' (e.g. `Do_not_evaluate_nodes.csv`). +#' @param processes Number of parallel processes used by TreeScan. +#' @param binary Path to the TreeScan binary (see [ts_binary()]). +#' @return A `ts_result` object (see [ts_results()]). +#' @export +#' @examples +#' \dontrun{ +#' dir <- tools::R_user_dir("treescanr", "data") +#' res <- read.csv("visits.csv") |> +#' ts_visits() |> +#' ts_counts(end_date = Sys.Date() - 1, tree_wide = "Tree_File_2026_wide_format.txt") |> +#' ts_run(tree = "Tree_File_2027.csv", dir = file.path(dir, Sys.Date(), "lag1")) +#' res +#' } +ts_run <- function( + counts, + tree, + dir = tempfile("treescanr_"), + prm = ts_prm_template(), + not_evaluated = NULL, + processes = 2L, + binary = ts_binary() +) { + end_date <- attr(counts, "end_date") + study_days <- attr(counts, "study_days") + if (is.null(end_date) || is.null(study_days)) + stop("`counts` must be the output of `ts_counts()`.", call. = FALSE) + if (!file.exists(tree)) + stop("Tree file not found: ", tree, call. = FALSE) + + dir.create(dir, recursive = TRUE, showWarnings = FALSE) + dir <- normalizePath(dir, winslash = "/") + files <- list( + counts = file.path(dir, "counts.txt"), + prm = file.path(dir, "parameters.prm"), + results = file.path(dir, "results.txt"), + log = file.path(dir, "treescan.log") + ) + + utils::write.table( + counts[, c("code", "date", "n")], files$counts, sep = "\t", + row.names = FALSE, quote = FALSE, fileEncoding = "ASCII" + ) + + range <- .prm_range(end_date - study_days, end_date) + prm <- ts_prm_set( + prm, + "tree-filename" = .prm_path(tree), + "count-filename" = .prm_path(files$counts), + "results-filename" = .prm_path(files$results), + "data-time-range" = range, + "window-start-range" = range, + "window-end-range" = range, + "parallel-processes" = as.integer(processes), + "restrict-evaluated-nodes" = !is.null(not_evaluated), + "not-evaluated-nodes-file" = if (is.null(not_evaluated)) "" else + .prm_path(not_evaluated) + ) + ts_prm_write(prm, files$prm) + + status <- system2(binary, shQuote(files$prm), stdout = files$log, + stderr = files$log) + if (!identical(as.integer(status), 0L)) { + log <- readLines(files$log, warn = FALSE) + stop("TreeScan failed (exit status ", status, "). Last lines of ", + files$log, ":\n", paste(utils::tail(log, 20L), collapse = "\n"), + call. = FALSE) + } + + ts_results(dir) +} diff --git a/R/treescanr-package.R b/R/treescanr-package.R new file mode 100644 index 0000000..b96efca --- /dev/null +++ b/R/treescanr-package.R @@ -0,0 +1,14 @@ +#' treescanr: Tree-Based Scan Statistics for Syndromic Surveillance +#' +#' A pipeable workflow around the 'TreeScan' command-line software: +#' [ts_visits()] -> [ts_counts()] -> [ts_run()] -> [ts_results()]. +#' +#' @import data.table +#' @keywords internal +"_PACKAGE" + +# data.table non-standard evaluation +utils::globalVariables(c( + ".", ".N", ".SD", "code", "date", "key", "severity", "diagnosis_codes", + "Level2", "Level3", "Name1", "visit_count", "searchf", "Freq", "n" +)) diff --git a/R/visits.R b/R/visits.R new file mode 100644 index 0000000..a656764 --- /dev/null +++ b/R/visits.R @@ -0,0 +1,64 @@ +#' Standardize visit-level data +#' +#' Turns visit-level emergency department data (one row per visit) into the +#' input expected by [ts_counts()]: a `data.table` with columns `key` +#' (patient identifier), `date`, `diagnosis_codes` (space-separated ICD-10-CM +#' codes), and `severity` (`"A"` = admitted, `"V"` = visit only). +#' +#' @param data A `data.frame` with one row per visit. +#' @param key,date,codes,admitted Names of the columns in `data` holding the +#' patient identifier, visit date (or date-time), diagnosis codes (separated +#' by spaces, commas, or semicolons), and admission status (logical, 0/1, or +#' `"A"`/`"V"`). Missing admission status is treated as not admitted. +#' @return A `data.table`. +#' @export +#' @examples +#' visits <- read.csv(system.file("extdata", "toy_visits.csv", package = "treescanr")) +#' ts_visits(visits) |> head() +ts_visits <- function( + data, + key = "key", + date = "date", + codes = "diagnosis_codes", + admitted = "severity" +) { + missing_cols <- setdiff(c(key, date, codes, admitted), names(data)) + if (length(missing_cols)) + stop("Columns not found in `data`: ", paste(missing_cols, collapse = ", "), + call. = FALSE) + + adm <- data[[admitted]] + if (!(is.character(adm) && all(adm %in% c("A", "V", NA)))) + adm <- ifelse(as.logical(as.integer(adm)) %in% TRUE, "A", "V") + adm[is.na(adm)] <- "V" + + dx <- strsplit(as.character(data[[codes]]), "[;,[:space:]]+") + dx <- vapply(dx, function(x) { + x <- unique(x[!is.na(x) & nzchar(x) & x != "NA"]) + if (length(x)) paste(x, collapse = " ") else NA_character_ + }, character(1)) + + out <- as.data.table(list( + key = as.character(data[[key]]), + date = as.Date(data[[date]]), + diagnosis_codes = dx, + severity = adm + )) + + out[!is.na(diagnosis_codes) & !is.na(date)] +} + +#' @rdname ts_visits +#' @details `ts_visits_nssp()` is a shortcut for NSSP ESSENCE DataDetails +#' extracts (columns `C_Unique_Patient_ID`, `C_Visit_Date_Time`, +#' `DischargeDiagnosis`, and `HasBeenAdmitted`). +#' @export +ts_visits_nssp <- function(data) { + ts_visits( + data, + key = "C_Unique_Patient_ID", + date = "C_Visit_Date_Time", + codes = "DischargeDiagnosis", + admitted = "HasBeenAdmitted" + ) +} diff --git a/README.md b/README.md index bcd6216..2e1e5d8 100644 --- a/README.md +++ b/README.md @@ -1,104 +1,94 @@ -## TreeScan for the World Cup -# 🌳 TreeScan Implementation -A full pipeline for running TreeScan-based analyses using R and the TreeScan software. -This project provides a structured workflow to prepare data, run TreeScan, and process results using an R-based pipeline. + -
+# treescanr -## 📦 Installation -### 1. Download this Repository -* Click the green **Code** button on GitHub -* Select **Download ZIP** -* Extract the ZIP file -* Locate the `treescan_project` subfolder -* Move `treescan_project` to your desired working directory +**treescanr** is a lightweight R interface to +[TreeScan](https://www.treescan.org), the tree-based scan statistic, for +syndromic surveillance with ICD-10-CM coded emergency department visits. +It packages the core of the epiENGAGE TreeScan implementation (see +`treescan_project/` for the original scripts) as a small set of pipeable +functions: -
+| Function | Purpose | +|----|----| +| `ts_visits()`, `ts_visits_nssp()` | Standardize visit-level data | +| `ts_counts()` | Build the count file of incident diagnoses | +| `ts_prm_template()`, `ts_prm_set()` | Build the TreeScan parameter file | +| `ts_run()` | Run TreeScan and read the results | +| `ts_results()` | Reload results from a previous run | -### 2. Install RStudio +## Installation -Download and install RStudio: -https://posit.co/download/rstudio-desktop/ - -
- -### 3. Install TreeScan - -Download TreeScan from: -https://www.treescan.org/download_treescan.html - -**⚠️ Important setup details:** - -* You must create an account before downloading -* Choose version based on your environment: - * **Windows** → if running locally - * **Linux** → if running on a server -* Select the **NON-graphical version** - * The standard (graphical) version may cause IT/access issues - -
+``` r +# install.packages("remotes") +remotes::install_github("EpiForeSITE/TreeScan") +``` -### 4. Place TreeScan in Project Folder +You also need the **command-line (non-graphical)** version of TreeScan +(\>= 2.4.1), available at + (account required). +Tell treescanr where it is: -After downloading: +``` r +options(treescanr.binary = "~/TreeScan/treescan64") # or set TREESCAN_BIN +``` -Move the TreeScan files into the correct subfolder inside `treescan_project`: -| Environment | Folder | -| ----------- | ------ | -| Windows | TS_windows/ | -| Linux | TS_linux/ | +## Quick start -
+The package ships a small synthetic dataset with a cluster of viral +gastroenteritis (A08.4) in the last days of June 2026: -## 🚀 Running the Pipeline -### 1. Open the Project in RStudio +``` r +library(treescanr) +ex <- function(f) system.file("extdata", f, package = "treescanr") -* Launch RStudio -* In the bottom-right file explorer: - * Navigate to: `treescan_project/code/` - * Open: `run_full_pipeline.R` +counts <- read.csv(ex("toy_visits.csv")) |> + ts_visits() |> + ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) -
+head(counts) +``` -### 2. Configure the Script + code date n + + 1: 0-A08.4 2026/06/22 4 + 2: 0-R11.2 2026/06/22 4 + 3: 0-A08.4 2026/06/21 3 + 4: 0-R11.2 2026/06/21 3 + 5: 0-A08.4 2026/06/25 4 + 6: 0-R11.2 2026/06/25 4 -Before running, update the following: +Running TreeScan takes one more step. Since treescanr is meant for +routine (daily or weekly) use, write the results to a **persistent +location** so you can reload them in later sessions: -**Set Working Directory** +``` r +dir <- tools::R_user_dir("treescanr", "data") -Update line 4 to match your local path: +res <- counts |> + ts_run(tree = ex("toy_tree.csv"), dir = file.path(dir, "2026-06-30", "lag1")) +res -```r -setwd("~/TreeScan-implementation/treescan_project") +# Later, in a new session +ts_results(file.path(dir, "2026-06-30", "lag1")) ``` -Replace with wherever you saved treescan_project. +See `vignette("treescanr")` for a complete routine workflow. -**Set Execution Mode** +## Development -Modify these variables depending on your setup: +A [devcontainer](.devcontainer/) with R, Quarto, and TreeScan is +available as the **private** image `ghcr.io/epiforesite/treescanr-dev` +(developers only, since TreeScan requires accepting its license). The +same image runs `R CMD check` in GitHub Actions, including the tests +that call TreeScan. To rebuild it after downloading a new TreeScan Linux +release: -```r -server <- FALSE # Set to TRUE if running on a server -first_time <- TRUE # Set to FALSE after first run +``` sh +.devcontainer/build.sh ~/Downloads/treescan.2.4.1.tar.gz ``` -
- -### 3. Run the Pipeline - -* Run the script in RStudio - -The pipeline will: -* Execute TreeScan -* Process outputs -* Complete the full analysis workflow - -
- -## ⚠️ Notes -* Ensure the correct TreeScan version is placed in the matching folder (`TS_windows` or `TS_linux`) -* Using the **non-graphical version is required** -* Incorrect working directory paths will cause errors +Please cite TreeScan and its methodology papers when publishing results; +see the TreeScan User Guide. diff --git a/README.qmd b/README.qmd new file mode 100644 index 0000000..a17d080 --- /dev/null +++ b/README.qmd @@ -0,0 +1,90 @@ +--- +format: gfm +--- + + + +```{r} +#| include: false +devtools::load_all(quiet = TRUE) +``` + +# treescanr + +**treescanr** is a lightweight R interface to +[TreeScan](https://www.treescan.org), the tree-based scan statistic, for +syndromic surveillance with ICD-10-CM coded emergency department visits. It +packages the core of the epiENGAGE TreeScan implementation (see +`treescan_project/` for the original scripts) as a small set of pipeable +functions: + +| Function | Purpose | +|---|---| +| `ts_visits()`, `ts_visits_nssp()` | Standardize visit-level data | +| `ts_counts()` | Build the count file of incident diagnoses | +| `ts_prm_template()`, `ts_prm_set()` | Build the TreeScan parameter file | +| `ts_run()` | Run TreeScan and read the results | +| `ts_results()` | Reload results from a previous run | + +## Installation + +```r +# install.packages("remotes") +remotes::install_github("EpiForeSITE/TreeScan") +``` + +You also need the **command-line (non-graphical)** version of TreeScan +(>= 2.4.1), available at +(account required). Tell treescanr where it is: + +```r +options(treescanr.binary = "~/TreeScan/treescan64") # or set TREESCAN_BIN +``` + +## Quick start + +The package ships a small synthetic dataset with a cluster of viral +gastroenteritis (A08.4) in the last days of June 2026: + +```{r} +library(treescanr) +ex <- function(f) system.file("extdata", f, package = "treescanr") + +counts <- read.csv(ex("toy_visits.csv")) |> + ts_visits() |> + ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) + +head(counts) +``` + +Running TreeScan takes one more step. Since treescanr is meant for routine +(daily or weekly) use, write the results to a **persistent location** so you +can reload them in later sessions: + +```r +dir <- tools::R_user_dir("treescanr", "data") + +res <- counts |> + ts_run(tree = ex("toy_tree.csv"), dir = file.path(dir, "2026-06-30", "lag1")) +res + +# Later, in a new session +ts_results(file.path(dir, "2026-06-30", "lag1")) +``` + +See `vignette("treescanr")` for a complete routine workflow. + +## Development + +A [devcontainer](.devcontainer/) with R, Quarto, and TreeScan is available as +the **private** image `ghcr.io/epiforesite/treescanr-dev` (developers only, +since TreeScan requires accepting its license). The same image runs +`R CMD check` in GitHub Actions, including the tests that call TreeScan. +To rebuild it after downloading a new TreeScan Linux release: + +```sh +.devcontainer/build.sh ~/Downloads/treescan.2.4.1.tar.gz +``` + +Please cite TreeScan and its methodology papers when publishing results; see +the TreeScan User Guide. diff --git a/data-raw/toy_data.R b/data-raw/toy_data.R new file mode 100644 index 0000000..d9dbb4f --- /dev/null +++ b/data-raw/toy_data.R @@ -0,0 +1,52 @@ +# Generates the small synthetic datasets in inst/extdata from the full tree +# files in treescan_project/data. Run from the repository root. +library(data.table) + +blocks <- c("A00-A09", "J00-J06", "R10-R19", "R50-R69") + +# Wide tree: all codes in the selected blocks +wide <- fread("treescan_project/data/Tree_File_2026_wide_format.txt") +wide <- wide[Level3 %in% blocks] +fwrite(wide, "inst/extdata/toy_tree_wide.txt", sep = "\t") + +# Long tree (TreeScan input): the selected nodes and all their ancestors +tree <- fread("treescan_project/data/Tree_File_2027.csv") +nodes <- c(outer(c("0-", "1-", "2-"), c(wide$Name, blocks, "Root"), paste0)) +repeat { + more <- setdiff(tree[child %in% nodes & parent != "", parent], nodes) + if (!length(more)) break + nodes <- c(nodes, more) +} +tree <- tree[child %in% nodes] +# Empty fields must be written empty (not as "") or TreeScan reads them as node ids +for (col in names(tree)) set(tree, which(tree[[col]] == ""), col, NA) +fwrite(tree, "inst/extdata/toy_tree.csv", na = "") + +# Synthetic visits: 16 months ending 2026-06-30 with a cluster of viral +# gastroenteritis (A08.4) in the last 10 days +set.seed(20260623) +codes <- c(sample(wide$Name, 60), "J45.909", "Z00.00", "U07.1") +dates <- seq(as.Date("2025-03-01"), as.Date("2026-06-30"), by = "day") + +n_pat <- 2000 +n_vis <- sample(1:4, n_pat, replace = TRUE, prob = c(.6, .25, .1, .05)) +visits <- as.data.table(list( + key = rep(sprintf("P%05d", seq_len(n_pat)), n_vis), + date = sample(dates, sum(n_vis), replace = TRUE) +)) +visits[, diagnosis_codes := vapply( + sample(1:3, .N, replace = TRUE), + function(k) paste(sample(codes, k), collapse = " "), character(1) +)] + +cluster <- as.data.table(list( + key = sprintf("C%05d", 1:40), + date = sample(as.Date("2026-06-21") + 0:9, 40, replace = TRUE), + diagnosis_codes = "A08.4 R11.2" +)) +visits <- rbind(visits, cluster) +visits[, severity := sample(c("A", "V"), .N, replace = TRUE, prob = c(.2, .8))] +# Mimic NSSP formatting: codes without dots for some visits +visits[sample(.N, .N %/% 2), diagnosis_codes := gsub(".", "", diagnosis_codes, fixed = TRUE)] +setorder(visits, date, key) +fwrite(visits, "inst/extdata/toy_visits.csv") diff --git a/inst/extdata/Parameter_File_template.prm b/inst/extdata/Parameter_File_template.prm new file mode 100644 index 0000000..b0409d7 --- /dev/null +++ b/inst/extdata/Parameter_File_template.prm @@ -0,0 +1,237 @@ +[Analysis] +;scan type (TREEONLY=0, TREETIME=1, TIMEONLY=2) +scan-type=1 +;probability model type (POISSON=0, BERNOULLI_TREE=1, UNIFORM=2, Not-Applicable=3) +probability-model=0 +;conditional type (UNCONDITIONAL=0, TOTALCASES=1, NODE=2, NODEANDTIME=3) +conditional-type=3 +;self control design - unconditional Bernoulli only (y/n) +self-control-design=n +;case probability (integer/integer) +event-probability=1/2 +;variable case probability - unconditional Bernoulli only (y/n) +variable-case-probability=n +;scan rate type (HIGHRATE=0, LOWRATE=1, HIGHORLOWRATE=2) +scan-rate-type=0 + +[Input] +;tree structure filename +tree-filename= +;source type (CSV=0) +tree-filename-SourceType=0 +;source field map (comma separated list of integers) +tree-filename-SourceFieldMap=3,4,1,2,5 +;csv source delimiter (leave empty for space or tab delimiter) +tree-filename-SourceDelimiter=, +;csv source group character +tree-filename-SourceGrouper=" +;csv source skip initial lines (i.e. meta data) +tree-filename-SourceSkip=0 +;csv source first row column header +tree-filename-SourceFirstRowHeader=y +;count data filename +count-filename= +;source type (CSV=0) +count-filename-SourceFieldMap=1,3,2 +count-filename-SourceDelimiter= +count-filename-SourceFirstRowHeader=y +;csv source skip initial lines (i.e. meta data) +count-filename-SourceSkip=0 +;csv source group character +count-filename-SourceGrouper=" +;csv source skip initial lines (i.e. meta data) +count-filename-SourceSkip=0 +;csv source first row column header +count-filename-SourceFirstRowHeader=y +;control data filename +control-filename= + ;date precision type (NONE=0, GENERIC=1, YEAR=2, MONTH=3, DAY=4) +date-precision=4 +;data time ranges: [integer,integer] or [yyyy/mm/dd,yyyy/mm/dd] +data-time-range= + +[Output] +;results filename +results-filename= +;create HTML results (y/n) +results-html=y +;create CSV results (y/n) +results-csv=y +;create NCBI Asn results (y/n) +results-asn=n +;create Newick File (y/n) +results-nwk=n +;output cluster window graph HTML file (y/n) +output-clusterwindow-graph-html=y + +[Advanced Input] +;cuts filename +cut-filename= + ;default cuts type (SIMPLE=0, PAIRS=1, TRIPLETS=2, ORDINAL=3, COMBINATORIAL=4) +cut-type=0 +;allow data only on tree leaves - (y/n) +data-only-on-leaves=n +;ignore cases outside study period - (y/n) +relaxed-study-data-period-checking=y +;allow multi-parent nodes - (y/n) +allow-multi-parent-nodes=y +;allow multiple root nodes - (y/n) +allow-multiple-roots=n +;minimum censor time (2 <= x) +minimum-censor-time=50 +;minimum censor time percentage of study period (0 < x <= 100.0) +min-censor-percentage=10 +;apply risk window restriction due to censoring - (y/n) +risk-window-restriction-censor=n +;risk window alternative censor denominator (integer) +risk-window-alt-censor-denominator=2 + +[Temporal Window] +;maximum temporal size as percentage of data time range (0 < x <= 50.0) +maximum-window-percentage=50 +;maximum temporal size as fixed time length (integer) +maximum-window-fixed=28 +;maximum temporal size selection (PERCENTAGE_WINDOW=0, FIXED_LENGTH=1) +maximum-window-type=1 +;minimum temporal size as fixed time length (integer) +minimum-window-fixed=1 +;apply risk window restriction - (y/n) +apply-risk-window-restriction=n +;risk window percentage (0 < x <= 100.0) +risk-window-percentage=20 +;prospective analysis (y/n) +prospective-analysis=y +;restrict temporal windows (y/n) +restricted-window-range=n +;start data time range: [integer,integer] or [yyyy/mm/dd,yyyy/mm/dd] +window-start-range= +;end data time range: [integer,integer] or [yyyy/mm/dd,yyyy/mm/dd] +window-end-range= + +[Adjustments] +;perform day of week adjustments (y/n) +perform-day-of-week-adjustments=y +;apply exclusion time ranges (y/n) +apply-exclusion-data-ranges=n +;exclusion time ranges (semi-colon separated list of ranges: [integer,integer];[integer,integer] or [yyyy/mm/dd,yyyy/mm/dd];[yyyy/mm/dd,yyyy/mm/dd]) +exclusion-data-ranges= + +[Inference] +;number of simulation replications (0, 9, 999, n999) +monte-carlo-replications=9999 +;restrict tree levels evaluated (y/n) +restrict-tree-levels=y +;tree levels excluded from evaluation (csv list of unsigned integers, root level is 1) +excluded-tree-levels=1,2,3 +;restrict tree nodes evaluated (y/n) +restrict-evaluated-nodes=n +;not evaluated tree nodes filename +not-evaluated-nodes-file= +;source type (CSV=0) +not-evaluated-nodes-file-SourceType=0 +;source field map (comma separated list of integers) +not-evaluated-nodes-file-SourceFieldMap=1 +;csv source delimiter (leave empty for space or tab delimiter) +not-evaluated-nodes-file-SourceDelimiter=, +;csv source group character +not-evaluated-nodes-file-SourceGrouper=" +;csv source skip initial lines (i.e. meta data) +not-evaluated-nodes-file-SourceSkip=0 +;csv source first row column header +not-evaluated-nodes-file-SourceFirstRowHeader=y +;randomization seed (integer) +randomization-seed=12345678 +;generate randomization seed (y/n) +random-randomization-seed=n +;minimum number of cases in a node (integer) +minimum-node-cases=3 +;p-value reporting type (STANDARD_PVALUE=0, TERMINATION_PVALUE) +pvalue-report-type=1 +;early termination threshold (> 0) +early-termination-threshold=5000 + +[Sequential Scan] +;perform sequential scan - time-only scan (y/n) +sequential-scan=n +;sequential scan maximum cases for signal (integer) +sequential-maximum-signal=200 +;sequential scan - minimum cases to signal (integer) +sequential-minimum-signal=3 +;sequential scan filename +sequential-filename= +;sequential alpha overall +sequential-alpha-overall=0.05 +;sequential alpha spending +sequential-alpha-spending=0.01 + +[Power Evaluations] +;perform power evaluations (y/n) +perform-power-evaluations=n +;power evaluation type (0=Analysis And Power Evaluation Together, 1=Only Power Evaluation With Count File, 2=Only Power Evaluation With Defined Total Cases) +power-evaluation-type=0 +;critical values type (0=Monte Carlo, 1=User Specified Values) +critical-values-type=0 +;power evaluation critical value .05 (> 0) +critical-value-05=0 +;power evaluation critical value .01 (> 0) +critical-value-01=0 +;power evaluation critical value .001 (> 0) +critical-value-001=0 +;total cases in power evaluation (integer) +power-evaluation-totalcases=600 +;number of replications in power step (integer) +power-evaluation-replications=1000 +;power evaluation alternative hypothesis filename +alternative-hypothesis-filename= +;power baseline probability (integer/integer) +baseline-probability=1/2 +;power z value (0 < z <= 0.01) +power-z=0.001 + +[Miscellaneous Analysis] +;frequency of prospective analyses type (0=Daily, 1=Weekly, 2=Monthy, 3=Quarterly, 4=Yearly) +prospective-frequency-type=0 +;frequency of prospective (integer) +prospective-frequency=1 + +[Temporal Output] +;output temporal graph HTML file (y/n) +output-temporal-graph-html=y +;temporal graph cluster reporting type (0=Only most likely cluster, 1=X most likely clusters, 2=Only significant clusters) +temporal-graph-type=1 +;number of most likely clusters to report in temporal graph (positive integer) +temporal-graph-most-mlc=100 +;significant clusters p-value cutoff to report in temporal graph (0.000-1.000) +temporal-graph-significance-cutoff=0.05 +;output cluster window graph HTML file (y/n) +output-clusterwindow-graph-html=y + +[Additional Output] +;create LLR results (y/n) +results-llr=n +;report critical values (y/n) +report-critical-values=y +;report attributable risk (y/n) +report-attributable-risk=n +;number of exposed attributable risk is based upon (positive integer) +attributable-risk-exposed=0 +;report parent cuts that match child cuts (y/n) +include-identical-parent-cuts=n + +[Power Simulations] +;input simulation data (y/n) +input-simulations=n +;input simulation filename +input-simulations-file= +;output simulation data (y/n) +output-simulations=n +;output simulation filename +output-simulations-file= + +[Run Options] +;number of parallel processes to execute (0=All Processors, x=At Most X Processors) +parallel-processes=2 + +[System] +;parameters version - do not modify +parameters-version=2.4.1 diff --git a/inst/extdata/toy_tree.csv b/inst/extdata/toy_tree.csv new file mode 100644 index 0000000..d19432f --- /dev/null +++ b/inst/extdata/toy_tree.csv @@ -0,0 +1,1876 @@ +distance_between,description,child,parent,do_not_evaluate +1,0-Cholera,0-A00,0-A00-A09,TRUE +1,0-Cholera,0-A00,2-A00,TRUE +1,0-Intestinal infectious diseases,0-A00-A09,0-A00-B99,TRUE +1,0-Intestinal infectious diseases,0-A00-A09,2-A00-A09,TRUE +1,0-Certain infectious and parasitic diseases,0-A00-B99,0-Root,TRUE +1,0-Certain infectious and parasitic diseases,0-A00-B99,2-A00-B99,TRUE +1,"0-Cholera due to Vibrio cholerae 01, biovar cholerae",0-A00.0,0-A00,TRUE +1,"0-Cholera due to Vibrio cholerae 01, biovar cholerae",0-A00.0,2-A00.0,TRUE +1,"0-Cholera due to Vibrio cholerae 01, biovar eltor",0-A00.1,0-A00,TRUE +1,"0-Cholera due to Vibrio cholerae 01, biovar eltor",0-A00.1,2-A00.1,TRUE +1,"0-Cholera, unspecified",0-A00.9,0-A00,TRUE +1,"0-Cholera, unspecified",0-A00.9,2-A00.9,TRUE +1,0-Typhoid and paratyphoid fevers,0-A01,0-A00-A09,TRUE +1,0-Typhoid and paratyphoid fevers,0-A01,2-A01,TRUE +1,0-Typhoid fever,0-A01.0,0-A01,TRUE +1,0-Typhoid fever,0-A01.0,2-A01.0,TRUE +1,"0-Typhoid fever, unspecified",0-A01.00,0-A01.0,TRUE +1,"0-Typhoid fever, unspecified",0-A01.00,2-A01.00,TRUE +1,0-Typhoid meningitis,0-A01.01,0-A01.0,TRUE +1,0-Typhoid meningitis,0-A01.01,2-A01.01,TRUE +1,0-Typhoid fever with heart involvement,0-A01.02,0-A01.0,TRUE +1,0-Typhoid fever with heart involvement,0-A01.02,2-A01.02,TRUE +1,0-Typhoid pneumonia,0-A01.03,0-A01.0,TRUE +1,0-Typhoid pneumonia,0-A01.03,2-A01.03,TRUE +1,0-Typhoid arthritis,0-A01.04,0-A01.0,TRUE +1,0-Typhoid arthritis,0-A01.04,2-A01.04,TRUE +1,0-Typhoid osteomyelitis,0-A01.05,0-A01.0,TRUE +1,0-Typhoid osteomyelitis,0-A01.05,2-A01.05,TRUE +1,0-Typhoid fever with other complications,0-A01.09,0-A01.0,TRUE +1,0-Typhoid fever with other complications,0-A01.09,2-A01.09,TRUE +1,0-Paratyphoid fever A,0-A01.1,0-A01,TRUE +1,0-Paratyphoid fever A,0-A01.1,2-A01.1,TRUE +1,0-Paratyphoid fever B,0-A01.2,0-A01,TRUE +1,0-Paratyphoid fever B,0-A01.2,2-A01.2,TRUE +1,0-Paratyphoid fever C,0-A01.3,0-A01,TRUE +1,0-Paratyphoid fever C,0-A01.3,2-A01.3,TRUE +1,"0-Paratyphoid fever, unspecified",0-A01.4,0-A01,TRUE +1,"0-Paratyphoid fever, unspecified",0-A01.4,2-A01.4,TRUE +1,0-Other salmonella infections,0-A02,0-A00-A09,TRUE +1,0-Other salmonella infections,0-A02,2-A02,TRUE +1,0-Salmonella enteritis,0-A02.0,0-A02,TRUE +1,0-Salmonella enteritis,0-A02.0,2-A02.0,TRUE +1,0-Salmonella sepsis,0-A02.1,0-A02,TRUE +1,0-Salmonella sepsis,0-A02.1,2-A02.1,TRUE +1,0-Localized salmonella infections,0-A02.2,0-A02,TRUE +1,0-Localized salmonella infections,0-A02.2,2-A02.2,TRUE +1,"0-Localized salmonella infection, unspecified",0-A02.20,0-A02.2,TRUE +1,"0-Localized salmonella infection, unspecified",0-A02.20,2-A02.20,TRUE +1,0-Salmonella meningitis,0-A02.21,0-A02.2,TRUE +1,0-Salmonella meningitis,0-A02.21,2-A02.21,TRUE +1,0-Salmonella pneumonia,0-A02.22,0-A02.2,TRUE +1,0-Salmonella pneumonia,0-A02.22,2-A02.22,TRUE +1,0-Salmonella arthritis,0-A02.23,0-A02.2,TRUE +1,0-Salmonella arthritis,0-A02.23,2-A02.23,TRUE +1,0-Salmonella osteomyelitis,0-A02.24,0-A02.2,TRUE +1,0-Salmonella osteomyelitis,0-A02.24,2-A02.24,TRUE +1,0-Salmonella pyelonephritis,0-A02.25,0-A02.2,TRUE +1,0-Salmonella pyelonephritis,0-A02.25,2-A02.25,TRUE +1,0-Salmonella with other localized infection,0-A02.29,0-A02.2,TRUE +1,0-Salmonella with other localized infection,0-A02.29,2-A02.29,TRUE +1,0-Other specified salmonella infections,0-A02.8,0-A02,TRUE +1,0-Other specified salmonella infections,0-A02.8,2-A02.8,TRUE +1,"0-Salmonella infection, unspecified",0-A02.9,0-A02,TRUE +1,"0-Salmonella infection, unspecified",0-A02.9,2-A02.9,TRUE +1,0-Shigellosis,0-A03,0-A00-A09,TRUE +1,0-Shigellosis,0-A03,2-A03,TRUE +1,0-Shigellosis due to Shigella dysenteriae,0-A03.0,0-A03,TRUE +1,0-Shigellosis due to Shigella dysenteriae,0-A03.0,2-A03.0,TRUE +1,0-Shigellosis due to Shigella flexneri,0-A03.1,0-A03,TRUE +1,0-Shigellosis due to Shigella flexneri,0-A03.1,2-A03.1,TRUE +1,0-Shigellosis due to Shigella boydii,0-A03.2,0-A03,TRUE +1,0-Shigellosis due to Shigella boydii,0-A03.2,2-A03.2,TRUE +1,0-Shigellosis due to Shigella sonnei,0-A03.3,0-A03,TRUE +1,0-Shigellosis due to Shigella sonnei,0-A03.3,2-A03.3,TRUE +1,0-Other shigellosis,0-A03.8,0-A03,TRUE +1,0-Other shigellosis,0-A03.8,2-A03.8,TRUE +1,"0-Shigellosis, unspecified",0-A03.9,0-A03,TRUE +1,"0-Shigellosis, unspecified",0-A03.9,2-A03.9,TRUE +1,0-Other bacterial intestinal infections,0-A04,0-A00-A09,TRUE +1,0-Other bacterial intestinal infections,0-A04,2-A04,TRUE +1,0-Enteropathogenic Escherichia coli infection,0-A04.0,0-A04,TRUE +1,0-Enteropathogenic Escherichia coli infection,0-A04.0,0-Escherichia coli,TRUE +1,0-Enteropathogenic Escherichia coli infection,0-A04.0,2-A04.0,TRUE +1,0-Enterotoxigenic Escherichia coli infection,0-A04.1,0-A04,TRUE +1,0-Enterotoxigenic Escherichia coli infection,0-A04.1,0-Escherichia coli,TRUE +1,0-Enterotoxigenic Escherichia coli infection,0-A04.1,2-A04.1,TRUE +1,0-Enteroinvasive Escherichia coli infection,0-A04.2,0-A04,TRUE +1,0-Enteroinvasive Escherichia coli infection,0-A04.2,0-Escherichia coli,TRUE +1,0-Enteroinvasive Escherichia coli infection,0-A04.2,2-A04.2,TRUE +1,0-Enterohemorrhagic Escherichia coli infection,0-A04.3,0-A04,TRUE +1,0-Enterohemorrhagic Escherichia coli infection,0-A04.3,0-Escherichia coli,TRUE +1,0-Enterohemorrhagic Escherichia coli infection,0-A04.3,2-A04.3,TRUE +1,0-Other intestinal Escherichia coli infections,0-A04.4,0-A04,TRUE +1,0-Other intestinal Escherichia coli infections,0-A04.4,0-Escherichia coli,TRUE +1,0-Other intestinal Escherichia coli infections,0-A04.4,2-A04.4,TRUE +1,0-Campylobacter enteritis,0-A04.5,0-A04,TRUE +1,0-Campylobacter enteritis,0-A04.5,2-A04.5,TRUE +1,0-Enteritis due to Yersinia enterocolitica,0-A04.6,0-A04,TRUE +1,0-Enteritis due to Yersinia enterocolitica,0-A04.6,2-A04.6,TRUE +1,0-Enterocolitis due to Clostridium difficile,0-A04.7,0-A04,TRUE +1,0-Enterocolitis due to Clostridium difficile,0-A04.7,2-A04.7,TRUE +1,"0-Enterocolitis due to Clostridium difficile, recurrent",0-A04.71,0-A04.7,TRUE +1,"0-Enterocolitis due to Clostridium difficile, recurrent",0-A04.71,2-A04.71,TRUE +1,"0-Enterocolitis due to Clostridium difficile, not specified as recurrent",0-A04.72,0-A04.7,TRUE +1,"0-Enterocolitis due to Clostridium difficile, not specified as recurrent",0-A04.72,2-A04.72,TRUE +1,0-Other specified bacterial intestinal infections,0-A04.8,0-A04,TRUE +1,0-Other specified bacterial intestinal infections,0-A04.8,2-A04.8,TRUE +1,"0-Bacterial intestinal infection, unspecified",0-A04.9,0-A04,TRUE +1,"0-Bacterial intestinal infection, unspecified",0-A04.9,2-A04.9,TRUE +1,"0-Other bacterial foodborne intoxications, not elsewhere classified",0-A05,0-A00-A09,TRUE +1,"0-Other bacterial foodborne intoxications, not elsewhere classified",0-A05,2-A05,TRUE +1,0-Foodborne staphylococcal intoxication,0-A05.0,0-A05,TRUE +1,0-Foodborne staphylococcal intoxication,0-A05.0,2-A05.0,TRUE +1,0-Botulism food poisoning,0-A05.1,0-A05,TRUE +1,0-Botulism food poisoning,0-A05.1,2-A05.1,TRUE +1,0-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,0-A05.2,0-A05,TRUE +1,0-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,0-A05.2,0-Clostridium perfringens,TRUE +1,0-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,0-A05.2,2-A05.2,TRUE +1,0-Foodborne Vibrio parahaemolyticus intoxication,0-A05.3,0-A05,TRUE +1,0-Foodborne Vibrio parahaemolyticus intoxication,0-A05.3,2-A05.3,TRUE +1,0-Foodborne Bacillus cereus intoxication,0-A05.4,0-A05,TRUE +1,0-Foodborne Bacillus cereus intoxication,0-A05.4,2-A05.4,TRUE +1,0-Foodborne Vibrio vulnificus intoxication,0-A05.5,0-A05,TRUE +1,0-Foodborne Vibrio vulnificus intoxication,0-A05.5,0-Vibrio vulnificus,TRUE +1,0-Foodborne Vibrio vulnificus intoxication,0-A05.5,2-A05.5,TRUE +1,0-Other specified bacterial foodborne intoxications,0-A05.8,0-A05,TRUE +1,0-Other specified bacterial foodborne intoxications,0-A05.8,2-A05.8,TRUE +1,"0-Bacterial foodborne intoxication, unspecified",0-A05.9,0-A05,TRUE +1,"0-Bacterial foodborne intoxication, unspecified",0-A05.9,2-A05.9,TRUE +1,0-Amebiasis,0-A06,0-A00-A09,TRUE +1,0-Amebiasis,0-A06,2-A06,TRUE +1,0-Acute amebic dysentery,0-A06.0,0-A06,TRUE +1,0-Acute amebic dysentery,0-A06.0,2-A06.0,TRUE +1,0-Chronic intestinal amebiasis,0-A06.1,0-A06,TRUE +1,0-Chronic intestinal amebiasis,0-A06.1,2-A06.1,TRUE +1,0-Amebic nondysenteric colitis,0-A06.2,0-A06,TRUE +1,0-Amebic nondysenteric colitis,0-A06.2,2-A06.2,TRUE +1,0-Ameboma of intestine,0-A06.3,0-A06,TRUE +1,0-Ameboma of intestine,0-A06.3,2-A06.3,TRUE +1,0-Amebic liver abscess,0-A06.4,0-A06,TRUE +1,0-Amebic liver abscess,0-A06.4,2-A06.4,TRUE +1,0-Amebic lung abscess,0-A06.5,0-A06,TRUE +1,0-Amebic lung abscess,0-A06.5,2-A06.5,TRUE +1,0-Amebic brain abscess,0-A06.6,0-A06,TRUE +1,0-Amebic brain abscess,0-A06.6,2-A06.6,TRUE +1,0-Cutaneous amebiasis,0-A06.7,0-A06,TRUE +1,0-Cutaneous amebiasis,0-A06.7,2-A06.7,TRUE +1,0-Amebic infection of other sites,0-A06.8,0-A06,TRUE +1,0-Amebic infection of other sites,0-A06.8,2-A06.8,TRUE +1,0-Amebic cystitis,0-A06.81,0-A06.8,TRUE +1,0-Amebic cystitis,0-A06.81,2-A06.81,TRUE +1,0-Other amebic genitourinary infections,0-A06.82,0-A06.8,TRUE +1,0-Other amebic genitourinary infections,0-A06.82,2-A06.82,TRUE +1,0-Other amebic infections,0-A06.89,0-A06.8,TRUE +1,0-Other amebic infections,0-A06.89,2-A06.89,TRUE +1,"0-Amebiasis, unspecified",0-A06.9,0-A06,TRUE +1,"0-Amebiasis, unspecified",0-A06.9,2-A06.9,TRUE +1,0-Other protozoal intestinal diseases,0-A07,0-A00-A09,TRUE +1,0-Other protozoal intestinal diseases,0-A07,2-A07,TRUE +1,0-Balantidiasis,0-A07.0,0-A07,TRUE +1,0-Balantidiasis,0-A07.0,2-A07.0,TRUE +1,0-Giardiasis [lambliasis],0-A07.1,0-A07,TRUE +1,0-Giardiasis [lambliasis],0-A07.1,2-A07.1,TRUE +1,0-Cryptosporidiosis,0-A07.2,0-A07,TRUE +1,0-Cryptosporidiosis,0-A07.2,2-A07.2,TRUE +1,0-Isosporiasis,0-A07.3,0-A07,TRUE +1,0-Isosporiasis,0-A07.3,2-A07.3,TRUE +1,0-Cyclosporiasis,0-A07.4,0-A07,TRUE +1,0-Cyclosporiasis,0-A07.4,2-A07.4,TRUE +1,0-Other specified protozoal intestinal diseases,0-A07.8,0-A07,TRUE +1,0-Other specified protozoal intestinal diseases,0-A07.8,2-A07.8,TRUE +1,"0-Protozoal intestinal disease, unspecified",0-A07.9,0-A07,TRUE +1,"0-Protozoal intestinal disease, unspecified",0-A07.9,2-A07.9,TRUE +1,0-Viral and other specified intestinal infections,0-A08,0-A00-A09,TRUE +1,0-Viral and other specified intestinal infections,0-A08,2-A08,TRUE +1,0-Rotaviral enteritis,0-A08.0,0-A08,TRUE +1,0-Rotaviral enteritis,0-A08.0,2-A08.0,TRUE +1,0-Acute gastroenteropathy due to Norwalk agent and other small round viruses,0-A08.1,0-A08,TRUE +1,0-Acute gastroenteropathy due to Norwalk agent and other small round viruses,0-A08.1,2-A08.1,TRUE +1,0-Acute gastroenteropathy due to Norwalk agent,0-A08.11,0-A08.1,TRUE +1,0-Acute gastroenteropathy due to Norwalk agent,0-A08.11,2-A08.11,TRUE +1,0-Acute gastroenteropathy due to other small round viruses,0-A08.19,0-A08.1,TRUE +1,0-Acute gastroenteropathy due to other small round viruses,0-A08.19,2-A08.19,TRUE +1,0-Adenoviral enteritis,0-A08.2,0-A08,TRUE +1,0-Adenoviral enteritis,0-A08.2,2-A08.2,TRUE +1,0-Other viral enteritis,0-A08.3,0-A08,TRUE +1,0-Other viral enteritis,0-A08.3,2-A08.3,TRUE +1,0-Calicivirus enteritis,0-A08.31,0-A08.3,TRUE +1,0-Calicivirus enteritis,0-A08.31,2-A08.31,TRUE +1,0-Astrovirus enteritis,0-A08.32,0-A08.3,TRUE +1,0-Astrovirus enteritis,0-A08.32,2-A08.32,TRUE +1,0-Other viral enteritis,0-A08.39,0-A08.3,TRUE +1,0-Other viral enteritis,0-A08.39,2-A08.39,TRUE +1,"0-Viral intestinal infection, unspecified",0-A08.4,0-A08,TRUE +1,"0-Viral intestinal infection, unspecified",0-A08.4,2-A08.4,TRUE +1,0-Other specified intestinal infections,0-A08.8,0-A08,TRUE +1,0-Other specified intestinal infections,0-A08.8,2-A08.8,TRUE +1,"0-Infectious gastroenteritis and colitis, unspecified",0-A09,0-A00-A09,TRUE +1,"0-Infectious gastroenteritis and colitis, unspecified",0-A09,2-A09,TRUE +1,,0-Clostridium perfringens,0-dummy2,TRUE +1,,0-Clostridium perfringens,2-Clostridium perfringens,TRUE +1,,0-Escherichia coli,0-dummy2,TRUE +1,,0-Escherichia coli,2-Escherichia coli,TRUE +1,0-Acute nasopharyngitis [common cold],0-J00,0-J00-J06,TRUE +1,0-Acute nasopharyngitis [common cold],0-J00,2-J00,TRUE +1,0-Acute upper respiratory infections,0-J00-J06,0-J00-J99,TRUE +1,0-Acute upper respiratory infections,0-J00-J06,2-J00-J06,TRUE +1,0-Diseases of the respiratory system,0-J00-J99,0-Root,TRUE +1,0-Diseases of the respiratory system,0-J00-J99,2-J00-J99,TRUE +1,0-Acute sinusitis,0-J01,0-J00-J06,TRUE +1,0-Acute sinusitis,0-J01,2-J01,TRUE +1,0-Acute maxillary sinusitis,0-J01.0,0-J01,TRUE +1,0-Acute maxillary sinusitis,0-J01.0,2-J01.0,TRUE +1,"0-Acute maxillary sinusitis, unspecified",0-J01.00,0-J01.0,TRUE +1,"0-Acute maxillary sinusitis, unspecified",0-J01.00,2-J01.00,TRUE +1,0-Acute recurrent maxillary sinusitis,0-J01.01,0-J01.0,TRUE +1,0-Acute recurrent maxillary sinusitis,0-J01.01,2-J01.01,TRUE +1,0-Acute frontal sinusitis,0-J01.1,0-J01,TRUE +1,0-Acute frontal sinusitis,0-J01.1,2-J01.1,TRUE +1,"0-Acute frontal sinusitis, unspecified",0-J01.10,0-J01.1,TRUE +1,"0-Acute frontal sinusitis, unspecified",0-J01.10,2-J01.10,TRUE +1,0-Acute recurrent frontal sinusitis,0-J01.11,0-J01.1,TRUE +1,0-Acute recurrent frontal sinusitis,0-J01.11,2-J01.11,TRUE +1,0-Acute ethmoidal sinusitis,0-J01.2,0-J01,TRUE +1,0-Acute ethmoidal sinusitis,0-J01.2,2-J01.2,TRUE +1,"0-Acute ethmoidal sinusitis, unspecified",0-J01.20,0-J01.2,TRUE +1,"0-Acute ethmoidal sinusitis, unspecified",0-J01.20,2-J01.20,TRUE +1,0-Acute recurrent ethmoidal sinusitis,0-J01.21,0-J01.2,TRUE +1,0-Acute recurrent ethmoidal sinusitis,0-J01.21,2-J01.21,TRUE +1,0-Acute sphenoidal sinusitis,0-J01.3,0-J01,TRUE +1,0-Acute sphenoidal sinusitis,0-J01.3,2-J01.3,TRUE +1,"0-Acute sphenoidal sinusitis, unspecified",0-J01.30,0-J01.3,TRUE +1,"0-Acute sphenoidal sinusitis, unspecified",0-J01.30,2-J01.30,TRUE +1,0-Acute recurrent sphenoidal sinusitis,0-J01.31,0-J01.3,TRUE +1,0-Acute recurrent sphenoidal sinusitis,0-J01.31,2-J01.31,TRUE +1,0-Acute pansinusitis,0-J01.4,0-J01,TRUE +1,0-Acute pansinusitis,0-J01.4,2-J01.4,TRUE +1,"0-Acute pansinusitis, unspecified",0-J01.40,0-J01.4,TRUE +1,"0-Acute pansinusitis, unspecified",0-J01.40,2-J01.40,TRUE +1,0-Acute recurrent pansinusitis,0-J01.41,0-J01.4,TRUE +1,0-Acute recurrent pansinusitis,0-J01.41,2-J01.41,TRUE +1,0-Other acute sinusitis,0-J01.8,0-J01,TRUE +1,0-Other acute sinusitis,0-J01.8,2-J01.8,TRUE +1,0-Other acute sinusitis,0-J01.80,0-J01.8,TRUE +1,0-Other acute sinusitis,0-J01.80,2-J01.80,TRUE +1,0-Other acute recurrent sinusitis,0-J01.81,0-J01.8,TRUE +1,0-Other acute recurrent sinusitis,0-J01.81,2-J01.81,TRUE +1,"0-Acute sinusitis, unspecified",0-J01.9,0-J01,TRUE +1,"0-Acute sinusitis, unspecified",0-J01.9,2-J01.9,TRUE +1,"0-Acute sinusitis, unspecified",0-J01.90,0-J01.9,TRUE +1,"0-Acute sinusitis, unspecified",0-J01.90,2-J01.90,TRUE +1,"0-Acute recurrent sinusitis, unspecified",0-J01.91,0-J01.9,TRUE +1,"0-Acute recurrent sinusitis, unspecified",0-J01.91,2-J01.91,TRUE +1,0-Acute pharyngitis,0-J02,0-J00-J06,TRUE +1,0-Acute pharyngitis,0-J02,2-J02,TRUE +1,0-Streptococcal pharyngitis,0-J02.0,0-J02,TRUE +1,0-Streptococcal pharyngitis,0-J02.0,0-Other streptococcus,TRUE +1,0-Streptococcal pharyngitis,0-J02.0,2-J02.0,TRUE +1,0-Acute pharyngitis due to other specified organisms,0-J02.8,0-J02,TRUE +1,0-Acute pharyngitis due to other specified organisms,0-J02.8,2-J02.8,TRUE +1,"0-Acute pharyngitis, unspecified",0-J02.9,0-J02,TRUE +1,"0-Acute pharyngitis, unspecified",0-J02.9,2-J02.9,TRUE +1,0-Acute tonsillitis,0-J03,0-J00-J06,TRUE +1,0-Acute tonsillitis,0-J03,2-J03,TRUE +1,0-Streptococcal tonsillitis,0-J03.0,0-J03,TRUE +1,0-Streptococcal tonsillitis,0-J03.0,0-Other streptococcus,TRUE +1,0-Streptococcal tonsillitis,0-J03.0,2-J03.0,TRUE +1,"0-Acute streptococcal tonsillitis, unspecified",0-J03.00,0-J03.0,TRUE +1,"0-Acute streptococcal tonsillitis, unspecified",0-J03.00,2-J03.00,TRUE +1,0-Acute recurrent streptococcal tonsillitis,0-J03.01,0-J03.0,TRUE +1,0-Acute recurrent streptococcal tonsillitis,0-J03.01,2-J03.01,TRUE +1,0-Acute tonsillitis due to other specified organisms,0-J03.8,0-J03,TRUE +1,0-Acute tonsillitis due to other specified organisms,0-J03.8,2-J03.8,TRUE +1,0-Acute tonsillitis due to other specified organisms,0-J03.80,0-J03.8,TRUE +1,0-Acute tonsillitis due to other specified organisms,0-J03.80,2-J03.80,TRUE +1,0-Acute recurrent tonsillitis due to other specified organisms,0-J03.81,0-J03.8,TRUE +1,0-Acute recurrent tonsillitis due to other specified organisms,0-J03.81,2-J03.81,TRUE +1,"0-Acute tonsillitis, unspecified",0-J03.9,0-J03,TRUE +1,"0-Acute tonsillitis, unspecified",0-J03.9,2-J03.9,TRUE +1,"0-Acute tonsillitis, unspecified",0-J03.90,0-J03.9,TRUE +1,"0-Acute tonsillitis, unspecified",0-J03.90,2-J03.90,TRUE +1,"0-Acute recurrent tonsillitis, unspecified",0-J03.91,0-J03.9,TRUE +1,"0-Acute recurrent tonsillitis, unspecified",0-J03.91,2-J03.91,TRUE +1,0-Acute laryngitis and tracheitis,0-J04,0-J00-J06,TRUE +1,0-Acute laryngitis and tracheitis,0-J04,2-J04,TRUE +1,0-Acute laryngitis,0-J04.0,0-J04,TRUE +1,0-Acute laryngitis,0-J04.0,2-J04.0,TRUE +1,0-Acute tracheitis,0-J04.1,0-J04,TRUE +1,0-Acute tracheitis,0-J04.1,2-J04.1,TRUE +1,0-Acute tracheitis without obstruction,0-J04.10,0-J04.1,TRUE +1,0-Acute tracheitis without obstruction,0-J04.10,2-J04.10,TRUE +1,0-Acute tracheitis with obstruction,0-J04.11,0-J04.1,TRUE +1,0-Acute tracheitis with obstruction,0-J04.11,2-J04.11,TRUE +1,0-Acute laryngotracheitis,0-J04.2,0-J04,TRUE +1,0-Acute laryngotracheitis,0-J04.2,2-J04.2,TRUE +1,"0-Supraglottitis, unspecified",0-J04.3,0-J04,TRUE +1,"0-Supraglottitis, unspecified",0-J04.3,2-J04.3,TRUE +1,"0-Supraglottitis, unspecified, without obstruction",0-J04.30,0-J04.3,TRUE +1,"0-Supraglottitis, unspecified, without obstruction",0-J04.30,2-J04.30,TRUE +1,"0-Supraglottitis, unspecified, with obstruction",0-J04.31,0-J04.3,TRUE +1,"0-Supraglottitis, unspecified, with obstruction",0-J04.31,2-J04.31,TRUE +1,0-Acute obstructive laryngitis [croup] and epiglottitis,0-J05,0-J00-J06,TRUE +1,0-Acute obstructive laryngitis [croup] and epiglottitis,0-J05,2-J05,TRUE +1,0-Acute obstructive laryngitis [croup],0-J05.0,0-J05,TRUE +1,0-Acute obstructive laryngitis [croup],0-J05.0,2-J05.0,TRUE +1,0-Acute epiglottitis,0-J05.1,0-J05,TRUE +1,0-Acute epiglottitis,0-J05.1,2-J05.1,TRUE +1,0-Acute epiglottitis without obstruction,0-J05.10,0-J05.1,TRUE +1,0-Acute epiglottitis without obstruction,0-J05.10,2-J05.10,TRUE +1,0-Acute epiglottitis with obstruction,0-J05.11,0-J05.1,TRUE +1,0-Acute epiglottitis with obstruction,0-J05.11,2-J05.11,TRUE +1,0-Acute upper respiratory infections of multiple and unspecified sites,0-J06,0-J00-J06,TRUE +1,0-Acute upper respiratory infections of multiple and unspecified sites,0-J06,2-J06,TRUE +1,0-Acute laryngopharyngitis,0-J06.0,0-J06,TRUE +1,0-Acute laryngopharyngitis,0-J06.0,2-J06.0,TRUE +1,"0-Acute upper respiratory infection, unspecified",0-J06.9,0-J06,TRUE +1,"0-Acute upper respiratory infection, unspecified",0-J06.9,2-J06.9,TRUE +1,,0-Other streptococcus,0-dummy2,TRUE +1,,0-Other streptococcus,2-Other streptococcus,TRUE +1,"0-Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",0-R00-R99,0-Root,TRUE +1,"0-Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",0-R00-R99,2-R00-R99,TRUE +1,0-Abdominal and pelvic pain,0-R10,0-R10-R19,TRUE +1,0-Abdominal and pelvic pain,0-R10,2-R10,TRUE +1,0-Symptoms and signs involving the digestive system and abdomen,0-R10-R19,0-R00-R99,TRUE +1,0-Symptoms and signs involving the digestive system and abdomen,0-R10-R19,2-R10-R19,TRUE +1,0-Acute abdomen,0-R10.0,0-R10,TRUE +1,0-Acute abdomen,0-R10.0,2-R10.0,TRUE +1,0-Pain localized to upper abdomen,0-R10.1,0-R10,TRUE +1,0-Pain localized to upper abdomen,0-R10.1,2-R10.1,TRUE +1,"0-Upper abdominal pain, unspecified",0-R10.10,0-R10.1,TRUE +1,"0-Upper abdominal pain, unspecified",0-R10.10,2-R10.10,TRUE +1,0-Right upper quadrant pain,0-R10.11,0-R10.1,TRUE +1,0-Right upper quadrant pain,0-R10.11,2-R10.11,TRUE +1,0-Left upper quadrant pain,0-R10.12,0-R10.1,TRUE +1,0-Left upper quadrant pain,0-R10.12,2-R10.12,TRUE +1,0-Epigastric pain,0-R10.13,0-R10.1,TRUE +1,0-Epigastric pain,0-R10.13,2-R10.13,TRUE +1,0-Pelvic and perineal pain,0-R10.2,0-R10,TRUE +1,0-Pelvic and perineal pain,0-R10.2,2-R10.2,TRUE +1,0-Pelvic and perineal pain unspecified side,0-R10.20,0-R10.2,TRUE +1,0-Pelvic and perineal pain unspecified side,0-R10.20,2-R10.20,TRUE +1,0-Pelvic and perineal pain right side,0-R10.21,0-R10.2,TRUE +1,0-Pelvic and perineal pain right side,0-R10.21,2-R10.21,TRUE +1,0-Pelvic and perineal pain left side,0-R10.22,0-R10.2,TRUE +1,0-Pelvic and perineal pain left side,0-R10.22,2-R10.22,TRUE +1,0-Pelvic and perineal pain bilateral,0-R10.23,0-R10.2,TRUE +1,0-Pelvic and perineal pain bilateral,0-R10.23,2-R10.23,TRUE +1,0-Suprapubic pain,0-R10.24,0-R10.2,TRUE +1,0-Suprapubic pain,0-R10.24,2-R10.24,TRUE +1,0-Pain localized to other parts of lower abdomen,0-R10.3,0-R10,TRUE +1,0-Pain localized to other parts of lower abdomen,0-R10.3,2-R10.3,TRUE +1,"0-Lower abdominal pain, unspecified",0-R10.30,0-R10.3,TRUE +1,"0-Lower abdominal pain, unspecified",0-R10.30,2-R10.30,TRUE +1,0-Right lower quadrant pain,0-R10.31,0-R10.3,TRUE +1,0-Right lower quadrant pain,0-R10.31,2-R10.31,TRUE +1,0-Left lower quadrant pain,0-R10.32,0-R10.3,TRUE +1,0-Left lower quadrant pain,0-R10.32,2-R10.32,TRUE +1,0-Periumbilical pain,0-R10.33,0-R10.3,TRUE +1,0-Periumbilical pain,0-R10.33,2-R10.33,TRUE +1,0-Other abdominal pain,0-R10.8,0-R10,TRUE +1,0-Other abdominal pain,0-R10.8,2-R10.8,TRUE +1,0-Abdominal tenderness,0-R10.81,0-R10.8,TRUE +1,0-Abdominal tenderness,0-R10.81,2-R10.81,TRUE +1,0-Right upper quadrant abdominal tenderness,0-R10.811,0-R10.81,TRUE +1,0-Right upper quadrant abdominal tenderness,0-R10.811,2-R10.811,TRUE +1,0-Left upper quadrant abdominal tenderness,0-R10.812,0-R10.81,TRUE +1,0-Left upper quadrant abdominal tenderness,0-R10.812,2-R10.812,TRUE +1,0-Right lower quadrant abdominal tenderness,0-R10.813,0-R10.81,TRUE +1,0-Right lower quadrant abdominal tenderness,0-R10.813,2-R10.813,TRUE +1,0-Left lower quadrant abdominal tenderness,0-R10.814,0-R10.81,TRUE +1,0-Left lower quadrant abdominal tenderness,0-R10.814,2-R10.814,TRUE +1,0-Periumbilic abdominal tenderness,0-R10.815,0-R10.81,TRUE +1,0-Periumbilic abdominal tenderness,0-R10.815,2-R10.815,TRUE +1,0-Epigastric abdominal tenderness,0-R10.816,0-R10.81,TRUE +1,0-Epigastric abdominal tenderness,0-R10.816,2-R10.816,TRUE +1,0-Generalized abdominal tenderness,0-R10.817,0-R10.81,TRUE +1,0-Generalized abdominal tenderness,0-R10.817,2-R10.817,TRUE +1,"0-Abdominal tenderness, unspecified site",0-R10.819,0-R10.81,TRUE +1,"0-Abdominal tenderness, unspecified site",0-R10.819,2-R10.819,TRUE +1,0-Rebound abdominal tenderness,0-R10.82,0-R10.8,TRUE +1,0-Rebound abdominal tenderness,0-R10.82,2-R10.82,TRUE +1,0-Right upper quadrant rebound abdominal tenderness,0-R10.821,0-R10.82,TRUE +1,0-Right upper quadrant rebound abdominal tenderness,0-R10.821,2-R10.821,TRUE +1,0-Left upper quadrant rebound abdominal tenderness,0-R10.822,0-R10.82,TRUE +1,0-Left upper quadrant rebound abdominal tenderness,0-R10.822,2-R10.822,TRUE +1,0-Right lower quadrant rebound abdominal tenderness,0-R10.823,0-R10.82,TRUE +1,0-Right lower quadrant rebound abdominal tenderness,0-R10.823,2-R10.823,TRUE +1,0-Left lower quadrant rebound abdominal tenderness,0-R10.824,0-R10.82,TRUE +1,0-Left lower quadrant rebound abdominal tenderness,0-R10.824,2-R10.824,TRUE +1,0-Periumbilic rebound abdominal tenderness,0-R10.825,0-R10.82,TRUE +1,0-Periumbilic rebound abdominal tenderness,0-R10.825,2-R10.825,TRUE +1,0-Epigastric rebound abdominal tenderness,0-R10.826,0-R10.82,TRUE +1,0-Epigastric rebound abdominal tenderness,0-R10.826,2-R10.826,TRUE +1,0-Generalized rebound abdominal tenderness,0-R10.827,0-R10.82,TRUE +1,0-Generalized rebound abdominal tenderness,0-R10.827,2-R10.827,TRUE +1,"0-Rebound abdominal tenderness, unspecified site",0-R10.829,0-R10.82,TRUE +1,"0-Rebound abdominal tenderness, unspecified site",0-R10.829,2-R10.829,TRUE +1,0-Colic,0-R10.83,0-R10.8,TRUE +1,0-Colic,0-R10.83,2-R10.83,TRUE +1,0-Generalized abdominal pain,0-R10.84,0-R10.8,TRUE +1,0-Generalized abdominal pain,0-R10.84,2-R10.84,TRUE +1,0-Abdominal pain of multiple sites,0-R10.85,0-R10.8,TRUE +1,0-Abdominal pain of multiple sites,0-R10.85,2-R10.85,TRUE +1,0-Flank tenderness,0-R10.8A,0-R10.8,TRUE +1,0-Flank tenderness,0-R10.8A,2-R10.8A,TRUE +1,0-Right flank tenderness,0-R10.8A1,0-R10.8A,TRUE +1,0-Right flank tenderness,0-R10.8A1,2-R10.8A1,TRUE +1,0-Left flank tenderness,0-R10.8A2,0-R10.8A,TRUE +1,0-Left flank tenderness,0-R10.8A2,2-R10.8A2,TRUE +1,0-Suprapubic tenderness,0-R10.8A3,0-R10.8A,TRUE +1,0-Suprapubic tenderness,0-R10.8A3,2-R10.8A3,TRUE +1,"0-Flank tenderness, unspecified",0-R10.8A9,0-R10.8A,TRUE +1,"0-Flank tenderness, unspecified",0-R10.8A9,2-R10.8A9,TRUE +1,0-Unspecified abdominal pain,0-R10.9,0-R10,TRUE +1,0-Unspecified abdominal pain,0-R10.9,2-R10.9,TRUE +1,0-Pain localized to flank,0-R10.A,0-R10,TRUE +1,0-Pain localized to flank,0-R10.A,2-R10.A,TRUE +1,"0-Flank pain, unspecified side",0-R10.A0,0-R10.A,TRUE +1,"0-Flank pain, unspecified side",0-R10.A0,2-R10.A0,TRUE +1,"0-Flank pain, right side",0-R10.A1,0-R10.A,TRUE +1,"0-Flank pain, right side",0-R10.A1,2-R10.A1,TRUE +1,"0-Flank pain, left side",0-R10.A2,0-R10.A,TRUE +1,"0-Flank pain, left side",0-R10.A2,2-R10.A2,TRUE +1,"0-Flank pain, bilateral",0-R10.A3,0-R10.A,TRUE +1,"0-Flank pain, bilateral",0-R10.A3,2-R10.A3,TRUE +1,0-Nausea and vomiting,0-R11,0-R10-R19,TRUE +1,0-Nausea and vomiting,0-R11,2-R11,TRUE +1,0-Nausea,0-R11.0,0-R11,TRUE +1,0-Nausea,0-R11.0,2-R11.0,TRUE +1,0-Vomiting,0-R11.1,0-R11,TRUE +1,0-Vomiting,0-R11.1,2-R11.1,TRUE +1,"0-Vomiting, unspecified",0-R11.10,0-R11.1,TRUE +1,"0-Vomiting, unspecified",0-R11.10,2-R11.10,TRUE +1,0-Vomiting without nausea,0-R11.11,0-R11.1,TRUE +1,0-Vomiting without nausea,0-R11.11,2-R11.11,TRUE +1,0-Projectile vomiting,0-R11.12,0-R11.1,TRUE +1,0-Projectile vomiting,0-R11.12,2-R11.12,TRUE +1,0-Vomiting of fecal matter,0-R11.13,0-R11.1,TRUE +1,0-Vomiting of fecal matter,0-R11.13,2-R11.13,TRUE +1,0-Bilious vomiting,0-R11.14,0-R11.1,TRUE +1,0-Bilious vomiting,0-R11.14,2-R11.14,TRUE +1,0-Cyclical vomiting syndrome unrelated to migraine,0-R11.15,0-R11.1,TRUE +1,0-Cyclical vomiting syndrome unrelated to migraine,0-R11.15,2-R11.15,TRUE +1,0-Cannabis hyperemesis syndrome,0-R11.16,0-R11.1,TRUE +1,0-Cannabis hyperemesis syndrome,0-R11.16,2-R11.16,TRUE +1,"0-Nausea with vomiting, unspecified",0-R11.2,0-R11,TRUE +1,"0-Nausea with vomiting, unspecified",0-R11.2,2-R11.2,TRUE +1,0-Heartburn,0-R12,0-R10-R19,TRUE +1,0-Heartburn,0-R12,2-R12,TRUE +1,0-Aphagia and dysphagia,0-R13,0-R10-R19,TRUE +1,0-Aphagia and dysphagia,0-R13,2-R13,TRUE +1,0-Aphagia,0-R13.0,0-R13,TRUE +1,0-Aphagia,0-R13.0,2-R13.0,TRUE +1,0-Dysphagia,0-R13.1,0-R13,TRUE +1,0-Dysphagia,0-R13.1,2-R13.1,TRUE +1,"0-Dysphagia, unspecified",0-R13.10,0-R13.1,TRUE +1,"0-Dysphagia, unspecified",0-R13.10,2-R13.10,TRUE +1,"0-Dysphagia, oral phase",0-R13.11,0-R13.1,TRUE +1,"0-Dysphagia, oral phase",0-R13.11,2-R13.11,TRUE +1,"0-Dysphagia, oropharyngeal phase",0-R13.12,0-R13.1,TRUE +1,"0-Dysphagia, oropharyngeal phase",0-R13.12,2-R13.12,TRUE +1,"0-Dysphagia, pharyngeal phase",0-R13.13,0-R13.1,TRUE +1,"0-Dysphagia, pharyngeal phase",0-R13.13,2-R13.13,TRUE +1,"0-Dysphagia, pharyngoesophageal phase",0-R13.14,0-R13.1,TRUE +1,"0-Dysphagia, pharyngoesophageal phase",0-R13.14,2-R13.14,TRUE +1,0-Other dysphagia,0-R13.19,0-R13.1,TRUE +1,0-Other dysphagia,0-R13.19,2-R13.19,TRUE +1,0-Flatulence and related conditions,0-R14,0-R10-R19,TRUE +1,0-Flatulence and related conditions,0-R14,2-R14,TRUE +1,0-Abdominal distension (gaseous),0-R14.0,0-R14,TRUE +1,0-Abdominal distension (gaseous),0-R14.0,2-R14.0,TRUE +1,0-Gas pain,0-R14.1,0-R14,TRUE +1,0-Gas pain,0-R14.1,2-R14.1,TRUE +1,0-Eructation,0-R14.2,0-R14,TRUE +1,0-Eructation,0-R14.2,2-R14.2,TRUE +1,0-Flatulence,0-R14.3,0-R14,TRUE +1,0-Flatulence,0-R14.3,2-R14.3,TRUE +1,0-Fecal incontinence,0-R15,0-R10-R19,TRUE +1,0-Fecal incontinence,0-R15,2-R15,TRUE +1,0-Incomplete defecation,0-R15.0,0-R15,TRUE +1,0-Incomplete defecation,0-R15.0,2-R15.0,TRUE +1,0-Fecal smearing,0-R15.1,0-R15,TRUE +1,0-Fecal smearing,0-R15.1,2-R15.1,TRUE +1,0-Fecal urgency,0-R15.2,0-R15,TRUE +1,0-Fecal urgency,0-R15.2,2-R15.2,TRUE +1,0-Full incontinence of feces,0-R15.9,0-R15,TRUE +1,0-Full incontinence of feces,0-R15.9,2-R15.9,TRUE +1,"0-Hepatomegaly and splenomegaly, not elsewhere classified",0-R16,0-R10-R19,TRUE +1,"0-Hepatomegaly and splenomegaly, not elsewhere classified",0-R16,2-R16,TRUE +1,"0-Hepatomegaly, not elsewhere classified",0-R16.0,0-R16,TRUE +1,"0-Hepatomegaly, not elsewhere classified",0-R16.0,2-R16.0,TRUE +1,"0-Splenomegaly, not elsewhere classified",0-R16.1,0-R16,TRUE +1,"0-Splenomegaly, not elsewhere classified",0-R16.1,2-R16.1,TRUE +1,"0-Hepatomegaly with splenomegaly, not elsewhere classified",0-R16.2,0-R16,TRUE +1,"0-Hepatomegaly with splenomegaly, not elsewhere classified",0-R16.2,2-R16.2,TRUE +1,0-Unspecified jaundice,0-R17,0-R10-R19,TRUE +1,0-Unspecified jaundice,0-R17,2-R17,TRUE +1,0-Ascites,0-R18,0-R10-R19,TRUE +1,0-Ascites,0-R18,2-R18,TRUE +1,0-Malignant ascites,0-R18.0,0-R18,TRUE +1,0-Malignant ascites,0-R18.0,2-R18.0,TRUE +1,0-Other ascites,0-R18.8,0-R18,TRUE +1,0-Other ascites,0-R18.8,2-R18.8,TRUE +1,0-Other symptoms and signs involving the digestive system and abdomen,0-R19,0-R10-R19,TRUE +1,0-Other symptoms and signs involving the digestive system and abdomen,0-R19,2-R19,TRUE +1,"0-Intra-abdominal and pelvic swelling, mass and lump",0-R19.0,0-R19,TRUE +1,"0-Intra-abdominal and pelvic swelling, mass and lump",0-R19.0,2-R19.0,TRUE +1,"0-Intra-abdominal and pelvic swelling, mass and lump, unspecified site",0-R19.00,0-R19.0,TRUE +1,"0-Intra-abdominal and pelvic swelling, mass and lump, unspecified site",0-R19.00,2-R19.00,TRUE +1,"0-Right upper quadrant abdominal swelling, mass and lump",0-R19.01,0-R19.0,TRUE +1,"0-Right upper quadrant abdominal swelling, mass and lump",0-R19.01,2-R19.01,TRUE +1,"0-Left upper quadrant abdominal swelling, mass and lump",0-R19.02,0-R19.0,TRUE +1,"0-Left upper quadrant abdominal swelling, mass and lump",0-R19.02,2-R19.02,TRUE +1,"0-Right lower quadrant abdominal swelling, mass and lump",0-R19.03,0-R19.0,TRUE +1,"0-Right lower quadrant abdominal swelling, mass and lump",0-R19.03,2-R19.03,TRUE +1,"0-Left lower quadrant abdominal swelling, mass and lump",0-R19.04,0-R19.0,TRUE +1,"0-Left lower quadrant abdominal swelling, mass and lump",0-R19.04,2-R19.04,TRUE +1,"0-Periumbilic swelling, mass or lump",0-R19.05,0-R19.0,TRUE +1,"0-Periumbilic swelling, mass or lump",0-R19.05,2-R19.05,TRUE +1,"0-Epigastric swelling, mass or lump",0-R19.06,0-R19.0,TRUE +1,"0-Epigastric swelling, mass or lump",0-R19.06,2-R19.06,TRUE +1,"0-Generalized intra-abdominal and pelvic swelling, mass and lump",0-R19.07,0-R19.0,TRUE +1,"0-Generalized intra-abdominal and pelvic swelling, mass and lump",0-R19.07,2-R19.07,TRUE +1,"0-Other intra-abdominal and pelvic swelling, mass and lump",0-R19.09,0-R19.0,TRUE +1,"0-Other intra-abdominal and pelvic swelling, mass and lump",0-R19.09,2-R19.09,TRUE +1,0-Abnormal bowel sounds,0-R19.1,0-R19,TRUE +1,0-Abnormal bowel sounds,0-R19.1,2-R19.1,TRUE +1,0-Absent bowel sounds,0-R19.11,0-R19.1,TRUE +1,0-Absent bowel sounds,0-R19.11,2-R19.11,TRUE +1,0-Hyperactive bowel sounds,0-R19.12,0-R19.1,TRUE +1,0-Hyperactive bowel sounds,0-R19.12,2-R19.12,TRUE +1,0-Other abnormal bowel sounds,0-R19.15,0-R19.1,TRUE +1,0-Other abnormal bowel sounds,0-R19.15,2-R19.15,TRUE +1,0-Visible peristalsis,0-R19.2,0-R19,TRUE +1,0-Visible peristalsis,0-R19.2,2-R19.2,TRUE +1,0-Abdominal rigidity,0-R19.3,0-R19,TRUE +1,0-Abdominal rigidity,0-R19.3,2-R19.3,TRUE +1,"0-Abdominal rigidity, unspecified site",0-R19.30,0-R19.3,TRUE +1,"0-Abdominal rigidity, unspecified site",0-R19.30,2-R19.30,TRUE +1,0-Right upper quadrant abdominal rigidity,0-R19.31,0-R19.3,TRUE +1,0-Right upper quadrant abdominal rigidity,0-R19.31,2-R19.31,TRUE +1,0-Left upper quadrant abdominal rigidity,0-R19.32,0-R19.3,TRUE +1,0-Left upper quadrant abdominal rigidity,0-R19.32,2-R19.32,TRUE +1,0-Right lower quadrant abdominal rigidity,0-R19.33,0-R19.3,TRUE +1,0-Right lower quadrant abdominal rigidity,0-R19.33,2-R19.33,TRUE +1,0-Left lower quadrant abdominal rigidity,0-R19.34,0-R19.3,TRUE +1,0-Left lower quadrant abdominal rigidity,0-R19.34,2-R19.34,TRUE +1,0-Periumbilic abdominal rigidity,0-R19.35,0-R19.3,TRUE +1,0-Periumbilic abdominal rigidity,0-R19.35,2-R19.35,TRUE +1,0-Epigastric abdominal rigidity,0-R19.36,0-R19.3,TRUE +1,0-Epigastric abdominal rigidity,0-R19.36,2-R19.36,TRUE +1,0-Generalized abdominal rigidity,0-R19.37,0-R19.3,TRUE +1,0-Generalized abdominal rigidity,0-R19.37,2-R19.37,TRUE +1,0-Change in bowel habit,0-R19.4,0-R19,TRUE +1,0-Change in bowel habit,0-R19.4,2-R19.4,TRUE +1,0-Other fecal abnormalities,0-R19.5,0-R19,TRUE +1,0-Other fecal abnormalities,0-R19.5,2-R19.5,TRUE +1,0-Halitosis,0-R19.6,0-R19,TRUE +1,0-Halitosis,0-R19.6,2-R19.6,TRUE +1,"0-Diarrhea, unspecified",0-R19.7,0-R19,TRUE +1,"0-Diarrhea, unspecified",0-R19.7,2-R19.7,TRUE +1,0-Other specified symptoms and signs involving the digestive system and abdomen,0-R19.8,0-R19,TRUE +1,0-Other specified symptoms and signs involving the digestive system and abdomen,0-R19.8,2-R19.8,TRUE +1,0-Fever of other and unknown origin,0-R50,0-R50-R69,TRUE +1,0-Fever of other and unknown origin,0-R50,2-R50,TRUE +1,0-General symptoms and signs,0-R50-R69,0-R00-R99,TRUE +1,0-General symptoms and signs,0-R50-R69,2-R50-R69,TRUE +1,0-Drug induced fever,0-R50.2,0-R50,TRUE +1,0-Drug induced fever,0-R50.2,2-R50.2,TRUE +1,0-Other specified fever,0-R50.8,0-R50,TRUE +1,0-Other specified fever,0-R50.8,2-R50.8,TRUE +1,0-Fever presenting with conditions classified elsewhere,0-R50.81,0-R50.8,TRUE +1,0-Fever presenting with conditions classified elsewhere,0-R50.81,2-R50.81,TRUE +1,0-Postprocedural fever,0-R50.82,0-R50.8,TRUE +1,0-Postprocedural fever,0-R50.82,2-R50.82,TRUE +1,0-Postvaccination fever,0-R50.83,0-R50.8,TRUE +1,0-Postvaccination fever,0-R50.83,2-R50.83,TRUE +1,0-Febrile nonhemolytic transfusion reaction,0-R50.84,0-R50.8,TRUE +1,0-Febrile nonhemolytic transfusion reaction,0-R50.84,2-R50.84,TRUE +1,"0-Fever, unspecified",0-R50.9,0-R50,TRUE +1,"0-Fever, unspecified",0-R50.9,2-R50.9,TRUE +1,0-Headache,0-R51,0-R50-R69,TRUE +1,0-Headache,0-R51,2-R51,TRUE +1,"0-Headache with orthostatic component, not elsewhere classified",0-R51.0,0-R51,TRUE +1,"0-Headache with orthostatic component, not elsewhere classified",0-R51.0,2-R51.0,TRUE +1,"0-Headache, unspecified",0-R51.9,0-R51,TRUE +1,"0-Headache, unspecified",0-R51.9,2-R51.9,TRUE +1,"0-Pain, unspecified",0-R52,0-R50-R69,TRUE +1,"0-Pain, unspecified",0-R52,2-R52,TRUE +1,0-Malaise and fatigue,0-R53,0-R50-R69,TRUE +1,0-Malaise and fatigue,0-R53,2-R53,TRUE +1,0-Neoplastic (malignant) related fatigue,0-R53.0,0-R53,TRUE +1,0-Neoplastic (malignant) related fatigue,0-R53.0,2-R53.0,TRUE +1,0-Weakness,0-R53.1,0-R53,TRUE +1,0-Weakness,0-R53.1,2-R53.1,TRUE +1,0-Functional quadriplegia,0-R53.2,0-R53,TRUE +1,0-Functional quadriplegia,0-R53.2,2-R53.2,TRUE +1,0-Other malaise and fatigue,0-R53.8,0-R53,TRUE +1,0-Other malaise and fatigue,0-R53.8,2-R53.8,TRUE +1,0-Other malaise,0-R53.81,0-R53.8,TRUE +1,0-Other malaise,0-R53.81,2-R53.81,TRUE +1,"0-Chronic fatigue, unspecified",0-R53.82,0-R53.8,TRUE +1,"0-Chronic fatigue, unspecified",0-R53.82,2-R53.82,TRUE +1,0-Other fatigue,0-R53.83,0-R53.8,TRUE +1,0-Other fatigue,0-R53.83,2-R53.83,TRUE +1,0-Age-related physical debility,0-R54,0-R50-R69,TRUE +1,0-Age-related physical debility,0-R54,2-R54,TRUE +1,0-Syncope and collapse,0-R55,0-R50-R69,TRUE +1,0-Syncope and collapse,0-R55,2-R55,TRUE +1,"0-Convulsions, not elsewhere classified",0-R56,0-R50-R69,TRUE +1,"0-Convulsions, not elsewhere classified",0-R56,2-R56,TRUE +1,0-Febrile convulsions,0-R56.0,0-R56,TRUE +1,0-Febrile convulsions,0-R56.0,2-R56.0,TRUE +1,0-Simple febrile convulsions,0-R56.00,0-R56.0,TRUE +1,0-Simple febrile convulsions,0-R56.00,2-R56.00,TRUE +1,0-Complex febrile convulsions,0-R56.01,0-R56.0,TRUE +1,0-Complex febrile convulsions,0-R56.01,2-R56.01,TRUE +1,0-Post traumatic seizures,0-R56.1,0-R56,TRUE +1,0-Post traumatic seizures,0-R56.1,2-R56.1,TRUE +1,0-Unspecified convulsions,0-R56.9,0-R56,TRUE +1,0-Unspecified convulsions,0-R56.9,2-R56.9,TRUE +1,"0-Shock, not elsewhere classified",0-R57,0-R50-R69,TRUE +1,"0-Shock, not elsewhere classified",0-R57,2-R57,TRUE +1,0-Cardiogenic shock,0-R57.0,0-R57,TRUE +1,0-Cardiogenic shock,0-R57.0,2-R57.0,TRUE +1,0-Hypovolemic shock,0-R57.1,0-R57,TRUE +1,0-Hypovolemic shock,0-R57.1,2-R57.1,TRUE +1,0-Other shock,0-R57.8,0-R57,TRUE +1,0-Other shock,0-R57.8,2-R57.8,TRUE +1,"0-Shock, unspecified",0-R57.9,0-R57,TRUE +1,"0-Shock, unspecified",0-R57.9,2-R57.9,TRUE +1,"0-Hemorrhage, not elsewhere classified",0-R58,0-R50-R69,TRUE +1,"0-Hemorrhage, not elsewhere classified",0-R58,2-R58,TRUE +1,0-Enlarged lymph nodes,0-R59,0-R50-R69,TRUE +1,0-Enlarged lymph nodes,0-R59,2-R59,TRUE +1,0-Localized enlarged lymph nodes,0-R59.0,0-R59,TRUE +1,0-Localized enlarged lymph nodes,0-R59.0,2-R59.0,TRUE +1,0-Generalized enlarged lymph nodes,0-R59.1,0-R59,TRUE +1,0-Generalized enlarged lymph nodes,0-R59.1,2-R59.1,TRUE +1,"0-Enlarged lymph nodes, unspecified",0-R59.9,0-R59,TRUE +1,"0-Enlarged lymph nodes, unspecified",0-R59.9,2-R59.9,TRUE +1,"0-Edema, not elsewhere classified",0-R60,0-R50-R69,TRUE +1,"0-Edema, not elsewhere classified",0-R60,2-R60,TRUE +1,0-Localized edema,0-R60.0,0-R60,TRUE +1,0-Localized edema,0-R60.0,2-R60.0,TRUE +1,0-Generalized edema,0-R60.1,0-R60,TRUE +1,0-Generalized edema,0-R60.1,2-R60.1,TRUE +1,"0-Edema, unspecified",0-R60.9,0-R60,TRUE +1,"0-Edema, unspecified",0-R60.9,2-R60.9,TRUE +1,0-Generalized hyperhidrosis,0-R61,0-R50-R69,TRUE +1,0-Generalized hyperhidrosis,0-R61,2-R61,TRUE +1,0-Lack of expected normal physiological development in childhood and adults,0-R62,0-R50-R69,TRUE +1,0-Lack of expected normal physiological development in childhood and adults,0-R62,2-R62,TRUE +1,0-Delayed milestone in childhood,0-R62.0,0-R62,TRUE +1,0-Delayed milestone in childhood,0-R62.0,2-R62.0,TRUE +1,0-Other and unspecified lack of expected normal physiological development in childhood,0-R62.5,0-R62,TRUE +1,0-Other and unspecified lack of expected normal physiological development in childhood,0-R62.5,2-R62.5,TRUE +1,0-Unspecified lack of expected normal physiological development in childhood,0-R62.50,0-R62.5,TRUE +1,0-Unspecified lack of expected normal physiological development in childhood,0-R62.50,2-R62.50,TRUE +1,0-Failure to thrive (child),0-R62.51,0-R62.5,TRUE +1,0-Failure to thrive (child),0-R62.51,2-R62.51,TRUE +1,0-Short stature (child),0-R62.52,0-R62.5,TRUE +1,0-Short stature (child),0-R62.52,2-R62.52,TRUE +1,0-Other lack of expected normal physiological development in childhood,0-R62.59,0-R62.5,TRUE +1,0-Other lack of expected normal physiological development in childhood,0-R62.59,2-R62.59,TRUE +1,0-Adult failure to thrive,0-R62.7,0-R62,TRUE +1,0-Adult failure to thrive,0-R62.7,2-R62.7,TRUE +1,0-Symptoms and signs concerning food and fluid intake,0-R63,0-R50-R69,TRUE +1,0-Symptoms and signs concerning food and fluid intake,0-R63,2-R63,TRUE +1,0-Anorexia,0-R63.0,0-R63,TRUE +1,0-Anorexia,0-R63.0,2-R63.0,TRUE +1,0-Polydipsia,0-R63.1,0-R63,TRUE +1,0-Polydipsia,0-R63.1,2-R63.1,TRUE +1,0-Polyphagia,0-R63.2,0-R63,TRUE +1,0-Polyphagia,0-R63.2,2-R63.2,TRUE +1,0-Feeding difficulties,0-R63.3,0-R63,TRUE +1,0-Feeding difficulties,0-R63.3,2-R63.3,TRUE +1,"0-Feeding difficulties, unspecified",0-R63.30,0-R63.3,TRUE +1,"0-Feeding difficulties, unspecified",0-R63.30,2-R63.30,TRUE +1,"0-Pediatric feeding disorder, acute",0-R63.31,0-R63.3,TRUE +1,"0-Pediatric feeding disorder, acute",0-R63.31,2-R63.31,TRUE +1,"0-Pediatric feeding disorder, chronic",0-R63.32,0-R63.3,TRUE +1,"0-Pediatric feeding disorder, chronic",0-R63.32,2-R63.32,TRUE +1,0-Other feeding difficulties,0-R63.39,0-R63.3,TRUE +1,0-Other feeding difficulties,0-R63.39,2-R63.39,TRUE +1,0-Abnormal weight loss,0-R63.4,0-R63,TRUE +1,0-Abnormal weight loss,0-R63.4,2-R63.4,TRUE +1,0-Abnormal weight gain,0-R63.5,0-R63,TRUE +1,0-Abnormal weight gain,0-R63.5,2-R63.5,TRUE +1,0-Underweight,0-R63.6,0-R63,TRUE +1,0-Underweight,0-R63.6,2-R63.6,TRUE +1,0-Other symptoms and signs concerning food and fluid intake,0-R63.8,0-R63,TRUE +1,0-Other symptoms and signs concerning food and fluid intake,0-R63.8,2-R63.8,TRUE +1,0-Cachexia,0-R64,0-R50-R69,TRUE +1,0-Cachexia,0-R64,2-R64,TRUE +1,0-Symptoms and signs specifically associated with systemic inflammation and infection,0-R65,0-R50-R69,TRUE +1,0-Symptoms and signs specifically associated with systemic inflammation and infection,0-R65,2-R65,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin,0-R65.1,0-R65,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin,0-R65.1,2-R65.1,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction,0-R65.10,0-R65.1,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction,0-R65.10,2-R65.10,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction,0-R65.11,0-R65.1,TRUE +1,0-Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction,0-R65.11,2-R65.11,TRUE +1,0-Severe sepsis,0-R65.2,0-R65,TRUE +1,0-Severe sepsis,0-R65.2,2-R65.2,TRUE +1,0-Severe sepsis without septic shock,0-R65.20,0-R65.2,TRUE +1,0-Severe sepsis without septic shock,0-R65.20,2-R65.20,TRUE +1,0-Severe sepsis with septic shock,0-R65.21,0-R65.2,TRUE +1,0-Severe sepsis with septic shock,0-R65.21,2-R65.21,TRUE +1,0-Other general symptoms and signs,0-R68,0-R50-R69,TRUE +1,0-Other general symptoms and signs,0-R68,2-R68,TRUE +1,"0-Hypothermia, not associated with low environmental temperature",0-R68.0,0-R68,TRUE +1,"0-Hypothermia, not associated with low environmental temperature",0-R68.0,2-R68.0,TRUE +1,0-Nonspecific symptoms peculiar to infancy,0-R68.1,0-R68,TRUE +1,0-Nonspecific symptoms peculiar to infancy,0-R68.1,2-R68.1,TRUE +1,0-Excessive crying of infant (baby),0-R68.11,0-R68.1,TRUE +1,0-Excessive crying of infant (baby),0-R68.11,2-R68.11,TRUE +1,0-Fussy infant (baby),0-R68.12,0-R68.1,TRUE +1,0-Fussy infant (baby),0-R68.12,2-R68.12,TRUE +1,0-Apparent life threatening event in infant (ALTE),0-R68.13,0-R68.1,TRUE +1,0-Apparent life threatening event in infant (ALTE),0-R68.13,2-R68.13,TRUE +1,0-Other nonspecific symptoms peculiar to infancy,0-R68.19,0-R68.1,TRUE +1,0-Other nonspecific symptoms peculiar to infancy,0-R68.19,2-R68.19,TRUE +1,"0-Dry mouth, unspecified",0-R68.2,0-R68,TRUE +1,"0-Dry mouth, unspecified",0-R68.2,2-R68.2,TRUE +1,0-Clubbing of fingers,0-R68.3,0-R68,TRUE +1,0-Clubbing of fingers,0-R68.3,2-R68.3,TRUE +1,0-Other general symptoms and signs,0-R68.8,0-R68,TRUE +1,0-Other general symptoms and signs,0-R68.8,2-R68.8,TRUE +1,0-Early satiety,0-R68.81,0-R68.8,TRUE +1,0-Early satiety,0-R68.81,2-R68.81,TRUE +1,0-Decreased libido,0-R68.82,0-R68.8,TRUE +1,0-Decreased libido,0-R68.82,2-R68.82,TRUE +1,0-Chills (without fever),0-R68.83,0-R68.8,TRUE +1,0-Chills (without fever),0-R68.83,2-R68.83,TRUE +1,0-Jaw pain,0-R68.84,0-R68.8,TRUE +1,0-Jaw pain,0-R68.84,2-R68.84,TRUE +1,0-Other general symptoms and signs,0-R68.89,0-R68.8,TRUE +1,0-Other general symptoms and signs,0-R68.89,2-R68.89,TRUE +1,"0-Illness, unspecified",0-R69,0-R50-R69,TRUE +1,"0-Illness, unspecified",0-R69,2-R69,TRUE +1,0-ICD-10 Root,0-Root,2-Root,TRUE +1,,0-Vibrio vulnificus,0-dummy2,TRUE +1,,0-Vibrio vulnificus,2-Vibrio vulnificus,TRUE +1,,0-dummy1,0-Root,TRUE +1,,0-dummy1,2-dummy1,TRUE +1,,0-dummy2,0-dummy1,TRUE +1,,0-dummy2,2-dummy2,TRUE +1,1-Cholera,1-A00,1-A00-A09, +1,1-Cholera,1-A00,2-A00, +1,1-Intestinal infectious diseases,1-A00-A09,1-A00-B99,TRUE +1,1-Intestinal infectious diseases,1-A00-A09,2-A00-A09,TRUE +1,1-Certain infectious and parasitic diseases,1-A00-B99,1-Root, +1,1-Certain infectious and parasitic diseases,1-A00-B99,2-A00-B99, +1,"1-Cholera due to Vibrio cholerae 01, biovar cholerae",1-A00.0,1-A00, +1,"1-Cholera due to Vibrio cholerae 01, biovar cholerae",1-A00.0,2-A00.0, +1,"1-Cholera due to Vibrio cholerae 01, biovar eltor",1-A00.1,1-A00, +1,"1-Cholera due to Vibrio cholerae 01, biovar eltor",1-A00.1,2-A00.1, +1,"1-Cholera, unspecified",1-A00.9,1-A00, +1,"1-Cholera, unspecified",1-A00.9,2-A00.9, +1,1-Typhoid and paratyphoid fevers,1-A01,1-A00-A09, +1,1-Typhoid and paratyphoid fevers,1-A01,2-A01, +1,1-Typhoid fever,1-A01.0,1-A01, +1,1-Typhoid fever,1-A01.0,2-A01.0, +1,"1-Typhoid fever, unspecified",1-A01.00,1-A01.0, +1,"1-Typhoid fever, unspecified",1-A01.00,2-A01.00, +1,1-Typhoid meningitis,1-A01.01,1-A01.0, +1,1-Typhoid meningitis,1-A01.01,2-A01.01, +1,1-Typhoid fever with heart involvement,1-A01.02,1-A01.0, +1,1-Typhoid fever with heart involvement,1-A01.02,2-A01.02, +1,1-Typhoid pneumonia,1-A01.03,1-A01.0, +1,1-Typhoid pneumonia,1-A01.03,2-A01.03, +1,1-Typhoid arthritis,1-A01.04,1-A01.0, +1,1-Typhoid arthritis,1-A01.04,2-A01.04, +1,1-Typhoid osteomyelitis,1-A01.05,1-A01.0, +1,1-Typhoid osteomyelitis,1-A01.05,2-A01.05, +1,1-Typhoid fever with other complications,1-A01.09,1-A01.0, +1,1-Typhoid fever with other complications,1-A01.09,2-A01.09, +1,1-Paratyphoid fever A,1-A01.1,1-A01, +1,1-Paratyphoid fever A,1-A01.1,2-A01.1, +1,1-Paratyphoid fever B,1-A01.2,1-A01, +1,1-Paratyphoid fever B,1-A01.2,2-A01.2, +1,1-Paratyphoid fever C,1-A01.3,1-A01, +1,1-Paratyphoid fever C,1-A01.3,2-A01.3, +1,"1-Paratyphoid fever, unspecified",1-A01.4,1-A01, +1,"1-Paratyphoid fever, unspecified",1-A01.4,2-A01.4, +1,1-Other salmonella infections,1-A02,1-A00-A09, +1,1-Other salmonella infections,1-A02,2-A02, +1,1-Salmonella enteritis,1-A02.0,1-A02, +1,1-Salmonella enteritis,1-A02.0,2-A02.0, +1,1-Salmonella sepsis,1-A02.1,1-A02, +1,1-Salmonella sepsis,1-A02.1,2-A02.1, +1,1-Localized salmonella infections,1-A02.2,1-A02, +1,1-Localized salmonella infections,1-A02.2,2-A02.2, +1,"1-Localized salmonella infection, unspecified",1-A02.20,1-A02.2, +1,"1-Localized salmonella infection, unspecified",1-A02.20,2-A02.20, +1,1-Salmonella meningitis,1-A02.21,1-A02.2, +1,1-Salmonella meningitis,1-A02.21,2-A02.21, +1,1-Salmonella pneumonia,1-A02.22,1-A02.2, +1,1-Salmonella pneumonia,1-A02.22,2-A02.22, +1,1-Salmonella arthritis,1-A02.23,1-A02.2, +1,1-Salmonella arthritis,1-A02.23,2-A02.23, +1,1-Salmonella osteomyelitis,1-A02.24,1-A02.2, +1,1-Salmonella osteomyelitis,1-A02.24,2-A02.24, +1,1-Salmonella pyelonephritis,1-A02.25,1-A02.2, +1,1-Salmonella pyelonephritis,1-A02.25,2-A02.25, +1,1-Salmonella with other localized infection,1-A02.29,1-A02.2, +1,1-Salmonella with other localized infection,1-A02.29,2-A02.29, +1,1-Other specified salmonella infections,1-A02.8,1-A02, +1,1-Other specified salmonella infections,1-A02.8,2-A02.8, +1,"1-Salmonella infection, unspecified",1-A02.9,1-A02, +1,"1-Salmonella infection, unspecified",1-A02.9,2-A02.9, +1,1-Shigellosis,1-A03,1-A00-A09, +1,1-Shigellosis,1-A03,2-A03, +1,1-Shigellosis due to Shigella dysenteriae,1-A03.0,1-A03, +1,1-Shigellosis due to Shigella dysenteriae,1-A03.0,2-A03.0, +1,1-Shigellosis due to Shigella flexneri,1-A03.1,1-A03, +1,1-Shigellosis due to Shigella flexneri,1-A03.1,2-A03.1, +1,1-Shigellosis due to Shigella boydii,1-A03.2,1-A03, +1,1-Shigellosis due to Shigella boydii,1-A03.2,2-A03.2, +1,1-Shigellosis due to Shigella sonnei,1-A03.3,1-A03, +1,1-Shigellosis due to Shigella sonnei,1-A03.3,2-A03.3, +1,1-Other shigellosis,1-A03.8,1-A03, +1,1-Other shigellosis,1-A03.8,2-A03.8, +1,"1-Shigellosis, unspecified",1-A03.9,1-A03, +1,"1-Shigellosis, unspecified",1-A03.9,2-A03.9, +1,1-Other bacterial intestinal infections,1-A04,1-A00-A09, +1,1-Other bacterial intestinal infections,1-A04,2-A04, +1,1-Enteropathogenic Escherichia coli infection,1-A04.0,1-A04, +1,1-Enteropathogenic Escherichia coli infection,1-A04.0,1-Escherichia coli, +1,1-Enteropathogenic Escherichia coli infection,1-A04.0,2-A04.0, +1,1-Enterotoxigenic Escherichia coli infection,1-A04.1,1-A04, +1,1-Enterotoxigenic Escherichia coli infection,1-A04.1,1-Escherichia coli, +1,1-Enterotoxigenic Escherichia coli infection,1-A04.1,2-A04.1, +1,1-Enteroinvasive Escherichia coli infection,1-A04.2,1-A04, +1,1-Enteroinvasive Escherichia coli infection,1-A04.2,1-Escherichia coli, +1,1-Enteroinvasive Escherichia coli infection,1-A04.2,2-A04.2, +1,1-Enterohemorrhagic Escherichia coli infection,1-A04.3,1-A04, +1,1-Enterohemorrhagic Escherichia coli infection,1-A04.3,1-Escherichia coli, +1,1-Enterohemorrhagic Escherichia coli infection,1-A04.3,2-A04.3, +1,1-Other intestinal Escherichia coli infections,1-A04.4,1-A04, +1,1-Other intestinal Escherichia coli infections,1-A04.4,1-Escherichia coli, +1,1-Other intestinal Escherichia coli infections,1-A04.4,2-A04.4, +1,1-Campylobacter enteritis,1-A04.5,1-A04, +1,1-Campylobacter enteritis,1-A04.5,2-A04.5, +1,1-Enteritis due to Yersinia enterocolitica,1-A04.6,1-A04, +1,1-Enteritis due to Yersinia enterocolitica,1-A04.6,2-A04.6, +1,1-Enterocolitis due to Clostridium difficile,1-A04.7,1-A04, +1,1-Enterocolitis due to Clostridium difficile,1-A04.7,2-A04.7, +1,"1-Enterocolitis due to Clostridium difficile, recurrent",1-A04.71,1-A04.7, +1,"1-Enterocolitis due to Clostridium difficile, recurrent",1-A04.71,2-A04.71, +1,"1-Enterocolitis due to Clostridium difficile, not specified as recurrent",1-A04.72,1-A04.7, +1,"1-Enterocolitis due to Clostridium difficile, not specified as recurrent",1-A04.72,2-A04.72, +1,1-Other specified bacterial intestinal infections,1-A04.8,1-A04, +1,1-Other specified bacterial intestinal infections,1-A04.8,2-A04.8, +1,"1-Bacterial intestinal infection, unspecified",1-A04.9,1-A04, +1,"1-Bacterial intestinal infection, unspecified",1-A04.9,2-A04.9, +1,"1-Other bacterial foodborne intoxications, not elsewhere classified",1-A05,1-A00-A09, +1,"1-Other bacterial foodborne intoxications, not elsewhere classified",1-A05,2-A05, +1,1-Foodborne staphylococcal intoxication,1-A05.0,1-A05, +1,1-Foodborne staphylococcal intoxication,1-A05.0,2-A05.0, +1,1-Botulism food poisoning,1-A05.1,1-A05, +1,1-Botulism food poisoning,1-A05.1,2-A05.1, +1,1-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,1-A05.2,1-A05, +1,1-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,1-A05.2,1-Clostridium perfringens, +1,1-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,1-A05.2,2-A05.2, +1,1-Foodborne Vibrio parahaemolyticus intoxication,1-A05.3,1-A05, +1,1-Foodborne Vibrio parahaemolyticus intoxication,1-A05.3,2-A05.3, +1,1-Foodborne Bacillus cereus intoxication,1-A05.4,1-A05, +1,1-Foodborne Bacillus cereus intoxication,1-A05.4,2-A05.4, +1,1-Foodborne Vibrio vulnificus intoxication,1-A05.5,1-A05, +1,1-Foodborne Vibrio vulnificus intoxication,1-A05.5,1-Vibrio vulnificus, +1,1-Foodborne Vibrio vulnificus intoxication,1-A05.5,2-A05.5, +1,1-Other specified bacterial foodborne intoxications,1-A05.8,1-A05, +1,1-Other specified bacterial foodborne intoxications,1-A05.8,2-A05.8, +1,"1-Bacterial foodborne intoxication, unspecified",1-A05.9,1-A05, +1,"1-Bacterial foodborne intoxication, unspecified",1-A05.9,2-A05.9, +1,1-Amebiasis,1-A06,1-A00-A09, +1,1-Amebiasis,1-A06,2-A06, +1,1-Acute amebic dysentery,1-A06.0,1-A06, +1,1-Acute amebic dysentery,1-A06.0,2-A06.0, +1,1-Chronic intestinal amebiasis,1-A06.1,1-A06, +1,1-Chronic intestinal amebiasis,1-A06.1,2-A06.1, +1,1-Amebic nondysenteric colitis,1-A06.2,1-A06, +1,1-Amebic nondysenteric colitis,1-A06.2,2-A06.2, +1,1-Ameboma of intestine,1-A06.3,1-A06, +1,1-Ameboma of intestine,1-A06.3,2-A06.3, +1,1-Amebic liver abscess,1-A06.4,1-A06, +1,1-Amebic liver abscess,1-A06.4,2-A06.4, +1,1-Amebic lung abscess,1-A06.5,1-A06, +1,1-Amebic lung abscess,1-A06.5,2-A06.5, +1,1-Amebic brain abscess,1-A06.6,1-A06, +1,1-Amebic brain abscess,1-A06.6,2-A06.6, +1,1-Cutaneous amebiasis,1-A06.7,1-A06, +1,1-Cutaneous amebiasis,1-A06.7,2-A06.7, +1,1-Amebic infection of other sites,1-A06.8,1-A06, +1,1-Amebic infection of other sites,1-A06.8,2-A06.8, +1,1-Amebic cystitis,1-A06.81,1-A06.8, +1,1-Amebic cystitis,1-A06.81,2-A06.81, +1,1-Other amebic genitourinary infections,1-A06.82,1-A06.8, +1,1-Other amebic genitourinary infections,1-A06.82,2-A06.82, +1,1-Other amebic infections,1-A06.89,1-A06.8, +1,1-Other amebic infections,1-A06.89,2-A06.89, +1,"1-Amebiasis, unspecified",1-A06.9,1-A06, +1,"1-Amebiasis, unspecified",1-A06.9,2-A06.9, +1,1-Other protozoal intestinal diseases,1-A07,1-A00-A09, +1,1-Other protozoal intestinal diseases,1-A07,2-A07, +1,1-Balantidiasis,1-A07.0,1-A07, +1,1-Balantidiasis,1-A07.0,2-A07.0, +1,1-Giardiasis [lambliasis],1-A07.1,1-A07, +1,1-Giardiasis [lambliasis],1-A07.1,2-A07.1, +1,1-Cryptosporidiosis,1-A07.2,1-A07, +1,1-Cryptosporidiosis,1-A07.2,2-A07.2, +1,1-Isosporiasis,1-A07.3,1-A07, +1,1-Isosporiasis,1-A07.3,2-A07.3, +1,1-Cyclosporiasis,1-A07.4,1-A07, +1,1-Cyclosporiasis,1-A07.4,2-A07.4, +1,1-Other specified protozoal intestinal diseases,1-A07.8,1-A07, +1,1-Other specified protozoal intestinal diseases,1-A07.8,2-A07.8, +1,"1-Protozoal intestinal disease, unspecified",1-A07.9,1-A07, +1,"1-Protozoal intestinal disease, unspecified",1-A07.9,2-A07.9, +1,1-Viral and other specified intestinal infections,1-A08,1-A00-A09, +1,1-Viral and other specified intestinal infections,1-A08,2-A08, +1,1-Rotaviral enteritis,1-A08.0,1-A08, +1,1-Rotaviral enteritis,1-A08.0,2-A08.0, +1,1-Acute gastroenteropathy due to Norwalk agent and other small round viruses,1-A08.1,1-A08, +1,1-Acute gastroenteropathy due to Norwalk agent and other small round viruses,1-A08.1,2-A08.1, +1,1-Acute gastroenteropathy due to Norwalk agent,1-A08.11,1-A08.1, +1,1-Acute gastroenteropathy due to Norwalk agent,1-A08.11,2-A08.11, +1,1-Acute gastroenteropathy due to other small round viruses,1-A08.19,1-A08.1, +1,1-Acute gastroenteropathy due to other small round viruses,1-A08.19,2-A08.19, +1,1-Adenoviral enteritis,1-A08.2,1-A08, +1,1-Adenoviral enteritis,1-A08.2,2-A08.2, +1,1-Other viral enteritis,1-A08.3,1-A08, +1,1-Other viral enteritis,1-A08.3,2-A08.3, +1,1-Calicivirus enteritis,1-A08.31,1-A08.3, +1,1-Calicivirus enteritis,1-A08.31,2-A08.31, +1,1-Astrovirus enteritis,1-A08.32,1-A08.3, +1,1-Astrovirus enteritis,1-A08.32,2-A08.32, +1,1-Other viral enteritis,1-A08.39,1-A08.3, +1,1-Other viral enteritis,1-A08.39,2-A08.39, +1,"1-Viral intestinal infection, unspecified",1-A08.4,1-A08, +1,"1-Viral intestinal infection, unspecified",1-A08.4,2-A08.4, +1,1-Other specified intestinal infections,1-A08.8,1-A08, +1,1-Other specified intestinal infections,1-A08.8,2-A08.8, +1,"1-Infectious gastroenteritis and colitis, unspecified",1-A09,1-A00-A09, +1,"1-Infectious gastroenteritis and colitis, unspecified",1-A09,2-A09, +1,,1-Clostridium perfringens,1-dummy2, +1,,1-Clostridium perfringens,2-Clostridium perfringens, +1,,1-Escherichia coli,1-dummy2, +1,,1-Escherichia coli,2-Escherichia coli, +1,1-Acute nasopharyngitis [common cold],1-J00,1-J00-J06, +1,1-Acute nasopharyngitis [common cold],1-J00,2-J00, +1,1-Acute upper respiratory infections,1-J00-J06,1-J00-J99,TRUE +1,1-Acute upper respiratory infections,1-J00-J06,2-J00-J06,TRUE +1,1-Diseases of the respiratory system,1-J00-J99,1-Root, +1,1-Diseases of the respiratory system,1-J00-J99,2-J00-J99, +1,1-Acute sinusitis,1-J01,1-J00-J06, +1,1-Acute sinusitis,1-J01,2-J01, +1,1-Acute maxillary sinusitis,1-J01.0,1-J01, +1,1-Acute maxillary sinusitis,1-J01.0,2-J01.0, +1,"1-Acute maxillary sinusitis, unspecified",1-J01.00,1-J01.0, +1,"1-Acute maxillary sinusitis, unspecified",1-J01.00,2-J01.00, +1,1-Acute recurrent maxillary sinusitis,1-J01.01,1-J01.0, +1,1-Acute recurrent maxillary sinusitis,1-J01.01,2-J01.01, +1,1-Acute frontal sinusitis,1-J01.1,1-J01, +1,1-Acute frontal sinusitis,1-J01.1,2-J01.1, +1,"1-Acute frontal sinusitis, unspecified",1-J01.10,1-J01.1, +1,"1-Acute frontal sinusitis, unspecified",1-J01.10,2-J01.10, +1,1-Acute recurrent frontal sinusitis,1-J01.11,1-J01.1, +1,1-Acute recurrent frontal sinusitis,1-J01.11,2-J01.11, +1,1-Acute ethmoidal sinusitis,1-J01.2,1-J01, +1,1-Acute ethmoidal sinusitis,1-J01.2,2-J01.2, +1,"1-Acute ethmoidal sinusitis, unspecified",1-J01.20,1-J01.2, +1,"1-Acute ethmoidal sinusitis, unspecified",1-J01.20,2-J01.20, +1,1-Acute recurrent ethmoidal sinusitis,1-J01.21,1-J01.2, +1,1-Acute recurrent ethmoidal sinusitis,1-J01.21,2-J01.21, +1,1-Acute sphenoidal sinusitis,1-J01.3,1-J01, +1,1-Acute sphenoidal sinusitis,1-J01.3,2-J01.3, +1,"1-Acute sphenoidal sinusitis, unspecified",1-J01.30,1-J01.3, +1,"1-Acute sphenoidal sinusitis, unspecified",1-J01.30,2-J01.30, +1,1-Acute recurrent sphenoidal sinusitis,1-J01.31,1-J01.3, +1,1-Acute recurrent sphenoidal sinusitis,1-J01.31,2-J01.31, +1,1-Acute pansinusitis,1-J01.4,1-J01, +1,1-Acute pansinusitis,1-J01.4,2-J01.4, +1,"1-Acute pansinusitis, unspecified",1-J01.40,1-J01.4, +1,"1-Acute pansinusitis, unspecified",1-J01.40,2-J01.40, +1,1-Acute recurrent pansinusitis,1-J01.41,1-J01.4, +1,1-Acute recurrent pansinusitis,1-J01.41,2-J01.41, +1,1-Other acute sinusitis,1-J01.8,1-J01, +1,1-Other acute sinusitis,1-J01.8,2-J01.8, +1,1-Other acute sinusitis,1-J01.80,1-J01.8, +1,1-Other acute sinusitis,1-J01.80,2-J01.80, +1,1-Other acute recurrent sinusitis,1-J01.81,1-J01.8, +1,1-Other acute recurrent sinusitis,1-J01.81,2-J01.81, +1,"1-Acute sinusitis, unspecified",1-J01.9,1-J01, +1,"1-Acute sinusitis, unspecified",1-J01.9,2-J01.9, +1,"1-Acute sinusitis, unspecified",1-J01.90,1-J01.9, +1,"1-Acute sinusitis, unspecified",1-J01.90,2-J01.90, +1,"1-Acute recurrent sinusitis, unspecified",1-J01.91,1-J01.9, +1,"1-Acute recurrent sinusitis, unspecified",1-J01.91,2-J01.91, +1,1-Acute pharyngitis,1-J02,1-J00-J06, +1,1-Acute pharyngitis,1-J02,2-J02, +1,1-Streptococcal pharyngitis,1-J02.0,1-J02, +1,1-Streptococcal pharyngitis,1-J02.0,1-Other streptococcus, +1,1-Streptococcal pharyngitis,1-J02.0,2-J02.0, +1,1-Acute pharyngitis due to other specified organisms,1-J02.8,1-J02, +1,1-Acute pharyngitis due to other specified organisms,1-J02.8,2-J02.8, +1,"1-Acute pharyngitis, unspecified",1-J02.9,1-J02, +1,"1-Acute pharyngitis, unspecified",1-J02.9,2-J02.9, +1,1-Acute tonsillitis,1-J03,1-J00-J06, +1,1-Acute tonsillitis,1-J03,2-J03, +1,1-Streptococcal tonsillitis,1-J03.0,1-J03, +1,1-Streptococcal tonsillitis,1-J03.0,1-Other streptococcus, +1,1-Streptococcal tonsillitis,1-J03.0,2-J03.0, +1,"1-Acute streptococcal tonsillitis, unspecified",1-J03.00,1-J03.0, +1,"1-Acute streptococcal tonsillitis, unspecified",1-J03.00,2-J03.00, +1,1-Acute recurrent streptococcal tonsillitis,1-J03.01,1-J03.0, +1,1-Acute recurrent streptococcal tonsillitis,1-J03.01,2-J03.01, +1,1-Acute tonsillitis due to other specified organisms,1-J03.8,1-J03, +1,1-Acute tonsillitis due to other specified organisms,1-J03.8,2-J03.8, +1,1-Acute tonsillitis due to other specified organisms,1-J03.80,1-J03.8, +1,1-Acute tonsillitis due to other specified organisms,1-J03.80,2-J03.80, +1,1-Acute recurrent tonsillitis due to other specified organisms,1-J03.81,1-J03.8, +1,1-Acute recurrent tonsillitis due to other specified organisms,1-J03.81,2-J03.81, +1,"1-Acute tonsillitis, unspecified",1-J03.9,1-J03, +1,"1-Acute tonsillitis, unspecified",1-J03.9,2-J03.9, +1,"1-Acute tonsillitis, unspecified",1-J03.90,1-J03.9, +1,"1-Acute tonsillitis, unspecified",1-J03.90,2-J03.90, +1,"1-Acute recurrent tonsillitis, unspecified",1-J03.91,1-J03.9, +1,"1-Acute recurrent tonsillitis, unspecified",1-J03.91,2-J03.91, +1,1-Acute laryngitis and tracheitis,1-J04,1-J00-J06, +1,1-Acute laryngitis and tracheitis,1-J04,2-J04, +1,1-Acute laryngitis,1-J04.0,1-J04, +1,1-Acute laryngitis,1-J04.0,2-J04.0, +1,1-Acute tracheitis,1-J04.1,1-J04, +1,1-Acute tracheitis,1-J04.1,2-J04.1, +1,1-Acute tracheitis without obstruction,1-J04.10,1-J04.1, +1,1-Acute tracheitis without obstruction,1-J04.10,2-J04.10, +1,1-Acute tracheitis with obstruction,1-J04.11,1-J04.1, +1,1-Acute tracheitis with obstruction,1-J04.11,2-J04.11, +1,1-Acute laryngotracheitis,1-J04.2,1-J04, +1,1-Acute laryngotracheitis,1-J04.2,2-J04.2, +1,"1-Supraglottitis, unspecified",1-J04.3,1-J04, +1,"1-Supraglottitis, unspecified",1-J04.3,2-J04.3, +1,"1-Supraglottitis, unspecified, without obstruction",1-J04.30,1-J04.3, +1,"1-Supraglottitis, unspecified, without obstruction",1-J04.30,2-J04.30, +1,"1-Supraglottitis, unspecified, with obstruction",1-J04.31,1-J04.3, +1,"1-Supraglottitis, unspecified, with obstruction",1-J04.31,2-J04.31, +1,1-Acute obstructive laryngitis [croup] and epiglottitis,1-J05,1-J00-J06, +1,1-Acute obstructive laryngitis [croup] and epiglottitis,1-J05,2-J05, +1,1-Acute obstructive laryngitis [croup],1-J05.0,1-J05, +1,1-Acute obstructive laryngitis [croup],1-J05.0,2-J05.0, +1,1-Acute epiglottitis,1-J05.1,1-J05, +1,1-Acute epiglottitis,1-J05.1,2-J05.1, +1,1-Acute epiglottitis without obstruction,1-J05.10,1-J05.1, +1,1-Acute epiglottitis without obstruction,1-J05.10,2-J05.10, +1,1-Acute epiglottitis with obstruction,1-J05.11,1-J05.1, +1,1-Acute epiglottitis with obstruction,1-J05.11,2-J05.11, +1,1-Acute upper respiratory infections of multiple and unspecified sites,1-J06,1-J00-J06, +1,1-Acute upper respiratory infections of multiple and unspecified sites,1-J06,2-J06, +1,1-Acute laryngopharyngitis,1-J06.0,1-J06, +1,1-Acute laryngopharyngitis,1-J06.0,2-J06.0, +1,"1-Acute upper respiratory infection, unspecified",1-J06.9,1-J06, +1,"1-Acute upper respiratory infection, unspecified",1-J06.9,2-J06.9, +1,,1-Other streptococcus,1-dummy2, +1,,1-Other streptococcus,2-Other streptococcus, +1,"1-Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",1-R00-R99,1-Root, +1,"1-Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",1-R00-R99,2-R00-R99, +1,1-Abdominal and pelvic pain,1-R10,1-R10-R19, +1,1-Abdominal and pelvic pain,1-R10,2-R10, +1,1-Symptoms and signs involving the digestive system and abdomen,1-R10-R19,1-R00-R99,TRUE +1,1-Symptoms and signs involving the digestive system and abdomen,1-R10-R19,2-R10-R19,TRUE +1,1-Acute abdomen,1-R10.0,1-R10, +1,1-Acute abdomen,1-R10.0,2-R10.0, +1,1-Pain localized to upper abdomen,1-R10.1,1-R10, +1,1-Pain localized to upper abdomen,1-R10.1,2-R10.1, +1,"1-Upper abdominal pain, unspecified",1-R10.10,1-R10.1, +1,"1-Upper abdominal pain, unspecified",1-R10.10,2-R10.10, +1,1-Right upper quadrant pain,1-R10.11,1-R10.1, +1,1-Right upper quadrant pain,1-R10.11,2-R10.11, +1,1-Left upper quadrant pain,1-R10.12,1-R10.1, +1,1-Left upper quadrant pain,1-R10.12,2-R10.12, +1,1-Epigastric pain,1-R10.13,1-R10.1, +1,1-Epigastric pain,1-R10.13,2-R10.13, +1,1-Pelvic and perineal pain,1-R10.2,1-R10, +1,1-Pelvic and perineal pain,1-R10.2,2-R10.2, +1,1-Pelvic and perineal pain unspecified side,1-R10.20,1-R10.2,TRUE +1,1-Pelvic and perineal pain unspecified side,1-R10.20,2-R10.20,TRUE +1,1-Pelvic and perineal pain right side,1-R10.21,1-R10.2,TRUE +1,1-Pelvic and perineal pain right side,1-R10.21,2-R10.21,TRUE +1,1-Pelvic and perineal pain left side,1-R10.22,1-R10.2,TRUE +1,1-Pelvic and perineal pain left side,1-R10.22,2-R10.22,TRUE +1,1-Pelvic and perineal pain bilateral,1-R10.23,1-R10.2,TRUE +1,1-Pelvic and perineal pain bilateral,1-R10.23,2-R10.23,TRUE +1,1-Suprapubic pain,1-R10.24,1-R10.2,TRUE +1,1-Suprapubic pain,1-R10.24,2-R10.24,TRUE +1,1-Pain localized to other parts of lower abdomen,1-R10.3,1-R10, +1,1-Pain localized to other parts of lower abdomen,1-R10.3,2-R10.3, +1,"1-Lower abdominal pain, unspecified",1-R10.30,1-R10.3, +1,"1-Lower abdominal pain, unspecified",1-R10.30,2-R10.30, +1,1-Right lower quadrant pain,1-R10.31,1-R10.3, +1,1-Right lower quadrant pain,1-R10.31,2-R10.31, +1,1-Left lower quadrant pain,1-R10.32,1-R10.3, +1,1-Left lower quadrant pain,1-R10.32,2-R10.32, +1,1-Periumbilical pain,1-R10.33,1-R10.3, +1,1-Periumbilical pain,1-R10.33,2-R10.33, +1,1-Other abdominal pain,1-R10.8,1-R10, +1,1-Other abdominal pain,1-R10.8,2-R10.8, +1,1-Abdominal tenderness,1-R10.81,1-R10.8, +1,1-Abdominal tenderness,1-R10.81,2-R10.81, +1,1-Right upper quadrant abdominal tenderness,1-R10.811,1-R10.81, +1,1-Right upper quadrant abdominal tenderness,1-R10.811,2-R10.811, +1,1-Left upper quadrant abdominal tenderness,1-R10.812,1-R10.81, +1,1-Left upper quadrant abdominal tenderness,1-R10.812,2-R10.812, +1,1-Right lower quadrant abdominal tenderness,1-R10.813,1-R10.81, +1,1-Right lower quadrant abdominal tenderness,1-R10.813,2-R10.813, +1,1-Left lower quadrant abdominal tenderness,1-R10.814,1-R10.81, +1,1-Left lower quadrant abdominal tenderness,1-R10.814,2-R10.814, +1,1-Periumbilic abdominal tenderness,1-R10.815,1-R10.81, +1,1-Periumbilic abdominal tenderness,1-R10.815,2-R10.815, +1,1-Epigastric abdominal tenderness,1-R10.816,1-R10.81, +1,1-Epigastric abdominal tenderness,1-R10.816,2-R10.816, +1,1-Generalized abdominal tenderness,1-R10.817,1-R10.81, +1,1-Generalized abdominal tenderness,1-R10.817,2-R10.817, +1,"1-Abdominal tenderness, unspecified site",1-R10.819,1-R10.81, +1,"1-Abdominal tenderness, unspecified site",1-R10.819,2-R10.819, +1,1-Rebound abdominal tenderness,1-R10.82,1-R10.8, +1,1-Rebound abdominal tenderness,1-R10.82,2-R10.82, +1,1-Right upper quadrant rebound abdominal tenderness,1-R10.821,1-R10.82, +1,1-Right upper quadrant rebound abdominal tenderness,1-R10.821,2-R10.821, +1,1-Left upper quadrant rebound abdominal tenderness,1-R10.822,1-R10.82, +1,1-Left upper quadrant rebound abdominal tenderness,1-R10.822,2-R10.822, +1,1-Right lower quadrant rebound abdominal tenderness,1-R10.823,1-R10.82, +1,1-Right lower quadrant rebound abdominal tenderness,1-R10.823,2-R10.823, +1,1-Left lower quadrant rebound abdominal tenderness,1-R10.824,1-R10.82, +1,1-Left lower quadrant rebound abdominal tenderness,1-R10.824,2-R10.824, +1,1-Periumbilic rebound abdominal tenderness,1-R10.825,1-R10.82, +1,1-Periumbilic rebound abdominal tenderness,1-R10.825,2-R10.825, +1,1-Epigastric rebound abdominal tenderness,1-R10.826,1-R10.82, +1,1-Epigastric rebound abdominal tenderness,1-R10.826,2-R10.826, +1,1-Generalized rebound abdominal tenderness,1-R10.827,1-R10.82, +1,1-Generalized rebound abdominal tenderness,1-R10.827,2-R10.827, +1,"1-Rebound abdominal tenderness, unspecified site",1-R10.829,1-R10.82, +1,"1-Rebound abdominal tenderness, unspecified site",1-R10.829,2-R10.829, +1,1-Colic,1-R10.83,1-R10.8, +1,1-Colic,1-R10.83,2-R10.83, +1,1-Generalized abdominal pain,1-R10.84,1-R10.8, +1,1-Generalized abdominal pain,1-R10.84,2-R10.84, +1,1-Abdominal pain of multiple sites,1-R10.85,1-R10.8, +1,1-Abdominal pain of multiple sites,1-R10.85,2-R10.85, +1,1-Flank tenderness,1-R10.8A,1-R10.8, +1,1-Flank tenderness,1-R10.8A,2-R10.8A, +1,1-Right flank tenderness,1-R10.8A1,1-R10.8A, +1,1-Right flank tenderness,1-R10.8A1,2-R10.8A1, +1,1-Left flank tenderness,1-R10.8A2,1-R10.8A, +1,1-Left flank tenderness,1-R10.8A2,2-R10.8A2, +1,1-Suprapubic tenderness,1-R10.8A3,1-R10.8A, +1,1-Suprapubic tenderness,1-R10.8A3,2-R10.8A3, +1,"1-Flank tenderness, unspecified",1-R10.8A9,1-R10.8A, +1,"1-Flank tenderness, unspecified",1-R10.8A9,2-R10.8A9, +1,1-Unspecified abdominal pain,1-R10.9,1-R10, +1,1-Unspecified abdominal pain,1-R10.9,2-R10.9, +1,1-Pain localized to flank,1-R10.A,1-R10, +1,1-Pain localized to flank,1-R10.A,2-R10.A, +1,"1-Flank pain, unspecified side",1-R10.A0,1-R10.A,TRUE +1,"1-Flank pain, unspecified side",1-R10.A0,2-R10.A0,TRUE +1,"1-Flank pain, right side",1-R10.A1,1-R10.A,TRUE +1,"1-Flank pain, right side",1-R10.A1,2-R10.A1,TRUE +1,"1-Flank pain, left side",1-R10.A2,1-R10.A,TRUE +1,"1-Flank pain, left side",1-R10.A2,2-R10.A2,TRUE +1,"1-Flank pain, bilateral",1-R10.A3,1-R10.A,TRUE +1,"1-Flank pain, bilateral",1-R10.A3,2-R10.A3,TRUE +1,1-Nausea and vomiting,1-R11,1-R10-R19, +1,1-Nausea and vomiting,1-R11,2-R11, +1,1-Nausea,1-R11.0,1-R11, +1,1-Nausea,1-R11.0,2-R11.0, +1,1-Vomiting,1-R11.1,1-R11, +1,1-Vomiting,1-R11.1,2-R11.1, +1,"1-Vomiting, unspecified",1-R11.10,1-R11.1, +1,"1-Vomiting, unspecified",1-R11.10,2-R11.10, +1,1-Vomiting without nausea,1-R11.11,1-R11.1, +1,1-Vomiting without nausea,1-R11.11,2-R11.11, +1,1-Projectile vomiting,1-R11.12,1-R11.1, +1,1-Projectile vomiting,1-R11.12,2-R11.12, +1,1-Vomiting of fecal matter,1-R11.13,1-R11.1, +1,1-Vomiting of fecal matter,1-R11.13,2-R11.13, +1,1-Bilious vomiting,1-R11.14,1-R11.1, +1,1-Bilious vomiting,1-R11.14,2-R11.14, +1,1-Cyclical vomiting syndrome unrelated to migraine,1-R11.15,1-R11.1, +1,1-Cyclical vomiting syndrome unrelated to migraine,1-R11.15,2-R11.15, +1,1-Cannabis hyperemesis syndrome,1-R11.16,1-R11.1, +1,1-Cannabis hyperemesis syndrome,1-R11.16,2-R11.16, +1,"1-Nausea with vomiting, unspecified",1-R11.2,1-R11, +1,"1-Nausea with vomiting, unspecified",1-R11.2,2-R11.2, +1,1-Heartburn,1-R12,1-R10-R19, +1,1-Heartburn,1-R12,2-R12, +1,1-Aphagia and dysphagia,1-R13,1-R10-R19, +1,1-Aphagia and dysphagia,1-R13,2-R13, +1,1-Aphagia,1-R13.0,1-R13, +1,1-Aphagia,1-R13.0,2-R13.0, +1,1-Dysphagia,1-R13.1,1-R13, +1,1-Dysphagia,1-R13.1,2-R13.1, +1,"1-Dysphagia, unspecified",1-R13.10,1-R13.1, +1,"1-Dysphagia, unspecified",1-R13.10,2-R13.10, +1,"1-Dysphagia, oral phase",1-R13.11,1-R13.1, +1,"1-Dysphagia, oral phase",1-R13.11,2-R13.11, +1,"1-Dysphagia, oropharyngeal phase",1-R13.12,1-R13.1, +1,"1-Dysphagia, oropharyngeal phase",1-R13.12,2-R13.12, +1,"1-Dysphagia, pharyngeal phase",1-R13.13,1-R13.1, +1,"1-Dysphagia, pharyngeal phase",1-R13.13,2-R13.13, +1,"1-Dysphagia, pharyngoesophageal phase",1-R13.14,1-R13.1, +1,"1-Dysphagia, pharyngoesophageal phase",1-R13.14,2-R13.14, +1,1-Other dysphagia,1-R13.19,1-R13.1, +1,1-Other dysphagia,1-R13.19,2-R13.19, +1,1-Flatulence and related conditions,1-R14,1-R10-R19, +1,1-Flatulence and related conditions,1-R14,2-R14, +1,1-Abdominal distension (gaseous),1-R14.0,1-R14, +1,1-Abdominal distension (gaseous),1-R14.0,2-R14.0, +1,1-Gas pain,1-R14.1,1-R14, +1,1-Gas pain,1-R14.1,2-R14.1, +1,1-Eructation,1-R14.2,1-R14, +1,1-Eructation,1-R14.2,2-R14.2, +1,1-Flatulence,1-R14.3,1-R14, +1,1-Flatulence,1-R14.3,2-R14.3, +1,1-Fecal incontinence,1-R15,1-R10-R19, +1,1-Fecal incontinence,1-R15,2-R15, +1,1-Incomplete defecation,1-R15.0,1-R15, +1,1-Incomplete defecation,1-R15.0,2-R15.0, +1,1-Fecal smearing,1-R15.1,1-R15, +1,1-Fecal smearing,1-R15.1,2-R15.1, +1,1-Fecal urgency,1-R15.2,1-R15, +1,1-Fecal urgency,1-R15.2,2-R15.2, +1,1-Full incontinence of feces,1-R15.9,1-R15, +1,1-Full incontinence of feces,1-R15.9,2-R15.9, +1,"1-Hepatomegaly and splenomegaly, not elsewhere classified",1-R16,1-R10-R19, +1,"1-Hepatomegaly and splenomegaly, not elsewhere classified",1-R16,2-R16, +1,"1-Hepatomegaly, not elsewhere classified",1-R16.0,1-R16, +1,"1-Hepatomegaly, not elsewhere classified",1-R16.0,2-R16.0, +1,"1-Splenomegaly, not elsewhere classified",1-R16.1,1-R16, +1,"1-Splenomegaly, not elsewhere classified",1-R16.1,2-R16.1, +1,"1-Hepatomegaly with splenomegaly, not elsewhere classified",1-R16.2,1-R16, +1,"1-Hepatomegaly with splenomegaly, not elsewhere classified",1-R16.2,2-R16.2, +1,1-Unspecified jaundice,1-R17,1-R10-R19, +1,1-Unspecified jaundice,1-R17,2-R17, +1,1-Ascites,1-R18,1-R10-R19, +1,1-Ascites,1-R18,2-R18, +1,1-Malignant ascites,1-R18.0,1-R18, +1,1-Malignant ascites,1-R18.0,2-R18.0, +1,1-Other ascites,1-R18.8,1-R18, +1,1-Other ascites,1-R18.8,2-R18.8, +1,1-Other symptoms and signs involving the digestive system and abdomen,1-R19,1-R10-R19, +1,1-Other symptoms and signs involving the digestive system and abdomen,1-R19,2-R19, +1,"1-Intra-abdominal and pelvic swelling, mass and lump",1-R19.0,1-R19, +1,"1-Intra-abdominal and pelvic swelling, mass and lump",1-R19.0,2-R19.0, +1,"1-Intra-abdominal and pelvic swelling, mass and lump, unspecified site",1-R19.00,1-R19.0, +1,"1-Intra-abdominal and pelvic swelling, mass and lump, unspecified site",1-R19.00,2-R19.00, +1,"1-Right upper quadrant abdominal swelling, mass and lump",1-R19.01,1-R19.0, +1,"1-Right upper quadrant abdominal swelling, mass and lump",1-R19.01,2-R19.01, +1,"1-Left upper quadrant abdominal swelling, mass and lump",1-R19.02,1-R19.0, +1,"1-Left upper quadrant abdominal swelling, mass and lump",1-R19.02,2-R19.02, +1,"1-Right lower quadrant abdominal swelling, mass and lump",1-R19.03,1-R19.0, +1,"1-Right lower quadrant abdominal swelling, mass and lump",1-R19.03,2-R19.03, +1,"1-Left lower quadrant abdominal swelling, mass and lump",1-R19.04,1-R19.0, +1,"1-Left lower quadrant abdominal swelling, mass and lump",1-R19.04,2-R19.04, +1,"1-Periumbilic swelling, mass or lump",1-R19.05,1-R19.0, +1,"1-Periumbilic swelling, mass or lump",1-R19.05,2-R19.05, +1,"1-Epigastric swelling, mass or lump",1-R19.06,1-R19.0, +1,"1-Epigastric swelling, mass or lump",1-R19.06,2-R19.06, +1,"1-Generalized intra-abdominal and pelvic swelling, mass and lump",1-R19.07,1-R19.0, +1,"1-Generalized intra-abdominal and pelvic swelling, mass and lump",1-R19.07,2-R19.07, +1,"1-Other intra-abdominal and pelvic swelling, mass and lump",1-R19.09,1-R19.0, +1,"1-Other intra-abdominal and pelvic swelling, mass and lump",1-R19.09,2-R19.09, +1,1-Abnormal bowel sounds,1-R19.1,1-R19, +1,1-Abnormal bowel sounds,1-R19.1,2-R19.1, +1,1-Absent bowel sounds,1-R19.11,1-R19.1, +1,1-Absent bowel sounds,1-R19.11,2-R19.11, +1,1-Hyperactive bowel sounds,1-R19.12,1-R19.1, +1,1-Hyperactive bowel sounds,1-R19.12,2-R19.12, +1,1-Other abnormal bowel sounds,1-R19.15,1-R19.1, +1,1-Other abnormal bowel sounds,1-R19.15,2-R19.15, +1,1-Visible peristalsis,1-R19.2,1-R19, +1,1-Visible peristalsis,1-R19.2,2-R19.2, +1,1-Abdominal rigidity,1-R19.3,1-R19, +1,1-Abdominal rigidity,1-R19.3,2-R19.3, +1,"1-Abdominal rigidity, unspecified site",1-R19.30,1-R19.3, +1,"1-Abdominal rigidity, unspecified site",1-R19.30,2-R19.30, +1,1-Right upper quadrant abdominal rigidity,1-R19.31,1-R19.3, +1,1-Right upper quadrant abdominal rigidity,1-R19.31,2-R19.31, +1,1-Left upper quadrant abdominal rigidity,1-R19.32,1-R19.3, +1,1-Left upper quadrant abdominal rigidity,1-R19.32,2-R19.32, +1,1-Right lower quadrant abdominal rigidity,1-R19.33,1-R19.3, +1,1-Right lower quadrant abdominal rigidity,1-R19.33,2-R19.33, +1,1-Left lower quadrant abdominal rigidity,1-R19.34,1-R19.3, +1,1-Left lower quadrant abdominal rigidity,1-R19.34,2-R19.34, +1,1-Periumbilic abdominal rigidity,1-R19.35,1-R19.3, +1,1-Periumbilic abdominal rigidity,1-R19.35,2-R19.35, +1,1-Epigastric abdominal rigidity,1-R19.36,1-R19.3, +1,1-Epigastric abdominal rigidity,1-R19.36,2-R19.36, +1,1-Generalized abdominal rigidity,1-R19.37,1-R19.3, +1,1-Generalized abdominal rigidity,1-R19.37,2-R19.37, +1,1-Change in bowel habit,1-R19.4,1-R19, +1,1-Change in bowel habit,1-R19.4,2-R19.4, +1,1-Other fecal abnormalities,1-R19.5,1-R19, +1,1-Other fecal abnormalities,1-R19.5,2-R19.5, +1,1-Halitosis,1-R19.6,1-R19, +1,1-Halitosis,1-R19.6,2-R19.6, +1,"1-Diarrhea, unspecified",1-R19.7,1-R19, +1,"1-Diarrhea, unspecified",1-R19.7,2-R19.7, +1,1-Other specified symptoms and signs involving the digestive system and abdomen,1-R19.8,1-R19, +1,1-Other specified symptoms and signs involving the digestive system and abdomen,1-R19.8,2-R19.8, +1,1-Fever of other and unknown origin,1-R50,1-R50-R69, +1,1-Fever of other and unknown origin,1-R50,2-R50, +1,1-General symptoms and signs,1-R50-R69,1-R00-R99,TRUE +1,1-General symptoms and signs,1-R50-R69,2-R50-R69,TRUE +1,1-Drug induced fever,1-R50.2,1-R50, +1,1-Drug induced fever,1-R50.2,2-R50.2, +1,1-Other specified fever,1-R50.8,1-R50, +1,1-Other specified fever,1-R50.8,2-R50.8, +1,1-Fever presenting with conditions classified elsewhere,1-R50.81,1-R50.8, +1,1-Fever presenting with conditions classified elsewhere,1-R50.81,2-R50.81, +1,1-Postprocedural fever,1-R50.82,1-R50.8, +1,1-Postprocedural fever,1-R50.82,2-R50.82, +1,1-Postvaccination fever,1-R50.83,1-R50.8, +1,1-Postvaccination fever,1-R50.83,2-R50.83, +1,1-Febrile nonhemolytic transfusion reaction,1-R50.84,1-R50.8, +1,1-Febrile nonhemolytic transfusion reaction,1-R50.84,2-R50.84, +1,"1-Fever, unspecified",1-R50.9,1-R50, +1,"1-Fever, unspecified",1-R50.9,2-R50.9, +1,1-Headache,1-R51,1-R50-R69, +1,1-Headache,1-R51,2-R51, +1,"1-Headache with orthostatic component, not elsewhere classified",1-R51.0,1-R51, +1,"1-Headache with orthostatic component, not elsewhere classified",1-R51.0,2-R51.0, +1,"1-Headache, unspecified",1-R51.9,1-R51, +1,"1-Headache, unspecified",1-R51.9,2-R51.9, +1,"1-Pain, unspecified",1-R52,1-R50-R69, +1,"1-Pain, unspecified",1-R52,2-R52, +1,1-Malaise and fatigue,1-R53,1-R50-R69, +1,1-Malaise and fatigue,1-R53,2-R53, +1,1-Neoplastic (malignant) related fatigue,1-R53.0,1-R53, +1,1-Neoplastic (malignant) related fatigue,1-R53.0,2-R53.0, +1,1-Weakness,1-R53.1,1-R53, +1,1-Weakness,1-R53.1,2-R53.1, +1,1-Functional quadriplegia,1-R53.2,1-R53, +1,1-Functional quadriplegia,1-R53.2,2-R53.2, +1,1-Other malaise and fatigue,1-R53.8,1-R53, +1,1-Other malaise and fatigue,1-R53.8,2-R53.8, +1,1-Other malaise,1-R53.81,1-R53.8, +1,1-Other malaise,1-R53.81,2-R53.81, +1,"1-Chronic fatigue, unspecified",1-R53.82,1-R53.8, +1,"1-Chronic fatigue, unspecified",1-R53.82,2-R53.82, +1,1-Other fatigue,1-R53.83,1-R53.8, +1,1-Other fatigue,1-R53.83,2-R53.83, +1,1-Age-related physical debility,1-R54,1-R50-R69, +1,1-Age-related physical debility,1-R54,2-R54, +1,1-Syncope and collapse,1-R55,1-R50-R69, +1,1-Syncope and collapse,1-R55,2-R55, +1,"1-Convulsions, not elsewhere classified",1-R56,1-R50-R69, +1,"1-Convulsions, not elsewhere classified",1-R56,2-R56, +1,1-Febrile convulsions,1-R56.0,1-R56, +1,1-Febrile convulsions,1-R56.0,2-R56.0, +1,1-Simple febrile convulsions,1-R56.00,1-R56.0, +1,1-Simple febrile convulsions,1-R56.00,2-R56.00, +1,1-Complex febrile convulsions,1-R56.01,1-R56.0, +1,1-Complex febrile convulsions,1-R56.01,2-R56.01, +1,1-Post traumatic seizures,1-R56.1,1-R56, +1,1-Post traumatic seizures,1-R56.1,2-R56.1, +1,1-Unspecified convulsions,1-R56.9,1-R56, +1,1-Unspecified convulsions,1-R56.9,2-R56.9, +1,"1-Shock, not elsewhere classified",1-R57,1-R50-R69, +1,"1-Shock, not elsewhere classified",1-R57,2-R57, +1,1-Cardiogenic shock,1-R57.0,1-R57, +1,1-Cardiogenic shock,1-R57.0,2-R57.0, +1,1-Hypovolemic shock,1-R57.1,1-R57, +1,1-Hypovolemic shock,1-R57.1,2-R57.1, +1,1-Other shock,1-R57.8,1-R57, +1,1-Other shock,1-R57.8,2-R57.8, +1,"1-Shock, unspecified",1-R57.9,1-R57, +1,"1-Shock, unspecified",1-R57.9,2-R57.9, +1,"1-Hemorrhage, not elsewhere classified",1-R58,1-R50-R69, +1,"1-Hemorrhage, not elsewhere classified",1-R58,2-R58, +1,1-Enlarged lymph nodes,1-R59,1-R50-R69, +1,1-Enlarged lymph nodes,1-R59,2-R59, +1,1-Localized enlarged lymph nodes,1-R59.0,1-R59, +1,1-Localized enlarged lymph nodes,1-R59.0,2-R59.0, +1,1-Generalized enlarged lymph nodes,1-R59.1,1-R59, +1,1-Generalized enlarged lymph nodes,1-R59.1,2-R59.1, +1,"1-Enlarged lymph nodes, unspecified",1-R59.9,1-R59, +1,"1-Enlarged lymph nodes, unspecified",1-R59.9,2-R59.9, +1,"1-Edema, not elsewhere classified",1-R60,1-R50-R69, +1,"1-Edema, not elsewhere classified",1-R60,2-R60, +1,1-Localized edema,1-R60.0,1-R60, +1,1-Localized edema,1-R60.0,2-R60.0, +1,1-Generalized edema,1-R60.1,1-R60, +1,1-Generalized edema,1-R60.1,2-R60.1, +1,"1-Edema, unspecified",1-R60.9,1-R60, +1,"1-Edema, unspecified",1-R60.9,2-R60.9, +1,1-Generalized hyperhidrosis,1-R61,1-R50-R69, +1,1-Generalized hyperhidrosis,1-R61,2-R61, +1,1-Lack of expected normal physiological development in childhood and adults,1-R62,1-R50-R69, +1,1-Lack of expected normal physiological development in childhood and adults,1-R62,2-R62, +1,1-Delayed milestone in childhood,1-R62.0,1-R62, +1,1-Delayed milestone in childhood,1-R62.0,2-R62.0, +1,1-Other and unspecified lack of expected normal physiological development in childhood,1-R62.5,1-R62, +1,1-Other and unspecified lack of expected normal physiological development in childhood,1-R62.5,2-R62.5, +1,1-Unspecified lack of expected normal physiological development in childhood,1-R62.50,1-R62.5, +1,1-Unspecified lack of expected normal physiological development in childhood,1-R62.50,2-R62.50, +1,1-Failure to thrive (child),1-R62.51,1-R62.5, +1,1-Failure to thrive (child),1-R62.51,2-R62.51, +1,1-Short stature (child),1-R62.52,1-R62.5, +1,1-Short stature (child),1-R62.52,2-R62.52, +1,1-Other lack of expected normal physiological development in childhood,1-R62.59,1-R62.5, +1,1-Other lack of expected normal physiological development in childhood,1-R62.59,2-R62.59, +1,1-Adult failure to thrive,1-R62.7,1-R62, +1,1-Adult failure to thrive,1-R62.7,2-R62.7, +1,1-Symptoms and signs concerning food and fluid intake,1-R63,1-R50-R69, +1,1-Symptoms and signs concerning food and fluid intake,1-R63,2-R63, +1,1-Anorexia,1-R63.0,1-R63, +1,1-Anorexia,1-R63.0,2-R63.0, +1,1-Polydipsia,1-R63.1,1-R63, +1,1-Polydipsia,1-R63.1,2-R63.1, +1,1-Polyphagia,1-R63.2,1-R63, +1,1-Polyphagia,1-R63.2,2-R63.2, +1,1-Feeding difficulties,1-R63.3,1-R63, +1,1-Feeding difficulties,1-R63.3,2-R63.3, +1,"1-Feeding difficulties, unspecified",1-R63.30,1-R63.3, +1,"1-Feeding difficulties, unspecified",1-R63.30,2-R63.30, +1,"1-Pediatric feeding disorder, acute",1-R63.31,1-R63.3, +1,"1-Pediatric feeding disorder, acute",1-R63.31,2-R63.31, +1,"1-Pediatric feeding disorder, chronic",1-R63.32,1-R63.3, +1,"1-Pediatric feeding disorder, chronic",1-R63.32,2-R63.32, +1,1-Other feeding difficulties,1-R63.39,1-R63.3, +1,1-Other feeding difficulties,1-R63.39,2-R63.39, +1,1-Abnormal weight loss,1-R63.4,1-R63, +1,1-Abnormal weight loss,1-R63.4,2-R63.4, +1,1-Abnormal weight gain,1-R63.5,1-R63, +1,1-Abnormal weight gain,1-R63.5,2-R63.5, +1,1-Underweight,1-R63.6,1-R63, +1,1-Underweight,1-R63.6,2-R63.6, +1,1-Other symptoms and signs concerning food and fluid intake,1-R63.8,1-R63, +1,1-Other symptoms and signs concerning food and fluid intake,1-R63.8,2-R63.8, +1,1-Cachexia,1-R64,1-R50-R69, +1,1-Cachexia,1-R64,2-R64, +1,1-Symptoms and signs specifically associated with systemic inflammation and infection,1-R65,1-R50-R69, +1,1-Symptoms and signs specifically associated with systemic inflammation and infection,1-R65,2-R65, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin,1-R65.1,1-R65, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin,1-R65.1,2-R65.1, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction,1-R65.10,1-R65.1, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction,1-R65.10,2-R65.10, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction,1-R65.11,1-R65.1, +1,1-Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction,1-R65.11,2-R65.11, +1,1-Severe sepsis,1-R65.2,1-R65, +1,1-Severe sepsis,1-R65.2,2-R65.2, +1,1-Severe sepsis without septic shock,1-R65.20,1-R65.2, +1,1-Severe sepsis without septic shock,1-R65.20,2-R65.20, +1,1-Severe sepsis with septic shock,1-R65.21,1-R65.2, +1,1-Severe sepsis with septic shock,1-R65.21,2-R65.21, +1,1-Other general symptoms and signs,1-R68,1-R50-R69, +1,1-Other general symptoms and signs,1-R68,2-R68, +1,"1-Hypothermia, not associated with low environmental temperature",1-R68.0,1-R68, +1,"1-Hypothermia, not associated with low environmental temperature",1-R68.0,2-R68.0, +1,1-Nonspecific symptoms peculiar to infancy,1-R68.1,1-R68, +1,1-Nonspecific symptoms peculiar to infancy,1-R68.1,2-R68.1, +1,1-Excessive crying of infant (baby),1-R68.11,1-R68.1, +1,1-Excessive crying of infant (baby),1-R68.11,2-R68.11, +1,1-Fussy infant (baby),1-R68.12,1-R68.1, +1,1-Fussy infant (baby),1-R68.12,2-R68.12, +1,1-Apparent life threatening event in infant (ALTE),1-R68.13,1-R68.1, +1,1-Apparent life threatening event in infant (ALTE),1-R68.13,2-R68.13, +1,1-Other nonspecific symptoms peculiar to infancy,1-R68.19,1-R68.1, +1,1-Other nonspecific symptoms peculiar to infancy,1-R68.19,2-R68.19, +1,"1-Dry mouth, unspecified",1-R68.2,1-R68, +1,"1-Dry mouth, unspecified",1-R68.2,2-R68.2, +1,1-Clubbing of fingers,1-R68.3,1-R68, +1,1-Clubbing of fingers,1-R68.3,2-R68.3, +1,1-Other general symptoms and signs,1-R68.8,1-R68, +1,1-Other general symptoms and signs,1-R68.8,2-R68.8, +1,1-Early satiety,1-R68.81,1-R68.8, +1,1-Early satiety,1-R68.81,2-R68.81, +1,1-Decreased libido,1-R68.82,1-R68.8, +1,1-Decreased libido,1-R68.82,2-R68.82, +1,1-Chills (without fever),1-R68.83,1-R68.8, +1,1-Chills (without fever),1-R68.83,2-R68.83, +1,1-Jaw pain,1-R68.84,1-R68.8, +1,1-Jaw pain,1-R68.84,2-R68.84, +1,1-Other general symptoms and signs,1-R68.89,1-R68.8, +1,1-Other general symptoms and signs,1-R68.89,2-R68.89, +1,"1-Illness, unspecified",1-R69,1-R50-R69, +1,"1-Illness, unspecified",1-R69,2-R69, +1,1-ICD-10 Root,1-Root,2-Root, +1,,1-Vibrio vulnificus,1-dummy2, +1,,1-Vibrio vulnificus,2-Vibrio vulnificus, +1,,1-dummy1,1-Root, +1,,1-dummy1,2-dummy1, +1,,1-dummy2,1-dummy1,TRUE +1,,1-dummy2,2-dummy2,TRUE +1,2-Cholera,2-A00,2-A00-A09, +1,2-Intestinal infectious diseases,2-A00-A09,2-A00-B99, +1,2-Certain infectious and parasitic diseases,2-A00-B99,2-Root, +1,"2-Cholera due to Vibrio cholerae 01, biovar cholerae",2-A00.0,2-A00, +1,"2-Cholera due to Vibrio cholerae 01, biovar eltor",2-A00.1,2-A00, +1,"2-Cholera, unspecified",2-A00.9,2-A00, +1,2-Typhoid and paratyphoid fevers,2-A01,2-A00-A09, +1,2-Typhoid fever,2-A01.0,2-A01, +1,"2-Typhoid fever, unspecified",2-A01.00,2-A01.0, +1,2-Typhoid meningitis,2-A01.01,2-A01.0, +1,2-Typhoid fever with heart involvement,2-A01.02,2-A01.0, +1,2-Typhoid pneumonia,2-A01.03,2-A01.0, +1,2-Typhoid arthritis,2-A01.04,2-A01.0, +1,2-Typhoid osteomyelitis,2-A01.05,2-A01.0, +1,2-Typhoid fever with other complications,2-A01.09,2-A01.0, +1,2-Paratyphoid fever A,2-A01.1,2-A01, +1,2-Paratyphoid fever B,2-A01.2,2-A01, +1,2-Paratyphoid fever C,2-A01.3,2-A01, +1,"2-Paratyphoid fever, unspecified",2-A01.4,2-A01, +1,2-Other salmonella infections,2-A02,2-A00-A09, +1,2-Salmonella enteritis,2-A02.0,2-A02, +1,2-Salmonella sepsis,2-A02.1,2-A02, +1,2-Localized salmonella infections,2-A02.2,2-A02, +1,"2-Localized salmonella infection, unspecified",2-A02.20,2-A02.2, +1,2-Salmonella meningitis,2-A02.21,2-A02.2, +1,2-Salmonella pneumonia,2-A02.22,2-A02.2, +1,2-Salmonella arthritis,2-A02.23,2-A02.2, +1,2-Salmonella osteomyelitis,2-A02.24,2-A02.2, +1,2-Salmonella pyelonephritis,2-A02.25,2-A02.2, +1,2-Salmonella with other localized infection,2-A02.29,2-A02.2, +1,2-Other specified salmonella infections,2-A02.8,2-A02, +1,"2-Salmonella infection, unspecified",2-A02.9,2-A02, +1,2-Shigellosis,2-A03,2-A00-A09, +1,2-Shigellosis due to Shigella dysenteriae,2-A03.0,2-A03, +1,2-Shigellosis due to Shigella flexneri,2-A03.1,2-A03, +1,2-Shigellosis due to Shigella boydii,2-A03.2,2-A03, +1,2-Shigellosis due to Shigella sonnei,2-A03.3,2-A03, +1,2-Other shigellosis,2-A03.8,2-A03, +1,"2-Shigellosis, unspecified",2-A03.9,2-A03, +1,2-Other bacterial intestinal infections,2-A04,2-A00-A09, +1,2-Enteropathogenic Escherichia coli infection,2-A04.0,2-A04, +1,2-Enteropathogenic Escherichia coli infection,2-A04.0,2-Escherichia coli, +1,2-Enterotoxigenic Escherichia coli infection,2-A04.1,2-A04, +1,2-Enterotoxigenic Escherichia coli infection,2-A04.1,2-Escherichia coli, +1,2-Enteroinvasive Escherichia coli infection,2-A04.2,2-A04, +1,2-Enteroinvasive Escherichia coli infection,2-A04.2,2-Escherichia coli, +1,2-Enterohemorrhagic Escherichia coli infection,2-A04.3,2-A04, +1,2-Enterohemorrhagic Escherichia coli infection,2-A04.3,2-Escherichia coli, +1,2-Other intestinal Escherichia coli infections,2-A04.4,2-A04, +1,2-Other intestinal Escherichia coli infections,2-A04.4,2-Escherichia coli, +1,2-Campylobacter enteritis,2-A04.5,2-A04, +1,2-Enteritis due to Yersinia enterocolitica,2-A04.6,2-A04, +1,2-Enterocolitis due to Clostridium difficile,2-A04.7,2-A04, +1,"2-Enterocolitis due to Clostridium difficile, recurrent",2-A04.71,2-A04.7, +1,"2-Enterocolitis due to Clostridium difficile, not specified as recurrent",2-A04.72,2-A04.7, +1,2-Other specified bacterial intestinal infections,2-A04.8,2-A04, +1,"2-Bacterial intestinal infection, unspecified",2-A04.9,2-A04, +1,"2-Other bacterial foodborne intoxications, not elsewhere classified",2-A05,2-A00-A09, +1,2-Foodborne staphylococcal intoxication,2-A05.0,2-A05, +1,2-Botulism food poisoning,2-A05.1,2-A05, +1,2-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,2-A05.2,2-A05, +1,2-Foodborne Clostridium perfringens [Clostridium welchii] intoxication,2-A05.2,2-Clostridium perfringens, +1,2-Foodborne Vibrio parahaemolyticus intoxication,2-A05.3,2-A05, +1,2-Foodborne Bacillus cereus intoxication,2-A05.4,2-A05, +1,2-Foodborne Vibrio vulnificus intoxication,2-A05.5,2-A05, +1,2-Foodborne Vibrio vulnificus intoxication,2-A05.5,2-Vibrio vulnificus, +1,2-Other specified bacterial foodborne intoxications,2-A05.8,2-A05, +1,"2-Bacterial foodborne intoxication, unspecified",2-A05.9,2-A05, +1,2-Amebiasis,2-A06,2-A00-A09, +1,2-Acute amebic dysentery,2-A06.0,2-A06, +1,2-Chronic intestinal amebiasis,2-A06.1,2-A06, +1,2-Amebic nondysenteric colitis,2-A06.2,2-A06, +1,2-Ameboma of intestine,2-A06.3,2-A06, +1,2-Amebic liver abscess,2-A06.4,2-A06, +1,2-Amebic lung abscess,2-A06.5,2-A06, +1,2-Amebic brain abscess,2-A06.6,2-A06, +1,2-Cutaneous amebiasis,2-A06.7,2-A06, +1,2-Amebic infection of other sites,2-A06.8,2-A06, +1,2-Amebic cystitis,2-A06.81,2-A06.8, +1,2-Other amebic genitourinary infections,2-A06.82,2-A06.8, +1,2-Other amebic infections,2-A06.89,2-A06.8, +1,"2-Amebiasis, unspecified",2-A06.9,2-A06, +1,2-Other protozoal intestinal diseases,2-A07,2-A00-A09, +1,2-Balantidiasis,2-A07.0,2-A07, +1,2-Giardiasis [lambliasis],2-A07.1,2-A07, +1,2-Cryptosporidiosis,2-A07.2,2-A07, +1,2-Isosporiasis,2-A07.3,2-A07, +1,2-Cyclosporiasis,2-A07.4,2-A07, +1,2-Other specified protozoal intestinal diseases,2-A07.8,2-A07, +1,"2-Protozoal intestinal disease, unspecified",2-A07.9,2-A07, +1,2-Viral and other specified intestinal infections,2-A08,2-A00-A09, +1,2-Rotaviral enteritis,2-A08.0,2-A08, +1,2-Acute gastroenteropathy due to Norwalk agent and other small round viruses,2-A08.1,2-A08, +1,2-Acute gastroenteropathy due to Norwalk agent,2-A08.11,2-A08.1, +1,2-Acute gastroenteropathy due to other small round viruses,2-A08.19,2-A08.1, +1,2-Adenoviral enteritis,2-A08.2,2-A08, +1,2-Other viral enteritis,2-A08.3,2-A08, +1,2-Calicivirus enteritis,2-A08.31,2-A08.3, +1,2-Astrovirus enteritis,2-A08.32,2-A08.3, +1,2-Other viral enteritis,2-A08.39,2-A08.3, +1,"2-Viral intestinal infection, unspecified",2-A08.4,2-A08, +1,2-Other specified intestinal infections,2-A08.8,2-A08, +1,"2-Infectious gastroenteritis and colitis, unspecified",2-A09,2-A00-A09, +1,,2-Clostridium perfringens,2-dummy2, +1,,2-Escherichia coli,2-dummy2, +1,2-Acute nasopharyngitis [common cold],2-J00,2-J00-J06, +1,2-Acute upper respiratory infections,2-J00-J06,2-J00-J99, +1,2-Diseases of the respiratory system,2-J00-J99,2-Root, +1,2-Acute sinusitis,2-J01,2-J00-J06, +1,2-Acute maxillary sinusitis,2-J01.0,2-J01, +1,"2-Acute maxillary sinusitis, unspecified",2-J01.00,2-J01.0, +1,2-Acute recurrent maxillary sinusitis,2-J01.01,2-J01.0, +1,2-Acute frontal sinusitis,2-J01.1,2-J01, +1,"2-Acute frontal sinusitis, unspecified",2-J01.10,2-J01.1, +1,2-Acute recurrent frontal sinusitis,2-J01.11,2-J01.1, +1,2-Acute ethmoidal sinusitis,2-J01.2,2-J01, +1,"2-Acute ethmoidal sinusitis, unspecified",2-J01.20,2-J01.2, +1,2-Acute recurrent ethmoidal sinusitis,2-J01.21,2-J01.2, +1,2-Acute sphenoidal sinusitis,2-J01.3,2-J01, +1,"2-Acute sphenoidal sinusitis, unspecified",2-J01.30,2-J01.3, +1,2-Acute recurrent sphenoidal sinusitis,2-J01.31,2-J01.3, +1,2-Acute pansinusitis,2-J01.4,2-J01, +1,"2-Acute pansinusitis, unspecified",2-J01.40,2-J01.4, +1,2-Acute recurrent pansinusitis,2-J01.41,2-J01.4, +1,2-Other acute sinusitis,2-J01.8,2-J01, +1,2-Other acute sinusitis,2-J01.80,2-J01.8, +1,2-Other acute recurrent sinusitis,2-J01.81,2-J01.8, +1,"2-Acute sinusitis, unspecified",2-J01.9,2-J01, +1,"2-Acute sinusitis, unspecified",2-J01.90,2-J01.9, +1,"2-Acute recurrent sinusitis, unspecified",2-J01.91,2-J01.9, +1,2-Acute pharyngitis,2-J02,2-J00-J06, +1,2-Streptococcal pharyngitis,2-J02.0,2-J02, +1,2-Streptococcal pharyngitis,2-J02.0,2-Other streptococcus, +1,2-Acute pharyngitis due to other specified organisms,2-J02.8,2-J02, +1,"2-Acute pharyngitis, unspecified",2-J02.9,2-J02, +1,2-Acute tonsillitis,2-J03,2-J00-J06, +1,2-Streptococcal tonsillitis,2-J03.0,2-J03, +1,2-Streptococcal tonsillitis,2-J03.0,2-Other streptococcus, +1,"2-Acute streptococcal tonsillitis, unspecified",2-J03.00,2-J03.0, +1,2-Acute recurrent streptococcal tonsillitis,2-J03.01,2-J03.0, +1,2-Acute tonsillitis due to other specified organisms,2-J03.8,2-J03, +1,2-Acute tonsillitis due to other specified organisms,2-J03.80,2-J03.8, +1,2-Acute recurrent tonsillitis due to other specified organisms,2-J03.81,2-J03.8, +1,"2-Acute tonsillitis, unspecified",2-J03.9,2-J03, +1,"2-Acute tonsillitis, unspecified",2-J03.90,2-J03.9, +1,"2-Acute recurrent tonsillitis, unspecified",2-J03.91,2-J03.9, +1,2-Acute laryngitis and tracheitis,2-J04,2-J00-J06, +1,2-Acute laryngitis,2-J04.0,2-J04, +1,2-Acute tracheitis,2-J04.1,2-J04, +1,2-Acute tracheitis without obstruction,2-J04.10,2-J04.1, +1,2-Acute tracheitis with obstruction,2-J04.11,2-J04.1, +1,2-Acute laryngotracheitis,2-J04.2,2-J04, +1,"2-Supraglottitis, unspecified",2-J04.3,2-J04, +1,"2-Supraglottitis, unspecified, without obstruction",2-J04.30,2-J04.3, +1,"2-Supraglottitis, unspecified, with obstruction",2-J04.31,2-J04.3, +1,2-Acute obstructive laryngitis [croup] and epiglottitis,2-J05,2-J00-J06, +1,2-Acute obstructive laryngitis [croup],2-J05.0,2-J05, +1,2-Acute epiglottitis,2-J05.1,2-J05, +1,2-Acute epiglottitis without obstruction,2-J05.10,2-J05.1, +1,2-Acute epiglottitis with obstruction,2-J05.11,2-J05.1, +1,2-Acute upper respiratory infections of multiple and unspecified sites,2-J06,2-J00-J06, +1,2-Acute laryngopharyngitis,2-J06.0,2-J06, +1,"2-Acute upper respiratory infection, unspecified",2-J06.9,2-J06, +1,,2-Other streptococcus,2-dummy2, +1,"2-Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",2-R00-R99,2-Root, +1,2-Abdominal and pelvic pain,2-R10,2-R10-R19, +1,2-Symptoms and signs involving the digestive system and abdomen,2-R10-R19,2-R00-R99, +1,2-Acute abdomen,2-R10.0,2-R10, +1,2-Pain localized to upper abdomen,2-R10.1,2-R10, +1,"2-Upper abdominal pain, unspecified",2-R10.10,2-R10.1, +1,2-Right upper quadrant pain,2-R10.11,2-R10.1, +1,2-Left upper quadrant pain,2-R10.12,2-R10.1, +1,2-Epigastric pain,2-R10.13,2-R10.1, +1,2-Pelvic and perineal pain,2-R10.2,2-R10, +1,2-Pelvic and perineal pain unspecified side,2-R10.20,2-R10.2,TRUE +1,2-Pelvic and perineal pain right side,2-R10.21,2-R10.2,TRUE +1,2-Pelvic and perineal pain left side,2-R10.22,2-R10.2,TRUE +1,2-Pelvic and perineal pain bilateral,2-R10.23,2-R10.2,TRUE +1,2-Suprapubic pain,2-R10.24,2-R10.2,TRUE +1,2-Pain localized to other parts of lower abdomen,2-R10.3,2-R10, +1,"2-Lower abdominal pain, unspecified",2-R10.30,2-R10.3, +1,2-Right lower quadrant pain,2-R10.31,2-R10.3, +1,2-Left lower quadrant pain,2-R10.32,2-R10.3, +1,2-Periumbilical pain,2-R10.33,2-R10.3, +1,2-Other abdominal pain,2-R10.8,2-R10, +1,2-Abdominal tenderness,2-R10.81,2-R10.8, +1,2-Right upper quadrant abdominal tenderness,2-R10.811,2-R10.81, +1,2-Left upper quadrant abdominal tenderness,2-R10.812,2-R10.81, +1,2-Right lower quadrant abdominal tenderness,2-R10.813,2-R10.81, +1,2-Left lower quadrant abdominal tenderness,2-R10.814,2-R10.81, +1,2-Periumbilic abdominal tenderness,2-R10.815,2-R10.81, +1,2-Epigastric abdominal tenderness,2-R10.816,2-R10.81, +1,2-Generalized abdominal tenderness,2-R10.817,2-R10.81, +1,"2-Abdominal tenderness, unspecified site",2-R10.819,2-R10.81, +1,2-Rebound abdominal tenderness,2-R10.82,2-R10.8, +1,2-Right upper quadrant rebound abdominal tenderness,2-R10.821,2-R10.82, +1,2-Left upper quadrant rebound abdominal tenderness,2-R10.822,2-R10.82, +1,2-Right lower quadrant rebound abdominal tenderness,2-R10.823,2-R10.82, +1,2-Left lower quadrant rebound abdominal tenderness,2-R10.824,2-R10.82, +1,2-Periumbilic rebound abdominal tenderness,2-R10.825,2-R10.82, +1,2-Epigastric rebound abdominal tenderness,2-R10.826,2-R10.82, +1,2-Generalized rebound abdominal tenderness,2-R10.827,2-R10.82, +1,"2-Rebound abdominal tenderness, unspecified site",2-R10.829,2-R10.82, +1,2-Colic,2-R10.83,2-R10.8, +1,2-Generalized abdominal pain,2-R10.84,2-R10.8, +1,2-Abdominal pain of multiple sites,2-R10.85,2-R10.8, +1,2-Flank tenderness,2-R10.8A,2-R10.8, +1,2-Right flank tenderness,2-R10.8A1,2-R10.8A, +1,2-Left flank tenderness,2-R10.8A2,2-R10.8A, +1,2-Suprapubic tenderness,2-R10.8A3,2-R10.8A, +1,"2-Flank tenderness, unspecified",2-R10.8A9,2-R10.8A, +1,2-Unspecified abdominal pain,2-R10.9,2-R10, +1,2-Pain localized to flank,2-R10.A,2-R10, +1,"2-Flank pain, unspecified side",2-R10.A0,2-R10.A,TRUE +1,"2-Flank pain, right side",2-R10.A1,2-R10.A,TRUE +1,"2-Flank pain, left side",2-R10.A2,2-R10.A,TRUE +1,"2-Flank pain, bilateral",2-R10.A3,2-R10.A,TRUE +1,2-Nausea and vomiting,2-R11,2-R10-R19, +1,2-Nausea,2-R11.0,2-R11, +1,2-Vomiting,2-R11.1,2-R11, +1,"2-Vomiting, unspecified",2-R11.10,2-R11.1, +1,2-Vomiting without nausea,2-R11.11,2-R11.1, +1,2-Projectile vomiting,2-R11.12,2-R11.1, +1,2-Vomiting of fecal matter,2-R11.13,2-R11.1, +1,2-Bilious vomiting,2-R11.14,2-R11.1, +1,2-Cyclical vomiting syndrome unrelated to migraine,2-R11.15,2-R11.1, +1,2-Cannabis hyperemesis syndrome,2-R11.16,2-R11.1, +1,"2-Nausea with vomiting, unspecified",2-R11.2,2-R11, +1,2-Heartburn,2-R12,2-R10-R19, +1,2-Aphagia and dysphagia,2-R13,2-R10-R19, +1,2-Aphagia,2-R13.0,2-R13, +1,2-Dysphagia,2-R13.1,2-R13, +1,"2-Dysphagia, unspecified",2-R13.10,2-R13.1, +1,"2-Dysphagia, oral phase",2-R13.11,2-R13.1, +1,"2-Dysphagia, oropharyngeal phase",2-R13.12,2-R13.1, +1,"2-Dysphagia, pharyngeal phase",2-R13.13,2-R13.1, +1,"2-Dysphagia, pharyngoesophageal phase",2-R13.14,2-R13.1, +1,2-Other dysphagia,2-R13.19,2-R13.1, +1,2-Flatulence and related conditions,2-R14,2-R10-R19, +1,2-Abdominal distension (gaseous),2-R14.0,2-R14, +1,2-Gas pain,2-R14.1,2-R14, +1,2-Eructation,2-R14.2,2-R14, +1,2-Flatulence,2-R14.3,2-R14, +1,2-Fecal incontinence,2-R15,2-R10-R19, +1,2-Incomplete defecation,2-R15.0,2-R15, +1,2-Fecal smearing,2-R15.1,2-R15, +1,2-Fecal urgency,2-R15.2,2-R15, +1,2-Full incontinence of feces,2-R15.9,2-R15, +1,"2-Hepatomegaly and splenomegaly, not elsewhere classified",2-R16,2-R10-R19, +1,"2-Hepatomegaly, not elsewhere classified",2-R16.0,2-R16, +1,"2-Splenomegaly, not elsewhere classified",2-R16.1,2-R16, +1,"2-Hepatomegaly with splenomegaly, not elsewhere classified",2-R16.2,2-R16, +1,2-Unspecified jaundice,2-R17,2-R10-R19, +1,2-Ascites,2-R18,2-R10-R19, +1,2-Malignant ascites,2-R18.0,2-R18, +1,2-Other ascites,2-R18.8,2-R18, +1,2-Other symptoms and signs involving the digestive system and abdomen,2-R19,2-R10-R19, +1,"2-Intra-abdominal and pelvic swelling, mass and lump",2-R19.0,2-R19, +1,"2-Intra-abdominal and pelvic swelling, mass and lump, unspecified site",2-R19.00,2-R19.0, +1,"2-Right upper quadrant abdominal swelling, mass and lump",2-R19.01,2-R19.0, +1,"2-Left upper quadrant abdominal swelling, mass and lump",2-R19.02,2-R19.0, +1,"2-Right lower quadrant abdominal swelling, mass and lump",2-R19.03,2-R19.0, +1,"2-Left lower quadrant abdominal swelling, mass and lump",2-R19.04,2-R19.0, +1,"2-Periumbilic swelling, mass or lump",2-R19.05,2-R19.0, +1,"2-Epigastric swelling, mass or lump",2-R19.06,2-R19.0, +1,"2-Generalized intra-abdominal and pelvic swelling, mass and lump",2-R19.07,2-R19.0, +1,"2-Other intra-abdominal and pelvic swelling, mass and lump",2-R19.09,2-R19.0, +1,2-Abnormal bowel sounds,2-R19.1,2-R19, +1,2-Absent bowel sounds,2-R19.11,2-R19.1, +1,2-Hyperactive bowel sounds,2-R19.12,2-R19.1, +1,2-Other abnormal bowel sounds,2-R19.15,2-R19.1, +1,2-Visible peristalsis,2-R19.2,2-R19, +1,2-Abdominal rigidity,2-R19.3,2-R19, +1,"2-Abdominal rigidity, unspecified site",2-R19.30,2-R19.3, +1,2-Right upper quadrant abdominal rigidity,2-R19.31,2-R19.3, +1,2-Left upper quadrant abdominal rigidity,2-R19.32,2-R19.3, +1,2-Right lower quadrant abdominal rigidity,2-R19.33,2-R19.3, +1,2-Left lower quadrant abdominal rigidity,2-R19.34,2-R19.3, +1,2-Periumbilic abdominal rigidity,2-R19.35,2-R19.3, +1,2-Epigastric abdominal rigidity,2-R19.36,2-R19.3, +1,2-Generalized abdominal rigidity,2-R19.37,2-R19.3, +1,2-Change in bowel habit,2-R19.4,2-R19, +1,2-Other fecal abnormalities,2-R19.5,2-R19, +1,2-Halitosis,2-R19.6,2-R19, +1,"2-Diarrhea, unspecified",2-R19.7,2-R19, +1,2-Other specified symptoms and signs involving the digestive system and abdomen,2-R19.8,2-R19, +1,2-Fever of other and unknown origin,2-R50,2-R50-R69, +1,2-General symptoms and signs,2-R50-R69,2-R00-R99, +1,2-Drug induced fever,2-R50.2,2-R50, +1,2-Other specified fever,2-R50.8,2-R50, +1,2-Fever presenting with conditions classified elsewhere,2-R50.81,2-R50.8, +1,2-Postprocedural fever,2-R50.82,2-R50.8, +1,2-Postvaccination fever,2-R50.83,2-R50.8, +1,2-Febrile nonhemolytic transfusion reaction,2-R50.84,2-R50.8, +1,"2-Fever, unspecified",2-R50.9,2-R50, +1,2-Headache,2-R51,2-R50-R69, +1,"2-Headache with orthostatic component, not elsewhere classified",2-R51.0,2-R51, +1,"2-Headache, unspecified",2-R51.9,2-R51, +1,"2-Pain, unspecified",2-R52,2-R50-R69, +1,2-Malaise and fatigue,2-R53,2-R50-R69, +1,2-Neoplastic (malignant) related fatigue,2-R53.0,2-R53, +1,2-Weakness,2-R53.1,2-R53, +1,2-Functional quadriplegia,2-R53.2,2-R53, +1,2-Other malaise and fatigue,2-R53.8,2-R53, +1,2-Other malaise,2-R53.81,2-R53.8, +1,"2-Chronic fatigue, unspecified",2-R53.82,2-R53.8, +1,2-Other fatigue,2-R53.83,2-R53.8, +1,2-Age-related physical debility,2-R54,2-R50-R69, +1,2-Syncope and collapse,2-R55,2-R50-R69, +1,"2-Convulsions, not elsewhere classified",2-R56,2-R50-R69, +1,2-Febrile convulsions,2-R56.0,2-R56, +1,2-Simple febrile convulsions,2-R56.00,2-R56.0, +1,2-Complex febrile convulsions,2-R56.01,2-R56.0, +1,2-Post traumatic seizures,2-R56.1,2-R56, +1,2-Unspecified convulsions,2-R56.9,2-R56, +1,"2-Shock, not elsewhere classified",2-R57,2-R50-R69, +1,2-Cardiogenic shock,2-R57.0,2-R57, +1,2-Hypovolemic shock,2-R57.1,2-R57, +1,2-Other shock,2-R57.8,2-R57, +1,"2-Shock, unspecified",2-R57.9,2-R57, +1,"2-Hemorrhage, not elsewhere classified",2-R58,2-R50-R69, +1,2-Enlarged lymph nodes,2-R59,2-R50-R69, +1,2-Localized enlarged lymph nodes,2-R59.0,2-R59, +1,2-Generalized enlarged lymph nodes,2-R59.1,2-R59, +1,"2-Enlarged lymph nodes, unspecified",2-R59.9,2-R59, +1,"2-Edema, not elsewhere classified",2-R60,2-R50-R69, +1,2-Localized edema,2-R60.0,2-R60, +1,2-Generalized edema,2-R60.1,2-R60, +1,"2-Edema, unspecified",2-R60.9,2-R60, +1,2-Generalized hyperhidrosis,2-R61,2-R50-R69, +1,2-Lack of expected normal physiological development in childhood and adults,2-R62,2-R50-R69, +1,2-Delayed milestone in childhood,2-R62.0,2-R62, +1,2-Other and unspecified lack of expected normal physiological development in childhood,2-R62.5,2-R62, +1,2-Unspecified lack of expected normal physiological development in childhood,2-R62.50,2-R62.5, +1,2-Failure to thrive (child),2-R62.51,2-R62.5, +1,2-Short stature (child),2-R62.52,2-R62.5, +1,2-Other lack of expected normal physiological development in childhood,2-R62.59,2-R62.5, +1,2-Adult failure to thrive,2-R62.7,2-R62, +1,2-Symptoms and signs concerning food and fluid intake,2-R63,2-R50-R69, +1,2-Anorexia,2-R63.0,2-R63, +1,2-Polydipsia,2-R63.1,2-R63, +1,2-Polyphagia,2-R63.2,2-R63, +1,2-Feeding difficulties,2-R63.3,2-R63, +1,"2-Feeding difficulties, unspecified",2-R63.30,2-R63.3, +1,"2-Pediatric feeding disorder, acute",2-R63.31,2-R63.3, +1,"2-Pediatric feeding disorder, chronic",2-R63.32,2-R63.3, +1,2-Other feeding difficulties,2-R63.39,2-R63.3, +1,2-Abnormal weight loss,2-R63.4,2-R63, +1,2-Abnormal weight gain,2-R63.5,2-R63, +1,2-Underweight,2-R63.6,2-R63, +1,2-Other symptoms and signs concerning food and fluid intake,2-R63.8,2-R63, +1,2-Cachexia,2-R64,2-R50-R69, +1,2-Symptoms and signs specifically associated with systemic inflammation and infection,2-R65,2-R50-R69, +1,2-Systemic inflammatory response syndrome (SIRS) of non-infectious origin,2-R65.1,2-R65, +1,2-Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction,2-R65.10,2-R65.1, +1,2-Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction,2-R65.11,2-R65.1, +1,2-Severe sepsis,2-R65.2,2-R65, +1,2-Severe sepsis without septic shock,2-R65.20,2-R65.2, +1,2-Severe sepsis with septic shock,2-R65.21,2-R65.2, +1,2-Other general symptoms and signs,2-R68,2-R50-R69, +1,"2-Hypothermia, not associated with low environmental temperature",2-R68.0,2-R68, +1,2-Nonspecific symptoms peculiar to infancy,2-R68.1,2-R68, +1,2-Excessive crying of infant (baby),2-R68.11,2-R68.1, +1,2-Fussy infant (baby),2-R68.12,2-R68.1, +1,2-Apparent life threatening event in infant (ALTE),2-R68.13,2-R68.1, +1,2-Other nonspecific symptoms peculiar to infancy,2-R68.19,2-R68.1, +1,"2-Dry mouth, unspecified",2-R68.2,2-R68, +1,2-Clubbing of fingers,2-R68.3,2-R68, +1,2-Other general symptoms and signs,2-R68.8,2-R68, +1,2-Early satiety,2-R68.81,2-R68.8, +1,2-Decreased libido,2-R68.82,2-R68.8, +1,2-Chills (without fever),2-R68.83,2-R68.8, +1,2-Jaw pain,2-R68.84,2-R68.8, +1,2-Other general symptoms and signs,2-R68.89,2-R68.8, +1,"2-Illness, unspecified",2-R69,2-R50-R69, +1,2-ICD-10 Root,2-Root,, +1,,2-Vibrio vulnificus,2-dummy2, +1,,2-dummy1,2-Root, +1,,2-dummy2,2-dummy1, diff --git a/inst/extdata/toy_tree_wide.txt b/inst/extdata/toy_tree_wide.txt new file mode 100644 index 0000000..605e1df --- /dev/null +++ b/inst/extdata/toy_tree_wide.txt @@ -0,0 +1,357 @@ +Name Name1 Desc Level1 Level2 Level3 Level4 Level5 Level6 Level7 Level8 V1 added +A00 A00 Cholera Root A00-B99 A00-A09 A00 "" "" "" "" 0 +A00.0 A000 Cholera due to Vibrio cholerae 01, biovar cholerae Root A00-B99 A00-A09 A00 A00.0 "" "" "" A000 Cholera due to Vibrio cholerae 01, biovar cholerae 0 +A00.1 A001 Cholera due to Vibrio cholerae 01, biovar eltor Root A00-B99 A00-A09 A00 A00.1 "" "" "" A001 Cholera due to Vibrio cholerae 01, biovar eltor 0 +A00.9 A009 Cholera, unspecified Root A00-B99 A00-A09 A00 A00.9 "" "" "" A009 Cholera, unspecified 0 +A01 A01 Typhoid and paratyphoid fevers Root A00-B99 A00-A09 A01 "" "" "" "" 0 +A01.0 A010 Typhoid fever Root A00-B99 A00-A09 A01 A01.0 "" "" "" 0 +A01.00 A0100 Typhoid fever, unspecified Root A00-B99 A00-A09 A01 A01.0 A01.00 "" "" A0100 Typhoid fever, unspecified 0 +A01.01 A0101 Typhoid meningitis Root A00-B99 A00-A09 A01 A01.0 A01.01 "" "" A0101 Typhoid meningitis 0 +A01.02 A0102 Typhoid fever with heart involvement Root A00-B99 A00-A09 A01 A01.0 A01.02 "" "" A0102 Typhoid fever with heart involvement 0 +A01.03 A0103 Typhoid pneumonia Root A00-B99 A00-A09 A01 A01.0 A01.03 "" "" A0103 Typhoid pneumonia 0 +A01.04 A0104 Typhoid arthritis Root A00-B99 A00-A09 A01 A01.0 A01.04 "" "" A0104 Typhoid arthritis 0 +A01.05 A0105 Typhoid osteomyelitis Root A00-B99 A00-A09 A01 A01.0 A01.05 "" "" A0105 Typhoid osteomyelitis 0 +A01.09 A0109 Typhoid fever with other complications Root A00-B99 A00-A09 A01 A01.0 A01.09 "" "" A0109 Typhoid fever with other complications 0 +A01.1 A011 Paratyphoid fever A Root A00-B99 A00-A09 A01 A01.1 "" "" "" A011 Paratyphoid fever A 0 +A01.2 A012 Paratyphoid fever B Root A00-B99 A00-A09 A01 A01.2 "" "" "" A012 Paratyphoid fever B 0 +A01.3 A013 Paratyphoid fever C Root A00-B99 A00-A09 A01 A01.3 "" "" "" A013 Paratyphoid fever C 0 +A01.4 A014 Paratyphoid fever, unspecified Root A00-B99 A00-A09 A01 A01.4 "" "" "" A014 Paratyphoid fever, unspecified 0 +A02 A02 Other salmonella infections Root A00-B99 A00-A09 A02 "" "" "" "" 0 +A02.0 A020 Salmonella enteritis Root A00-B99 A00-A09 A02 A02.0 "" "" "" A020 Salmonella enteritis 0 +A02.1 A021 Salmonella sepsis Root A00-B99 A00-A09 A02 A02.1 "" "" "" A021 Salmonella sepsis 0 +A02.2 A022 Localized salmonella infections Root A00-B99 A00-A09 A02 A02.2 "" "" "" 0 +A02.20 A0220 Localized salmonella infection, unspecified Root A00-B99 A00-A09 A02 A02.2 A02.20 "" "" A0220 Localized salmonella infection, unspecified 0 +A02.21 A0221 Salmonella meningitis Root A00-B99 A00-A09 A02 A02.2 A02.21 "" "" A0221 Salmonella meningitis 0 +A02.22 A0222 Salmonella pneumonia Root A00-B99 A00-A09 A02 A02.2 A02.22 "" "" A0222 Salmonella pneumonia 0 +A02.23 A0223 Salmonella arthritis Root A00-B99 A00-A09 A02 A02.2 A02.23 "" "" A0223 Salmonella arthritis 0 +A02.24 A0224 Salmonella osteomyelitis Root A00-B99 A00-A09 A02 A02.2 A02.24 "" "" A0224 Salmonella osteomyelitis 0 +A02.25 A0225 Salmonella pyelonephritis Root A00-B99 A00-A09 A02 A02.2 A02.25 "" "" A0225 Salmonella pyelonephritis 0 +A02.29 A0229 Salmonella with other localized infection Root A00-B99 A00-A09 A02 A02.2 A02.29 "" "" A0229 Salmonella with other localized infection 0 +A02.8 A028 Other specified salmonella infections Root A00-B99 A00-A09 A02 A02.8 "" "" "" A028 Other specified salmonella infections 0 +A02.9 A029 Salmonella infection, unspecified Root A00-B99 A00-A09 A02 A02.9 "" "" "" A029 Salmonella infection, unspecified 0 +A03 A03 Shigellosis Root A00-B99 A00-A09 A03 "" "" "" "" 0 +A03.0 A030 Shigellosis due to Shigella dysenteriae Root A00-B99 A00-A09 A03 A03.0 "" "" "" A030 Shigellosis due to Shigella dysenteriae 0 +A03.1 A031 Shigellosis due to Shigella flexneri Root A00-B99 A00-A09 A03 A03.1 "" "" "" A031 Shigellosis due to Shigella flexneri 0 +A03.2 A032 Shigellosis due to Shigella boydii Root A00-B99 A00-A09 A03 A03.2 "" "" "" A032 Shigellosis due to Shigella boydii 0 +A03.3 A033 Shigellosis due to Shigella sonnei Root A00-B99 A00-A09 A03 A03.3 "" "" "" A033 Shigellosis due to Shigella sonnei 0 +A03.8 A038 Other shigellosis Root A00-B99 A00-A09 A03 A03.8 "" "" "" A038 Other shigellosis 0 +A03.9 A039 Shigellosis, unspecified Root A00-B99 A00-A09 A03 A03.9 "" "" "" A039 Shigellosis, unspecified 0 +A04 A04 Other bacterial intestinal infections Root A00-B99 A00-A09 A04 "" "" "" "" 0 +A04.0 A040 Enteropathogenic Escherichia coli infection Root A00-B99 A00-A09 A04 A04.0 "" "" "" A040 Enteropathogenic Escherichia coli infection 0 +A04.1 A041 Enterotoxigenic Escherichia coli infection Root A00-B99 A00-A09 A04 A04.1 "" "" "" A041 Enterotoxigenic Escherichia coli infection 0 +A04.2 A042 Enteroinvasive Escherichia coli infection Root A00-B99 A00-A09 A04 A04.2 "" "" "" A042 Enteroinvasive Escherichia coli infection 0 +A04.3 A043 Enterohemorrhagic Escherichia coli infection Root A00-B99 A00-A09 A04 A04.3 "" "" "" A043 Enterohemorrhagic Escherichia coli infection 0 +A04.4 A044 Other intestinal Escherichia coli infections Root A00-B99 A00-A09 A04 A04.4 "" "" "" A044 Other intestinal Escherichia coli infections 0 +A04.5 A045 Campylobacter enteritis Root A00-B99 A00-A09 A04 A04.5 "" "" "" A045 Campylobacter enteritis 0 +A04.6 A046 Enteritis due to Yersinia enterocolitica Root A00-B99 A00-A09 A04 A04.6 "" "" "" A046 Enteritis due to Yersinia enterocolitica 0 +A04.7 A047 Enterocolitis due to Clostridium difficile Root A00-B99 A00-A09 A04 A04.7 "" "" "" 0 +A04.71 A0471 Enterocolitis due to Clostridium difficile, recurrent Root A00-B99 A00-A09 A04 A04.7 A04.71 "" "" A0471 Enterocolitis due to Clostridium difficile, recurrent 0 +A04.72 A0472 Enterocolitis due to Clostridium difficile, not specified as recurrent Root A00-B99 A00-A09 A04 A04.7 A04.72 "" "" A0472 Enterocolitis due to Clostridium difficile, not specified as recurrent 0 +A04.8 A048 Other specified bacterial intestinal infections Root A00-B99 A00-A09 A04 A04.8 "" "" "" A048 Other specified bacterial intestinal infections 0 +A04.9 A049 Bacterial intestinal infection, unspecified Root A00-B99 A00-A09 A04 A04.9 "" "" "" A049 Bacterial intestinal infection, unspecified 0 +A05 A05 Other bacterial foodborne intoxications, not elsewhere classified Root A00-B99 A00-A09 A05 "" "" "" "" 0 +A05.0 A050 Foodborne staphylococcal intoxication Root A00-B99 A00-A09 A05 A05.0 "" "" "" A050 Foodborne staphylococcal intoxication 0 +A05.1 A051 Botulism food poisoning Root A00-B99 A00-A09 A05 A05.1 "" "" "" A051 Botulism food poisoning 0 +A05.2 A052 Foodborne Clostridium perfringens [Clostridium welchii] intoxication Root A00-B99 A00-A09 A05 A05.2 "" "" "" A052 Foodborne Clostridium perfringens [Clostridium welchii] intoxication 0 +A05.3 A053 Foodborne Vibrio parahaemolyticus intoxication Root A00-B99 A00-A09 A05 A05.3 "" "" "" A053 Foodborne Vibrio parahaemolyticus intoxication 0 +A05.4 A054 Foodborne Bacillus cereus intoxication Root A00-B99 A00-A09 A05 A05.4 "" "" "" A054 Foodborne Bacillus cereus intoxication 0 +A05.5 A055 Foodborne Vibrio vulnificus intoxication Root A00-B99 A00-A09 A05 A05.5 "" "" "" A055 Foodborne Vibrio vulnificus intoxication 0 +A05.8 A058 Other specified bacterial foodborne intoxications Root A00-B99 A00-A09 A05 A05.8 "" "" "" A058 Other specified bacterial foodborne intoxications 0 +A05.9 A059 Bacterial foodborne intoxication, unspecified Root A00-B99 A00-A09 A05 A05.9 "" "" "" A059 Bacterial foodborne intoxication, unspecified 0 +A06 A06 Amebiasis Root A00-B99 A00-A09 A06 "" "" "" "" 0 +A06.0 A060 Acute amebic dysentery Root A00-B99 A00-A09 A06 A06.0 "" "" "" A060 Acute amebic dysentery 0 +A06.1 A061 Chronic intestinal amebiasis Root A00-B99 A00-A09 A06 A06.1 "" "" "" A061 Chronic intestinal amebiasis 0 +A06.2 A062 Amebic nondysenteric colitis Root A00-B99 A00-A09 A06 A06.2 "" "" "" A062 Amebic nondysenteric colitis 0 +A06.3 A063 Ameboma of intestine Root A00-B99 A00-A09 A06 A06.3 "" "" "" A063 Ameboma of intestine 0 +A06.4 A064 Amebic liver abscess Root A00-B99 A00-A09 A06 A06.4 "" "" "" A064 Amebic liver abscess 0 +A06.5 A065 Amebic lung abscess Root A00-B99 A00-A09 A06 A06.5 "" "" "" A065 Amebic lung abscess 0 +A06.6 A066 Amebic brain abscess Root A00-B99 A00-A09 A06 A06.6 "" "" "" A066 Amebic brain abscess 0 +A06.7 A067 Cutaneous amebiasis Root A00-B99 A00-A09 A06 A06.7 "" "" "" A067 Cutaneous amebiasis 0 +A06.8 A068 Amebic infection of other sites Root A00-B99 A00-A09 A06 A06.8 "" "" "" 0 +A06.81 A0681 Amebic cystitis Root A00-B99 A00-A09 A06 A06.8 A06.81 "" "" A0681 Amebic cystitis 0 +A06.82 A0682 Other amebic genitourinary infections Root A00-B99 A00-A09 A06 A06.8 A06.82 "" "" A0682 Other amebic genitourinary infections 0 +A06.89 A0689 Other amebic infections Root A00-B99 A00-A09 A06 A06.8 A06.89 "" "" A0689 Other amebic infections 0 +A06.9 A069 Amebiasis, unspecified Root A00-B99 A00-A09 A06 A06.9 "" "" "" A069 Amebiasis, unspecified 0 +A07 A07 Other protozoal intestinal diseases Root A00-B99 A00-A09 A07 "" "" "" "" 0 +A07.0 A070 Balantidiasis Root A00-B99 A00-A09 A07 A07.0 "" "" "" A070 Balantidiasis 0 +A07.1 A071 Giardiasis [lambliasis] Root A00-B99 A00-A09 A07 A07.1 "" "" "" A071 Giardiasis [lambliasis] 0 +A07.2 A072 Cryptosporidiosis Root A00-B99 A00-A09 A07 A07.2 "" "" "" A072 Cryptosporidiosis 0 +A07.3 A073 Isosporiasis Root A00-B99 A00-A09 A07 A07.3 "" "" "" A073 Isosporiasis 0 +A07.4 A074 Cyclosporiasis Root A00-B99 A00-A09 A07 A07.4 "" "" "" A074 Cyclosporiasis 0 +A07.8 A078 Other specified protozoal intestinal diseases Root A00-B99 A00-A09 A07 A07.8 "" "" "" A078 Other specified protozoal intestinal diseases 0 +A07.9 A079 Protozoal intestinal disease, unspecified Root A00-B99 A00-A09 A07 A07.9 "" "" "" A079 Protozoal intestinal disease, unspecified 0 +A08 A08 Viral and other specified intestinal infections Root A00-B99 A00-A09 A08 "" "" "" "" 0 +A08.0 A080 Rotaviral enteritis Root A00-B99 A00-A09 A08 A08.0 "" "" "" A080 Rotaviral enteritis 0 +A08.1 A081 Acute gastroenteropathy due to Norwalk agent and other small round viruses Root A00-B99 A00-A09 A08 A08.1 "" "" "" 0 +A08.11 A0811 Acute gastroenteropathy due to Norwalk agent Root A00-B99 A00-A09 A08 A08.1 A08.11 "" "" A0811 Acute gastroenteropathy due to Norwalk agent 0 +A08.19 A0819 Acute gastroenteropathy due to other small round viruses Root A00-B99 A00-A09 A08 A08.1 A08.19 "" "" A0819 Acute gastroenteropathy due to other small round viruses 0 +A08.2 A082 Adenoviral enteritis Root A00-B99 A00-A09 A08 A08.2 "" "" "" A082 Adenoviral enteritis 0 +A08.3 A083 Other viral enteritis Root A00-B99 A00-A09 A08 A08.3 "" "" "" 0 +A08.31 A0831 Calicivirus enteritis Root A00-B99 A00-A09 A08 A08.3 A08.31 "" "" A0831 Calicivirus enteritis 0 +A08.32 A0832 Astrovirus enteritis Root A00-B99 A00-A09 A08 A08.3 A08.32 "" "" A0832 Astrovirus enteritis 0 +A08.39 A0839 Other viral enteritis Root A00-B99 A00-A09 A08 A08.3 A08.39 "" "" A0839 Other viral enteritis 0 +A08.4 A084 Viral intestinal infection, unspecified Root A00-B99 A00-A09 A08 A08.4 "" "" "" A084 Viral intestinal infection, unspecified 0 +A08.8 A088 Other specified intestinal infections Root A00-B99 A00-A09 A08 A08.8 "" "" "" A088 Other specified intestinal infections 0 +A09 A09 Infectious gastroenteritis and colitis, unspecified Root A00-B99 A00-A09 A09 "" "" "" "" A09 Infectious gastroenteritis and colitis, unspecified 0 +J00 J00 Acute nasopharyngitis [common cold] Root J00-J99 J00-J06 J00 "" "" "" "" J00 Acute nasopharyngitis [common cold] 0 +J01 J01 Acute sinusitis Root J00-J99 J00-J06 J01 "" "" "" "" 0 +J01.0 J010 Acute maxillary sinusitis Root J00-J99 J00-J06 J01 J01.0 "" "" "" 0 +J01.00 J0100 Acute maxillary sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.0 J01.00 "" "" J0100 Acute maxillary sinusitis, unspecified 0 +J01.01 J0101 Acute recurrent maxillary sinusitis Root J00-J99 J00-J06 J01 J01.0 J01.01 "" "" J0101 Acute recurrent maxillary sinusitis 0 +J01.1 J011 Acute frontal sinusitis Root J00-J99 J00-J06 J01 J01.1 "" "" "" 0 +J01.10 J0110 Acute frontal sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.1 J01.10 "" "" J0110 Acute frontal sinusitis, unspecified 0 +J01.11 J0111 Acute recurrent frontal sinusitis Root J00-J99 J00-J06 J01 J01.1 J01.11 "" "" J0111 Acute recurrent frontal sinusitis 0 +J01.2 J012 Acute ethmoidal sinusitis Root J00-J99 J00-J06 J01 J01.2 "" "" "" 0 +J01.20 J0120 Acute ethmoidal sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.2 J01.20 "" "" J0120 Acute ethmoidal sinusitis, unspecified 0 +J01.21 J0121 Acute recurrent ethmoidal sinusitis Root J00-J99 J00-J06 J01 J01.2 J01.21 "" "" J0121 Acute recurrent ethmoidal sinusitis 0 +J01.3 J013 Acute sphenoidal sinusitis Root J00-J99 J00-J06 J01 J01.3 "" "" "" 0 +J01.30 J0130 Acute sphenoidal sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.3 J01.30 "" "" J0130 Acute sphenoidal sinusitis, unspecified 0 +J01.31 J0131 Acute recurrent sphenoidal sinusitis Root J00-J99 J00-J06 J01 J01.3 J01.31 "" "" J0131 Acute recurrent sphenoidal sinusitis 0 +J01.4 J014 Acute pansinusitis Root J00-J99 J00-J06 J01 J01.4 "" "" "" 0 +J01.40 J0140 Acute pansinusitis, unspecified Root J00-J99 J00-J06 J01 J01.4 J01.40 "" "" J0140 Acute pansinusitis, unspecified 0 +J01.41 J0141 Acute recurrent pansinusitis Root J00-J99 J00-J06 J01 J01.4 J01.41 "" "" J0141 Acute recurrent pansinusitis 0 +J01.8 J018 Other acute sinusitis Root J00-J99 J00-J06 J01 J01.8 "" "" "" 0 +J01.80 J0180 Other acute sinusitis Root J00-J99 J00-J06 J01 J01.8 J01.80 "" "" J0180 Other acute sinusitis 0 +J01.81 J0181 Other acute recurrent sinusitis Root J00-J99 J00-J06 J01 J01.8 J01.81 "" "" J0181 Other acute recurrent sinusitis 0 +J01.9 J019 Acute sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.9 "" "" "" 0 +J01.90 J0190 Acute sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.9 J01.90 "" "" J0190 Acute sinusitis, unspecified 0 +J01.91 J0191 Acute recurrent sinusitis, unspecified Root J00-J99 J00-J06 J01 J01.9 J01.91 "" "" J0191 Acute recurrent sinusitis, unspecified 0 +J02 J02 Acute pharyngitis Root J00-J99 J00-J06 J02 "" "" "" "" 0 +J02.0 J020 Streptococcal pharyngitis Root J00-J99 J00-J06 J02 J02.0 "" "" "" J020 Streptococcal pharyngitis 0 +J02.8 J028 Acute pharyngitis due to other specified organisms Root J00-J99 J00-J06 J02 J02.8 "" "" "" J028 Acute pharyngitis due to other specified organisms 0 +J02.9 J029 Acute pharyngitis, unspecified Root J00-J99 J00-J06 J02 J02.9 "" "" "" J029 Acute pharyngitis, unspecified 0 +J03 J03 Acute tonsillitis Root J00-J99 J00-J06 J03 "" "" "" "" 0 +J03.0 J030 Streptococcal tonsillitis Root J00-J99 J00-J06 J03 J03.0 "" "" "" 0 +J03.00 J0300 Acute streptococcal tonsillitis, unspecified Root J00-J99 J00-J06 J03 J03.0 J03.00 "" "" J0300 Acute streptococcal tonsillitis, unspecified 0 +J03.01 J0301 Acute recurrent streptococcal tonsillitis Root J00-J99 J00-J06 J03 J03.0 J03.01 "" "" J0301 Acute recurrent streptococcal tonsillitis 0 +J03.8 J038 Acute tonsillitis due to other specified organisms Root J00-J99 J00-J06 J03 J03.8 "" "" "" 0 +J03.80 J0380 Acute tonsillitis due to other specified organisms Root J00-J99 J00-J06 J03 J03.8 J03.80 "" "" J0380 Acute tonsillitis due to other specified organisms 0 +J03.81 J0381 Acute recurrent tonsillitis due to other specified organisms Root J00-J99 J00-J06 J03 J03.8 J03.81 "" "" J0381 Acute recurrent tonsillitis due to other specified organisms 0 +J03.9 J039 Acute tonsillitis, unspecified Root J00-J99 J00-J06 J03 J03.9 "" "" "" 0 +J03.90 J0390 Acute tonsillitis, unspecified Root J00-J99 J00-J06 J03 J03.9 J03.90 "" "" J0390 Acute tonsillitis, unspecified 0 +J03.91 J0391 Acute recurrent tonsillitis, unspecified Root J00-J99 J00-J06 J03 J03.9 J03.91 "" "" J0391 Acute recurrent tonsillitis, unspecified 0 +J04 J04 Acute laryngitis and tracheitis Root J00-J99 J00-J06 J04 "" "" "" "" 0 +J04.0 J040 Acute laryngitis Root J00-J99 J00-J06 J04 J04.0 "" "" "" J040 Acute laryngitis 0 +J04.1 J041 Acute tracheitis Root J00-J99 J00-J06 J04 J04.1 "" "" "" 0 +J04.10 J0410 Acute tracheitis without obstruction Root J00-J99 J00-J06 J04 J04.1 J04.10 "" "" J0410 Acute tracheitis without obstruction 0 +J04.11 J0411 Acute tracheitis with obstruction Root J00-J99 J00-J06 J04 J04.1 J04.11 "" "" J0411 Acute tracheitis with obstruction 0 +J04.2 J042 Acute laryngotracheitis Root J00-J99 J00-J06 J04 J04.2 "" "" "" J042 Acute laryngotracheitis 0 +J04.3 J043 Supraglottitis, unspecified Root J00-J99 J00-J06 J04 J04.3 "" "" "" 0 +J04.30 J0430 Supraglottitis, unspecified, without obstruction Root J00-J99 J00-J06 J04 J04.3 J04.30 "" "" J0430 Supraglottitis, unspecified, without obstruction 0 +J04.31 J0431 Supraglottitis, unspecified, with obstruction Root J00-J99 J00-J06 J04 J04.3 J04.31 "" "" J0431 Supraglottitis, unspecified, with obstruction 0 +J05 J05 Acute obstructive laryngitis [croup] and epiglottitis Root J00-J99 J00-J06 J05 "" "" "" "" 0 +J05.0 J050 Acute obstructive laryngitis [croup] Root J00-J99 J00-J06 J05 J05.0 "" "" "" J050 Acute obstructive laryngitis [croup] 0 +J05.1 J051 Acute epiglottitis Root J00-J99 J00-J06 J05 J05.1 "" "" "" 0 +J05.10 J0510 Acute epiglottitis without obstruction Root J00-J99 J00-J06 J05 J05.1 J05.10 "" "" J0510 Acute epiglottitis without obstruction 0 +J05.11 J0511 Acute epiglottitis with obstruction Root J00-J99 J00-J06 J05 J05.1 J05.11 "" "" J0511 Acute epiglottitis with obstruction 0 +J06 J06 Acute upper respiratory infections of multiple and unspecified sites Root J00-J99 J00-J06 J06 "" "" "" "" 0 +J06.0 J060 Acute laryngopharyngitis Root J00-J99 J00-J06 J06 J06.0 "" "" "" J060 Acute laryngopharyngitis 0 +J06.9 J069 Acute upper respiratory infection, unspecified Root J00-J99 J00-J06 J06 J06.9 "" "" "" J069 Acute upper respiratory infection, unspecified 0 +R10 R10 Abdominal and pelvic pain Root R00-R99 R10-R19 R10 "" "" "" "" 0 +R10.0 R100 Acute abdomen Root R00-R99 R10-R19 R10 R10.0 "" "" "" R100 Acute abdomen 0 +R10.1 R101 Pain localized to upper abdomen Root R00-R99 R10-R19 R10 R10.1 "" "" "" 0 +R10.10 R1010 Upper abdominal pain, unspecified Root R00-R99 R10-R19 R10 R10.1 R10.10 "" "" R1010 Upper abdominal pain, unspecified 0 +R10.11 R1011 Right upper quadrant pain Root R00-R99 R10-R19 R10 R10.1 R10.11 "" "" R1011 Right upper quadrant pain 0 +R10.12 R1012 Left upper quadrant pain Root R00-R99 R10-R19 R10 R10.1 R10.12 "" "" R1012 Left upper quadrant pain 0 +R10.13 R1013 Epigastric pain Root R00-R99 R10-R19 R10 R10.1 R10.13 "" "" R1013 Epigastric pain 0 +R10.2 R102 Pelvic and perineal pain Root R00-R99 R10-R19 R10 R10.2 "" "" "" R102 Pelvic and perineal pain 0 +R10.20 R1020 Pelvic and perineal pain unspecified side Root R00-R99 R10-R19 R10 R10.2 R10.20 "" "" R1020 Pelvic and perineal pain unspecified side 0 +R10.21 R1021 Pelvic and perineal pain right side Root R00-R99 R10-R19 R10 R10.2 R10.21 "" "" R1021 Pelvic and perineal pain right side 0 +R10.22 R1022 Pelvic and perineal pain left side Root R00-R99 R10-R19 R10 R10.2 R10.22 "" "" R1022 Pelvic and perineal pain left side 0 +R10.23 R1023 Pelvic and perineal pain bilateral Root R00-R99 R10-R19 R10 R10.2 R10.23 "" "" R1023 Pelvic and perineal pain bilateral 0 +R10.24 R1024 Suprapubic pain Root R00-R99 R10-R19 R10 R10.2 R10.24 "" "" R1024 Suprapubic pain 0 +R10.3 R103 Pain localized to other parts of lower abdomen Root R00-R99 R10-R19 R10 R10.3 "" "" "" 0 +R10.30 R1030 Lower abdominal pain, unspecified Root R00-R99 R10-R19 R10 R10.3 R10.30 "" "" R1030 Lower abdominal pain, unspecified 0 +R10.31 R1031 Right lower quadrant pain Root R00-R99 R10-R19 R10 R10.3 R10.31 "" "" R1031 Right lower quadrant pain 0 +R10.32 R1032 Left lower quadrant pain Root R00-R99 R10-R19 R10 R10.3 R10.32 "" "" R1032 Left lower quadrant pain 0 +R10.33 R1033 Periumbilical pain Root R00-R99 R10-R19 R10 R10.3 R10.33 "" "" R1033 Periumbilical pain 0 +R10.8 R108 Other abdominal pain Root R00-R99 R10-R19 R10 R10.8 "" "" "" 0 +R10.81 R1081 Abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 "" "" 0 +R10.811 R10811 Right upper quadrant abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.811 "" R10811 Right upper quadrant abdominal tenderness 0 +R10.812 R10812 Left upper quadrant abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.812 "" R10812 Left upper quadrant abdominal tenderness 0 +R10.813 R10813 Right lower quadrant abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.813 "" R10813 Right lower quadrant abdominal tenderness 0 +R10.814 R10814 Left lower quadrant abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.814 "" R10814 Left lower quadrant abdominal tenderness 0 +R10.815 R10815 Periumbilic abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.815 "" R10815 Periumbilic abdominal tenderness 0 +R10.816 R10816 Epigastric abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.816 "" R10816 Epigastric abdominal tenderness 0 +R10.817 R10817 Generalized abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.817 "" R10817 Generalized abdominal tenderness 0 +R10.819 R10819 Abdominal tenderness, unspecified site Root R00-R99 R10-R19 R10 R10.8 R10.81 R10.819 "" R10819 Abdominal tenderness, unspecified site 0 +R10.82 R1082 Rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 "" "" 0 +R10.821 R10821 Right upper quadrant rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.821 "" R10821 Right upper quadrant rebound abdominal tenderness 0 +R10.822 R10822 Left upper quadrant rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.822 "" R10822 Left upper quadrant rebound abdominal tenderness 0 +R10.823 R10823 Right lower quadrant rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.823 "" R10823 Right lower quadrant rebound abdominal tenderness 0 +R10.824 R10824 Left lower quadrant rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.824 "" R10824 Left lower quadrant rebound abdominal tenderness 0 +R10.825 R10825 Periumbilic rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.825 "" R10825 Periumbilic rebound abdominal tenderness 0 +R10.826 R10826 Epigastric rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.826 "" R10826 Epigastric rebound abdominal tenderness 0 +R10.827 R10827 Generalized rebound abdominal tenderness Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.827 "" R10827 Generalized rebound abdominal tenderness 0 +R10.829 R10829 Rebound abdominal tenderness, unspecified site Root R00-R99 R10-R19 R10 R10.8 R10.82 R10.829 "" R10829 Rebound abdominal tenderness, unspecified site 0 +R10.83 R1083 Colic Root R00-R99 R10-R19 R10 R10.8 R10.83 "" "" R1083 Colic 0 +R10.84 R1084 Generalized abdominal pain Root R00-R99 R10-R19 R10 R10.8 R10.84 "" "" R1084 Generalized abdominal pain 0 +R10.85 R1085 Abdominal pain of multiple sites Root R00-R99 R10-R19 R10 R10.8 R10.85 "" "" R1085 Abdominal pain of multiple sites 0 +R10.8A R108A Flank tenderness Root R00-R99 R10-R19 R10 R10.8 R10.8A "" "" 0 +R10.8A1 R108A1 Right flank tenderness Root R00-R99 R10-R19 R10 R10.8 R10.8A R10.8A1 "" R108A1 Right flank tenderness 0 +R10.8A2 R108A2 Left flank tenderness Root R00-R99 R10-R19 R10 R10.8 R10.8A R10.8A2 "" R108A2 Left flank tenderness 0 +R10.8A3 R108A3 Suprapubic tenderness Root R00-R99 R10-R19 R10 R10.8 R10.8A R10.8A3 "" R108A3 Suprapubic tenderness 0 +R10.8A9 R108A9 Flank tenderness, unspecified Root R00-R99 R10-R19 R10 R10.8 R10.8A R10.8A9 "" R108A9 Flank tenderness, unspecified 0 +R10.9 R109 Unspecified abdominal pain Root R00-R99 R10-R19 R10 R10.9 "" "" "" R109 Unspecified abdominal pain 0 +R10.A R10A Pain localized to flank Root R00-R99 R10-R19 R10 R10.A "" "" "" 0 +R10.A0 R10A0 Flank pain, unspecified side Root R00-R99 R10-R19 R10 R10.A R10.A0 "" "" R10A0 Flank pain, unspecified side 0 +R10.A1 R10A1 Flank pain, right side Root R00-R99 R10-R19 R10 R10.A R10.A1 "" "" R10A1 Flank pain, right side 0 +R10.A2 R10A2 Flank pain, left side Root R00-R99 R10-R19 R10 R10.A R10.A2 "" "" R10A2 Flank pain, left side 0 +R10.A3 R10A3 Flank pain, bilateral Root R00-R99 R10-R19 R10 R10.A R10.A3 "" "" R10A3 Flank pain, bilateral 0 +R11 R11 Nausea and vomiting Root R00-R99 R10-R19 R11 "" "" "" "" 0 +R11.0 R110 Nausea Root R00-R99 R10-R19 R11 R11.0 "" "" "" R110 Nausea 0 +R11.1 R111 Vomiting Root R00-R99 R10-R19 R11 R11.1 "" "" "" 0 +R11.10 R1110 Vomiting, unspecified Root R00-R99 R10-R19 R11 R11.1 R11.10 "" "" R1110 Vomiting, unspecified 0 +R11.11 R1111 Vomiting without nausea Root R00-R99 R10-R19 R11 R11.1 R11.11 "" "" R1111 Vomiting without nausea 0 +R11.12 R1112 Projectile vomiting Root R00-R99 R10-R19 R11 R11.1 R11.12 "" "" R1112 Projectile vomiting 0 +R11.13 R1113 Vomiting of fecal matter Root R00-R99 R10-R19 R11 R11.1 R11.13 "" "" R1113 Vomiting of fecal matter 0 +R11.14 R1114 Bilious vomiting Root R00-R99 R10-R19 R11 R11.1 R11.14 "" "" R1114 Bilious vomiting 0 +R11.15 R1115 Cyclical vomiting syndrome unrelated to migraine Root R00-R99 R10-R19 R11 R11.1 R11.15 "" "" R1115 Cyclical vomiting syndrome unrelated to migraine 0 +R11.16 R1116 Cannabis hyperemesis syndrome Root R00-R99 R10-R19 R11 R11.1 R11.16 "" "" R1116 Cannabis hyperemesis syndrome 0 +R11.2 R112 Nausea with vomiting, unspecified Root R00-R99 R10-R19 R11 R11.2 "" "" "" R112 Nausea with vomiting, unspecified 0 +R12 R12 Heartburn Root R00-R99 R10-R19 R12 "" "" "" "" R12 Heartburn 0 +R13 R13 Aphagia and dysphagia Root R00-R99 R10-R19 R13 "" "" "" "" 0 +R13.0 R130 Aphagia Root R00-R99 R10-R19 R13 R13.0 "" "" "" R130 Aphagia 0 +R13.1 R131 Dysphagia Root R00-R99 R10-R19 R13 R13.1 "" "" "" 0 +R13.10 R1310 Dysphagia, unspecified Root R00-R99 R10-R19 R13 R13.1 R13.10 "" "" R1310 Dysphagia, unspecified 0 +R13.11 R1311 Dysphagia, oral phase Root R00-R99 R10-R19 R13 R13.1 R13.11 "" "" R1311 Dysphagia, oral phase 0 +R13.12 R1312 Dysphagia, oropharyngeal phase Root R00-R99 R10-R19 R13 R13.1 R13.12 "" "" R1312 Dysphagia, oropharyngeal phase 0 +R13.13 R1313 Dysphagia, pharyngeal phase Root R00-R99 R10-R19 R13 R13.1 R13.13 "" "" R1313 Dysphagia, pharyngeal phase 0 +R13.14 R1314 Dysphagia, pharyngoesophageal phase Root R00-R99 R10-R19 R13 R13.1 R13.14 "" "" R1314 Dysphagia, pharyngoesophageal phase 0 +R13.19 R1319 Other dysphagia Root R00-R99 R10-R19 R13 R13.1 R13.19 "" "" R1319 Other dysphagia 0 +R14 R14 Flatulence and related conditions Root R00-R99 R10-R19 R14 "" "" "" "" 0 +R14.0 R140 Abdominal distension (gaseous) Root R00-R99 R10-R19 R14 R14.0 "" "" "" R140 Abdominal distension (gaseous) 0 +R14.1 R141 Gas pain Root R00-R99 R10-R19 R14 R14.1 "" "" "" R141 Gas pain 0 +R14.2 R142 Eructation Root R00-R99 R10-R19 R14 R14.2 "" "" "" R142 Eructation 0 +R14.3 R143 Flatulence Root R00-R99 R10-R19 R14 R14.3 "" "" "" R143 Flatulence 0 +R15 R15 Fecal incontinence Root R00-R99 R10-R19 R15 "" "" "" "" 0 +R15.0 R150 Incomplete defecation Root R00-R99 R10-R19 R15 R15.0 "" "" "" R150 Incomplete defecation 0 +R15.1 R151 Fecal smearing Root R00-R99 R10-R19 R15 R15.1 "" "" "" R151 Fecal smearing 0 +R15.2 R152 Fecal urgency Root R00-R99 R10-R19 R15 R15.2 "" "" "" R152 Fecal urgency 0 +R15.9 R159 Full incontinence of feces Root R00-R99 R10-R19 R15 R15.9 "" "" "" R159 Full incontinence of feces 0 +R16 R16 Hepatomegaly and splenomegaly, not elsewhere classified Root R00-R99 R10-R19 R16 "" "" "" "" 0 +R16.0 R160 Hepatomegaly, not elsewhere classified Root R00-R99 R10-R19 R16 R16.0 "" "" "" R160 Hepatomegaly, not elsewhere classified 0 +R16.1 R161 Splenomegaly, not elsewhere classified Root R00-R99 R10-R19 R16 R16.1 "" "" "" R161 Splenomegaly, not elsewhere classified 0 +R16.2 R162 Hepatomegaly with splenomegaly, not elsewhere classified Root R00-R99 R10-R19 R16 R16.2 "" "" "" R162 Hepatomegaly with splenomegaly, not elsewhere classified 0 +R17 R17 Unspecified jaundice Root R00-R99 R10-R19 R17 "" "" "" "" R17 Unspecified jaundice 0 +R18 R18 Ascites Root R00-R99 R10-R19 R18 "" "" "" "" 0 +R18.0 R180 Malignant ascites Root R00-R99 R10-R19 R18 R18.0 "" "" "" R180 Malignant ascites 0 +R18.8 R188 Other ascites Root R00-R99 R10-R19 R18 R18.8 "" "" "" R188 Other ascites 0 +R19 R19 Other symptoms and signs involving the digestive system and abdomen Root R00-R99 R10-R19 R19 "" "" "" "" 0 +R19.0 R190 Intra-abdominal and pelvic swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 "" "" "" 0 +R19.00 R1900 Intra-abdominal and pelvic swelling, mass and lump, unspecified site Root R00-R99 R10-R19 R19 R19.0 R19.00 "" "" R1900 Intra-abdominal and pelvic swelling, mass and lump, unspecified site 0 +R19.01 R1901 Right upper quadrant abdominal swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.01 "" "" R1901 Right upper quadrant abdominal swelling, mass and lump 0 +R19.02 R1902 Left upper quadrant abdominal swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.02 "" "" R1902 Left upper quadrant abdominal swelling, mass and lump 0 +R19.03 R1903 Right lower quadrant abdominal swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.03 "" "" R1903 Right lower quadrant abdominal swelling, mass and lump 0 +R19.04 R1904 Left lower quadrant abdominal swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.04 "" "" R1904 Left lower quadrant abdominal swelling, mass and lump 0 +R19.05 R1905 Periumbilic swelling, mass or lump Root R00-R99 R10-R19 R19 R19.0 R19.05 "" "" R1905 Periumbilic swelling, mass or lump 0 +R19.06 R1906 Epigastric swelling, mass or lump Root R00-R99 R10-R19 R19 R19.0 R19.06 "" "" R1906 Epigastric swelling, mass or lump 0 +R19.07 R1907 Generalized intra-abdominal and pelvic swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.07 "" "" R1907 Generalized intra-abdominal and pelvic swelling, mass and lump 0 +R19.09 R1909 Other intra-abdominal and pelvic swelling, mass and lump Root R00-R99 R10-R19 R19 R19.0 R19.09 "" "" R1909 Other intra-abdominal and pelvic swelling, mass and lump 0 +R19.1 R191 Abnormal bowel sounds Root R00-R99 R10-R19 R19 R19.1 "" "" "" 0 +R19.11 R1911 Absent bowel sounds Root R00-R99 R10-R19 R19 R19.1 R19.11 "" "" R1911 Absent bowel sounds 0 +R19.12 R1912 Hyperactive bowel sounds Root R00-R99 R10-R19 R19 R19.1 R19.12 "" "" R1912 Hyperactive bowel sounds 0 +R19.15 R1915 Other abnormal bowel sounds Root R00-R99 R10-R19 R19 R19.1 R19.15 "" "" R1915 Other abnormal bowel sounds 0 +R19.2 R192 Visible peristalsis Root R00-R99 R10-R19 R19 R19.2 "" "" "" R192 Visible peristalsis 0 +R19.3 R193 Abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 "" "" "" 0 +R19.30 R1930 Abdominal rigidity, unspecified site Root R00-R99 R10-R19 R19 R19.3 R19.30 "" "" R1930 Abdominal rigidity, unspecified site 0 +R19.31 R1931 Right upper quadrant abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.31 "" "" R1931 Right upper quadrant abdominal rigidity 0 +R19.32 R1932 Left upper quadrant abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.32 "" "" R1932 Left upper quadrant abdominal rigidity 0 +R19.33 R1933 Right lower quadrant abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.33 "" "" R1933 Right lower quadrant abdominal rigidity 0 +R19.34 R1934 Left lower quadrant abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.34 "" "" R1934 Left lower quadrant abdominal rigidity 0 +R19.35 R1935 Periumbilic abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.35 "" "" R1935 Periumbilic abdominal rigidity 0 +R19.36 R1936 Epigastric abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.36 "" "" R1936 Epigastric abdominal rigidity 0 +R19.37 R1937 Generalized abdominal rigidity Root R00-R99 R10-R19 R19 R19.3 R19.37 "" "" R1937 Generalized abdominal rigidity 0 +R19.4 R194 Change in bowel habit Root R00-R99 R10-R19 R19 R19.4 "" "" "" R194 Change in bowel habit 0 +R19.5 R195 Other fecal abnormalities Root R00-R99 R10-R19 R19 R19.5 "" "" "" R195 Other fecal abnormalities 0 +R19.6 R196 Halitosis Root R00-R99 R10-R19 R19 R19.6 "" "" "" R196 Halitosis 0 +R19.7 R197 Diarrhea, unspecified Root R00-R99 R10-R19 R19 R19.7 "" "" "" R197 Diarrhea, unspecified 0 +R19.8 R198 Other specified symptoms and signs involving the digestive system and abdomen Root R00-R99 R10-R19 R19 R19.8 "" "" "" R198 Other specified symptoms and signs involving the digestive system and abdomen 0 +R50 R50 Fever of other and unknown origin Root R00-R99 R50-R69 R50 "" "" "" "" 0 +R50.2 R502 Drug induced fever Root R00-R99 R50-R69 R50 R50.2 "" "" "" R502 Drug induced fever 0 +R50.8 R508 Other specified fever Root R00-R99 R50-R69 R50 R50.8 "" "" "" 0 +R50.81 R5081 Fever presenting with conditions classified elsewhere Root R00-R99 R50-R69 R50 R50.8 R50.81 "" "" R5081 Fever presenting with conditions classified elsewhere 0 +R50.82 R5082 Postprocedural fever Root R00-R99 R50-R69 R50 R50.8 R50.82 "" "" R5082 Postprocedural fever 0 +R50.83 R5083 Postvaccination fever Root R00-R99 R50-R69 R50 R50.8 R50.83 "" "" R5083 Postvaccination fever 0 +R50.84 R5084 Febrile nonhemolytic transfusion reaction Root R00-R99 R50-R69 R50 R50.8 R50.84 "" "" R5084 Febrile nonhemolytic transfusion reaction 0 +R50.9 R509 Fever, unspecified Root R00-R99 R50-R69 R50 R50.9 "" "" "" R509 Fever, unspecified 0 +R51 R51 Headache Root R00-R99 R50-R69 R51 "" "" "" "" 0 +R51.0 R510 Headache with orthostatic component, not elsewhere classified Root R00-R99 R50-R69 R51 R51.0 "" "" "" R510 Headache with orthostatic component, not elsewhere classified 0 +R51.9 R519 Headache, unspecified Root R00-R99 R50-R69 R51 R51.9 "" "" "" R519 Headache, unspecified 0 +R52 R52 Pain, unspecified Root R00-R99 R50-R69 R52 "" "" "" "" R52 Pain, unspecified 0 +R53 R53 Malaise and fatigue Root R00-R99 R50-R69 R53 "" "" "" "" 0 +R53.0 R530 Neoplastic (malignant) related fatigue Root R00-R99 R50-R69 R53 R53.0 "" "" "" R530 Neoplastic (malignant) related fatigue 0 +R53.1 R531 Weakness Root R00-R99 R50-R69 R53 R53.1 "" "" "" R531 Weakness 0 +R53.2 R532 Functional quadriplegia Root R00-R99 R50-R69 R53 R53.2 "" "" "" R532 Functional quadriplegia 0 +R53.8 R538 Other malaise and fatigue Root R00-R99 R50-R69 R53 R53.8 "" "" "" 0 +R53.81 R5381 Other malaise Root R00-R99 R50-R69 R53 R53.8 R53.81 "" "" R5381 Other malaise 0 +R53.82 R5382 Chronic fatigue, unspecified Root R00-R99 R50-R69 R53 R53.8 R53.82 "" "" R5382 Chronic fatigue, unspecified 0 +R53.83 R5383 Other fatigue Root R00-R99 R50-R69 R53 R53.8 R53.83 "" "" R5383 Other fatigue 0 +R54 R54 Age-related physical debility Root R00-R99 R50-R69 R54 "" "" "" "" R54 Age-related physical debility 0 +R55 R55 Syncope and collapse Root R00-R99 R50-R69 R55 "" "" "" "" R55 Syncope and collapse 0 +R56 R56 Convulsions, not elsewhere classified Root R00-R99 R50-R69 R56 "" "" "" "" 0 +R56.0 R560 Febrile convulsions Root R00-R99 R50-R69 R56 R56.0 "" "" "" 0 +R56.00 R5600 Simple febrile convulsions Root R00-R99 R50-R69 R56 R56.0 R56.00 "" "" R5600 Simple febrile convulsions 0 +R56.01 R5601 Complex febrile convulsions Root R00-R99 R50-R69 R56 R56.0 R56.01 "" "" R5601 Complex febrile convulsions 0 +R56.1 R561 Post traumatic seizures Root R00-R99 R50-R69 R56 R56.1 "" "" "" R561 Post traumatic seizures 0 +R56.9 R569 Unspecified convulsions Root R00-R99 R50-R69 R56 R56.9 "" "" "" R569 Unspecified convulsions 0 +R57 R57 Shock, not elsewhere classified Root R00-R99 R50-R69 R57 "" "" "" "" 0 +R57.0 R570 Cardiogenic shock Root R00-R99 R50-R69 R57 R57.0 "" "" "" R570 Cardiogenic shock 0 +R57.1 R571 Hypovolemic shock Root R00-R99 R50-R69 R57 R57.1 "" "" "" R571 Hypovolemic shock 0 +R57.8 R578 Other shock Root R00-R99 R50-R69 R57 R57.8 "" "" "" R578 Other shock 0 +R57.9 R579 Shock, unspecified Root R00-R99 R50-R69 R57 R57.9 "" "" "" R579 Shock, unspecified 0 +R58 R58 Hemorrhage, not elsewhere classified Root R00-R99 R50-R69 R58 "" "" "" "" R58 Hemorrhage, not elsewhere classified 0 +R59 R59 Enlarged lymph nodes Root R00-R99 R50-R69 R59 "" "" "" "" 0 +R59.0 R590 Localized enlarged lymph nodes Root R00-R99 R50-R69 R59 R59.0 "" "" "" R590 Localized enlarged lymph nodes 0 +R59.1 R591 Generalized enlarged lymph nodes Root R00-R99 R50-R69 R59 R59.1 "" "" "" R591 Generalized enlarged lymph nodes 0 +R59.9 R599 Enlarged lymph nodes, unspecified Root R00-R99 R50-R69 R59 R59.9 "" "" "" R599 Enlarged lymph nodes, unspecified 0 +R60 R60 Edema, not elsewhere classified Root R00-R99 R50-R69 R60 "" "" "" "" 0 +R60.0 R600 Localized edema Root R00-R99 R50-R69 R60 R60.0 "" "" "" R600 Localized edema 0 +R60.1 R601 Generalized edema Root R00-R99 R50-R69 R60 R60.1 "" "" "" R601 Generalized edema 0 +R60.9 R609 Edema, unspecified Root R00-R99 R50-R69 R60 R60.9 "" "" "" R609 Edema, unspecified 0 +R61 R61 Generalized hyperhidrosis Root R00-R99 R50-R69 R61 "" "" "" "" R61 Generalized hyperhidrosis 0 +R62 R62 Lack of expected normal physiological development in childhood and adults Root R00-R99 R50-R69 R62 "" "" "" "" 0 +R62.0 R620 Delayed milestone in childhood Root R00-R99 R50-R69 R62 R62.0 "" "" "" R620 Delayed milestone in childhood 0 +R62.5 R625 Other and unspecified lack of expected normal physiological development in childhood Root R00-R99 R50-R69 R62 R62.5 "" "" "" 0 +R62.50 R6250 Unspecified lack of expected normal physiological development in childhood Root R00-R99 R50-R69 R62 R62.5 R62.50 "" "" R6250 Unspecified lack of expected normal physiological development in childhood 0 +R62.51 R6251 Failure to thrive (child) Root R00-R99 R50-R69 R62 R62.5 R62.51 "" "" R6251 Failure to thrive (child) 0 +R62.52 R6252 Short stature (child) Root R00-R99 R50-R69 R62 R62.5 R62.52 "" "" R6252 Short stature (child) 0 +R62.59 R6259 Other lack of expected normal physiological development in childhood Root R00-R99 R50-R69 R62 R62.5 R62.59 "" "" R6259 Other lack of expected normal physiological development in childhood 0 +R62.7 R627 Adult failure to thrive Root R00-R99 R50-R69 R62 R62.7 "" "" "" R627 Adult failure to thrive 0 +R63 R63 Symptoms and signs concerning food and fluid intake Root R00-R99 R50-R69 R63 "" "" "" "" 0 +R63.0 R630 Anorexia Root R00-R99 R50-R69 R63 R63.0 "" "" "" R630 Anorexia 0 +R63.1 R631 Polydipsia Root R00-R99 R50-R69 R63 R63.1 "" "" "" R631 Polydipsia 0 +R63.2 R632 Polyphagia Root R00-R99 R50-R69 R63 R63.2 "" "" "" R632 Polyphagia 0 +R63.3 R633 Feeding difficulties Root R00-R99 R50-R69 R63 R63.3 "" "" "" 0 +R63.30 R6330 Feeding difficulties, unspecified Root R00-R99 R50-R69 R63 R63.3 R63.30 "" "" R6330 Feeding difficulties, unspecified 0 +R63.31 R6331 Pediatric feeding disorder, acute Root R00-R99 R50-R69 R63 R63.3 R63.31 "" "" R6331 Pediatric feeding disorder, acute 0 +R63.32 R6332 Pediatric feeding disorder, chronic Root R00-R99 R50-R69 R63 R63.3 R63.32 "" "" R6332 Pediatric feeding disorder, chronic 0 +R63.39 R6339 Other feeding difficulties Root R00-R99 R50-R69 R63 R63.3 R63.39 "" "" R6339 Other feeding difficulties 0 +R63.4 R634 Abnormal weight loss Root R00-R99 R50-R69 R63 R63.4 "" "" "" R634 Abnormal weight loss 0 +R63.5 R635 Abnormal weight gain Root R00-R99 R50-R69 R63 R63.5 "" "" "" R635 Abnormal weight gain 0 +R63.6 R636 Underweight Root R00-R99 R50-R69 R63 R63.6 "" "" "" R636 Underweight 0 +R63.8 R638 Other symptoms and signs concerning food and fluid intake Root R00-R99 R50-R69 R63 R63.8 "" "" "" R638 Other symptoms and signs concerning food and fluid intake 0 +R64 R64 Cachexia Root R00-R99 R50-R69 R64 "" "" "" "" R64 Cachexia 0 +R65 R65 Symptoms and signs specifically associated with systemic inflammation and infection Root R00-R99 R50-R69 R65 "" "" "" "" 0 +R65.1 R651 Systemic inflammatory response syndrome (SIRS) of non-infectious origin Root R00-R99 R50-R69 R65 R65.1 "" "" "" 0 +R65.10 R6510 Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction Root R00-R99 R50-R69 R65 R65.1 R65.10 "" "" R6510 Systemic inflammatory response syndrome (SIRS) of non-infectious origin without acute organ dysfunction 0 +R65.11 R6511 Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction Root R00-R99 R50-R69 R65 R65.1 R65.11 "" "" R6511 Systemic inflammatory response syndrome (SIRS) of non-infectious origin with acute organ dysfunction 0 +R65.2 R652 Severe sepsis Root R00-R99 R50-R69 R65 R65.2 "" "" "" 0 +R65.20 R6520 Severe sepsis without septic shock Root R00-R99 R50-R69 R65 R65.2 R65.20 "" "" R6520 Severe sepsis without septic shock 0 +R65.21 R6521 Severe sepsis with septic shock Root R00-R99 R50-R69 R65 R65.2 R65.21 "" "" R6521 Severe sepsis with septic shock 0 +R68 R68 Other general symptoms and signs Root R00-R99 R50-R69 R68 "" "" "" "" 0 +R68.0 R680 Hypothermia, not associated with low environmental temperature Root R00-R99 R50-R69 R68 R68.0 "" "" "" R680 Hypothermia, not associated with low environmental temperature 0 +R68.1 R681 Nonspecific symptoms peculiar to infancy Root R00-R99 R50-R69 R68 R68.1 "" "" "" 0 +R68.11 R6811 Excessive crying of infant (baby) Root R00-R99 R50-R69 R68 R68.1 R68.11 "" "" R6811 Excessive crying of infant (baby) 0 +R68.12 R6812 Fussy infant (baby) Root R00-R99 R50-R69 R68 R68.1 R68.12 "" "" R6812 Fussy infant (baby) 0 +R68.13 R6813 Apparent life threatening event in infant (ALTE) Root R00-R99 R50-R69 R68 R68.1 R68.13 "" "" R6813 Apparent life threatening event in infant (ALTE) 0 +R68.19 R6819 Other nonspecific symptoms peculiar to infancy Root R00-R99 R50-R69 R68 R68.1 R68.19 "" "" R6819 Other nonspecific symptoms peculiar to infancy 0 +R68.2 R682 Dry mouth, unspecified Root R00-R99 R50-R69 R68 R68.2 "" "" "" R682 Dry mouth, unspecified 0 +R68.3 R683 Clubbing of fingers Root R00-R99 R50-R69 R68 R68.3 "" "" "" R683 Clubbing of fingers 0 +R68.8 R688 Other general symptoms and signs Root R00-R99 R50-R69 R68 R68.8 "" "" "" 0 +R68.81 R6881 Early satiety Root R00-R99 R50-R69 R68 R68.8 R68.81 "" "" R6881 Early satiety 0 +R68.82 R6882 Decreased libido Root R00-R99 R50-R69 R68 R68.8 R68.82 "" "" R6882 Decreased libido 0 +R68.83 R6883 Chills (without fever) Root R00-R99 R50-R69 R68 R68.8 R68.83 "" "" R6883 Chills (without fever) 0 +R68.84 R6884 Jaw pain Root R00-R99 R50-R69 R68 R68.8 R68.84 "" "" R6884 Jaw pain 0 +R68.89 R6889 Other general symptoms and signs Root R00-R99 R50-R69 R68 R68.8 R68.89 "" "" R6889 Other general symptoms and signs 0 +R69 R69 Illness, unspecified Root R00-R99 R50-R69 R69 "" "" "" "" R69 Illness, unspecified 0 diff --git a/inst/extdata/toy_visits.csv b/inst/extdata/toy_visits.csv new file mode 100644 index 0000000..36572c9 --- /dev/null +++ b/inst/extdata/toy_visits.csv @@ -0,0 +1,3235 @@ +key,date,diagnosis_codes,severity +P00016,2025-03-01,R10822 A0221,A +P00027,2025-03-01,R62.59,V +P01136,2025-03-01,R62.51 A08.11 R19.0,V +P01366,2025-03-01,R1931 A0811 R1905,V +P01420,2025-03-01,R19.2,V +P01585,2025-03-01,R6883 A0811 R1902,V +P01800,2025-03-01,R19.2 R11.0 J04.10,V +P01892,2025-03-01,R62.51,V +P00600,2025-03-02,R10 U071 R6883,V +P00630,2025-03-02,R15.2 A07.1 A03,V +P00665,2025-03-02,R152 R680 R61,V +P01571,2025-03-02,A0811,V +P01989,2025-03-02,R10.A A08.39,V +P00061,2025-03-03,A02.21 R10.813,V +P00072,2025-03-03,R62.51,V +P00366,2025-03-03,R6520 R57 J0300,V +P01332,2025-03-03,J01.81 A05 J03.0,V +P00211,2025-03-04,A03 J45909 R601,V +P00389,2025-03-04,R190,V +P00525,2025-03-04,R19.2 A07.1,V +P00742,2025-03-04,J45.909,V +P01063,2025-03-04,R68.83,A +P01511,2025-03-04,R630,A +P01827,2025-03-04,A08.39,V +P00053,2025-03-05,A00,V +P00097,2025-03-05,A051 R601 R630,V +P00395,2025-03-05,J030,V +P01732,2025-03-05,J03.0,V +P00508,2025-03-06,R15.2,V +P01538,2025-03-06,U071,V +P01965,2025-03-06,A07.1,V +P00119,2025-03-07,R6259 R6520,A +P00336,2025-03-07,Z0000 R152,V +P01221,2025-03-07,R61,V +P01558,2025-03-07,J030 R569,V +P01886,2025-03-07,A06.81 R57 J04.3,V +P01950,2025-03-07,R11.13 A05,V +P01951,2025-03-07,R192 A0811,V +P00034,2025-03-08,R6883 A0471,V +P00144,2025-03-08,R19.2 R10.813,V +P00269,2025-03-08,R1023 A071,V +P00498,2025-03-08,R62.59 A08.11 J45.909,V +P00964,2025-03-08,R6520 J0390,A +P01384,2025-03-08,J010,V +P01480,2025-03-08,R11.13,A +P00130,2025-03-09,R19.2 A00,A +P00484,2025-03-09,J04.3,V +P00759,2025-03-09,R10.822 A06.0,A +P00799,2025-03-09,R60 R62.51 A03,V +P01150,2025-03-09,R15.2,V +P01244,2025-03-09,R569 A060 J010,V +P01360,2025-03-09,R15.2 R13.12 A00.1,V +P01391,2025-03-09,J010 R6882,V +P01512,2025-03-09,A06.0,V +P00357,2025-03-10,R630 R1023 J0300,V +P00686,2025-03-10,A05.2 A03.1 A06.0,V +P00764,2025-03-10,A021,V +P00930,2025-03-10,J45909 J043,V +P01132,2025-03-10,R197 R6882,V +P01630,2025-03-10,A00,V +P00424,2025-03-11,A01.1 R19.09,V +P00585,2025-03-11,J043,V +P00883,2025-03-11,J03.0,V +P00949,2025-03-11,R57 J03.00 A00,V +P01171,2025-03-11,A021,V +P01528,2025-03-11,A071,V +P01826,2025-03-11,R19.7 J01.0 J45.909,V +P00147,2025-03-12,R19.2,V +P00640,2025-03-12,J45.909 R10.82,A +P00753,2025-03-12,R10,A +P00856,2025-03-12,R1012,V +P01576,2025-03-12,R1312 R10A,V +P01577,2025-03-12,A00,V +P00376,2025-03-13,A0471 R1312 J0390,A +P00807,2025-03-13,A02.22 J04.3 R19.05,V +P01033,2025-03-13,R57 A0811,V +P01418,2025-03-13,R1312,A +P01663,2025-03-13,R19.2 R11.10,A +P00249,2025-03-14,R61,V +P00360,2025-03-14,R6520 A060 J0181,A +P00363,2025-03-14,R10.12 R19.7,A +P00789,2025-03-14,A052,V +P01191,2025-03-14,J45909,A +P01585,2025-03-14,R6251 R569,V +P01922,2025-03-14,R68.83 A03 A06.81,V +P01987,2025-03-14,A08.39 A06.0,V +P00353,2025-03-15,J01.0 R60.1 R60,V +P00545,2025-03-15,R16 A011 R1023,V +P00695,2025-03-15,R63,V +P00825,2025-03-15,A0681 R6882 R197,V +P01042,2025-03-15,R10.813 R10.A J04.3,V +P00139,2025-03-16,R19.05,V +P01914,2025-03-16,R11.10,V +P01945,2025-03-16,A02.21 R63,V +P00653,2025-03-17,R19.7,V +P00669,2025-03-17,A03.1 J03.90,V +P00840,2025-03-17,R10 A07.1 R61,V +P01236,2025-03-17,A0221,V +P01374,2025-03-17,R19.05 A06.0,V +P01742,2025-03-17,J0410 R6251 R1012,V +P01936,2025-03-17,A0471,V +P01972,2025-03-17,A06.0 A00,V +P00012,2025-03-18,R60.1 J01,V +P00763,2025-03-18,R6251 R1082 J45909,A +P00879,2025-03-18,R13.12,V +P00966,2025-03-18,A03 U071,V 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a/inst/tinytest/test-pipeline.R b/inst/tinytest/test-pipeline.R new file mode 100644 index 0000000..656c690 --- /dev/null +++ b/inst/tinytest/test-pipeline.R @@ -0,0 +1,64 @@ +# Integration tests: the full treescanr pipeline on the bundled toy data. +# Everything is written to temporary directories. +ex <- function(f) system.file("extdata", f, package = "treescanr") + +# Visits -> counts ------------------------------------------------------------ +visits <- read.csv(ex("toy_visits.csv")) |> ts_visits() +expect_equal(names(visits), c("key", "date", "diagnosis_codes", "severity")) +expect_true(all(visits$severity %in% c("A", "V"))) + +counts <- visits |> + ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) + +# Same output as the legacy script (treescan_project/code/3_create_count_file.R) +# run on the same data with set.seed(1) +legacy <- data.table::fread("legacy_counts_lag1.txt", colClasses = "character") +legacy[, n := as.integer(n)] +data.table::setorder(legacy, code, date) +expect_equal( + as.data.frame(counts[order(code, date), list(code, date, n)]), + as.data.frame(legacy) +) +expect_equal(attr(counts, "end_date"), as.Date("2026-06-30")) +expect_true(all(as.Date(counts$date, "%Y/%m/%d") > as.Date("2026-06-30") - 90)) + +# Seed does not alter the global RNG state +set.seed(123); before <- runif(1) +set.seed(123); invisible(ts_counts(visits, "2026-06-30", ex("toy_tree_wide.txt"), seed = 1)) +expect_equal(runif(1), before) + +# NSSP adapter +nssp <- data.frame( + C_Unique_Patient_ID = c("a", "b"), + C_Visit_Date_Time = c("2026-01-01 10:00:00", "2026-01-02 08:00:00"), + DischargeDiagnosis = c(";A084;R112;", ";J069;;"), + HasBeenAdmitted = c(1, NA) +) +expect_equal(ts_visits_nssp(nssp)$diagnosis_codes, c("A084 R112", "J069")) +expect_equal(ts_visits_nssp(nssp)$severity, c("A", "V")) + +# Parameter files --------------------------------------------------------------- +prm_file <- tempfile(fileext = ".prm") +prm <- ts_prm_template() |> + ts_prm_set("monte-carlo-replications" = 999, "data-time-range" = "[2026/04/01,2026/06/30]") +ts_prm_write(prm, prm_file) +expect_identical(ts_prm_read(prm_file), prm) +expect_equal(ts_prm_get(prm, "monte-carlo-replications"), "999") +expect_equal(ts_prm_get(prm, "parallel-processes"), "2") +expect_error(ts_prm_set(prm, "not-a-parameter" = 1), "Unknown") + +# Running TreeScan (only when the binary is available) -------------------------- +if (nzchar(Sys.getenv("TREESCAN_BIN"))) { + dir <- tempfile("treescanr_") + res <- counts |> + ts_run(tree = ex("toy_tree.csv"), dir = dir, + prm = ts_prm_set(ts_prm_template(), "monte-carlo-replications" = 999, + "early-termination-threshold" = 50)) + expect_inherits(res, "ts_result") + expect_true(nrow(res$results) > 0) + # The injected A08.4 cluster is the most likely cut + top <- res$results[order(res$results$P.value), "Node.Identifier"][1:5] + expect_true(any(grepl("A08", top))) + expect_true(file.exists(file.path(dir, "parameters.prm"))) + expect_equal(nrow(ts_results(dir)$results), nrow(res$results)) +} diff --git a/man/treescanr-package.Rd b/man/treescanr-package.Rd new file mode 100644 index 0000000..21614a9 --- /dev/null +++ b/man/treescanr-package.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/treescanr-package.R +\docType{package} +\name{treescanr-package} +\alias{treescanr} +\alias{treescanr-package} +\title{treescanr: Tree-Based Scan Statistics for Syndromic Surveillance} +\description{ +A pipeable workflow around the 'TreeScan' command-line software: +\code{\link[=ts_visits]{ts_visits()}} -> \code{\link[=ts_counts]{ts_counts()}} -> \code{\link[=ts_run]{ts_run()}} -> \code{\link[=ts_results]{ts_results()}}. +} +\author{ +\strong{Maintainer}: George G. Vega Yon \email{g.vegayon@gmail.com} + +Authors: +\itemize{ + \item George G. Vega Yon \email{g.vegayon@gmail.com} +} + +} +\keyword{internal} diff --git a/man/ts_binary.Rd b/man/ts_binary.Rd new file mode 100644 index 0000000..54569b2 --- /dev/null +++ b/man/ts_binary.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/binary.R +\name{ts_binary} +\alias{ts_binary} +\title{Locate the TreeScan command-line binary} +\usage{ +ts_binary(path = getOption("treescanr.binary", Sys.getenv("TREESCAN_BIN"))) +} +\arguments{ +\item{path}{Path to the binary (e.g., \code{treescan64} or \code{treescan64.exe}). +Defaults to the \code{treescanr.binary} option, then the \code{TREESCAN_BIN} +environment variable, then \code{treescan64} on the \code{PATH}.} +} +\value{ +The normalized path to the binary. +} +\description{ +Checks that the TreeScan binary exists and is executable. The non-graphical +(command-line) version of TreeScan can be downloaded from +\url{https://www.treescan.org/download_treescan.html}. +} +\examples{ +\dontrun{ +options(treescanr.binary = "~/TreeScan/treescan64") +ts_binary() +} +} diff --git a/man/ts_counts.Rd b/man/ts_counts.Rd new file mode 100644 index 0000000..d9d9cfa --- /dev/null +++ b/man/ts_counts.Rd @@ -0,0 +1,72 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/counts.R +\name{ts_counts} +\alias{ts_counts} +\alias{ts_ineligible_pattern} +\title{Build a TreeScan count file of incident diagnoses} +\usage{ +ts_counts( + visits, + end_date, + tree_wide, + study_days = 90L, + lookback_days = 365L, + ineligible = ts_ineligible_pattern(), + seed = NULL +) + +ts_ineligible_pattern() +} +\arguments{ +\item{visits}{Output of \code{\link[=ts_visits]{ts_visits()}}.} + +\item{end_date}{Last day of the study period (e.g., \code{Sys.Date() - lag}).} + +\item{tree_wide}{Wide-format tree (path or \code{data.frame}) with columns +\code{Name1} (code without dot), \code{Level2}, and \code{Level3}.} + +\item{study_days}{Length of the study period in days.} + +\item{lookback_days}{Window used to define incident diagnoses.} + +\item{ineligible}{Regular expression of codes to exclude.} + +\item{seed}{Optional seed for the tie-break. The global RNG state is +restored on exit.} +} +\value{ +A \code{data.table} with columns \code{code}, \code{date} (\code{yyyy/mm/dd}), and \code{n}, +with attributes \code{end_date}, \code{study_days}, and \code{incident} (the incident +visit-code table, one row per \code{date}, \code{key}, \code{dispo}, \code{code}). +} +\description{ +Port of the epiENGAGE count-file algorithm (Ramona Lall and Alison +Levin-Rector, NYC DOHMH). Starting from visit-level data it: +} +\details{ +\enumerate{ +\item splits diagnosis codes and removes ineligible ones (\code{ineligible}); +\item keeps codes present in the tree and looks up their level-3 parent; +\item keeps only \strong{incident} diagnoses: a level-3 group seen for the same +patient within \code{lookback_days} is dropped, with special handling of +admissions; +\item restricts to the \code{study_days} ending on \code{end_date}; +\item keeps the rarest code per level-3 group within a visit (random +tie-break, see \code{seed}); +\item aggregates counts by node (\verb{0-} = not admitted, \verb{1-} = admitted) and day. +} + +\code{visits} should cover \code{study_days + lookback_days} so every day in the study +period has a full lookback. + +\code{ts_ineligible_pattern()} returns the default exclusions: COVID-19, +influenza, allergic rhinitis, asthma, anaphylaxis, most Z codes, neoplasms, +and congenital malformations. +} +\examples{ +ex <- function(f) system.file("extdata", f, package = "treescanr") +counts <- read.csv(ex("toy_visits.csv")) |> + ts_visits() |> + ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) +head(counts) +} diff --git a/man/ts_prm.Rd b/man/ts_prm.Rd new file mode 100644 index 0000000..e3d2f65 --- /dev/null +++ b/man/ts_prm.Rd @@ -0,0 +1,51 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prm.R +\name{ts_prm} +\alias{ts_prm} +\alias{ts_prm_read} +\alias{ts_prm_template} +\alias{ts_prm_set} +\alias{ts_prm_get} +\alias{ts_prm_write} +\title{TreeScan parameter files} +\usage{ +ts_prm_read(path) + +ts_prm_template() + +ts_prm_set(prm, ...) + +ts_prm_get(prm, key) + +ts_prm_write(prm, path) +} +\arguments{ +\item{path}{Path to a \code{.prm} file.} + +\item{prm}{A \code{ts_prm} object.} + +\item{...}{Named values to set, e.g. \code{"monte-carlo-replications" = 999}. +Dates are formatted as \code{yyyy/mm/dd}, logicals as \code{y}/\code{n}.} + +\item{key}{Parameter name.} +} +\value{ +\code{ts_prm_read()}, \code{ts_prm_template()}, and \code{ts_prm_set()} return a +\code{ts_prm} object. \code{ts_prm_get()} returns a character value. +\code{ts_prm_write()} returns \code{path} invisibly. +} +\description{ +A parameter file (\code{.prm}) is stored as its raw lines (comments included) +with class \code{ts_prm}. Values are set by key name, without needing to know +the \verb{[Section]} they belong to. +} +\details{ +\code{ts_prm_template()} returns the template bundled with the package +(TreeScan v2.4.1, tree-temporal Poisson scan, 9,999 replications). +} +\examples{ +prm <- ts_prm_template() |> + ts_prm_set("monte-carlo-replications" = 999) +ts_prm_get(prm, "monte-carlo-replications") +ts_prm_write(prm, tempfile(fileext = ".prm")) +} diff --git a/man/ts_results.Rd b/man/ts_results.Rd new file mode 100644 index 0000000..d283e2f --- /dev/null +++ b/man/ts_results.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/results.R +\name{ts_results} +\alias{ts_results} +\title{Read TreeScan results} +\usage{ +ts_results(path) +} +\arguments{ +\item{path}{A directory created by \code{\link[=ts_run]{ts_run()}} or a TreeScan results \code{.csv}.} +} +\value{ +A \code{ts_result} object: a list with \code{results} (a \code{data.frame}, one row +per cut, as written by TreeScan), \code{dir}, \code{files}, and \code{prm} (the +parameter file used, if found). +} +\description{ +Reads the CSV results written by TreeScan, e.g., from a previous +\code{\link[=ts_run]{ts_run()}} stored in a persistent directory. +} +\examples{ +\dontrun{ +dir <- tools::R_user_dir("treescanr", "data") +ts_results(file.path(dir, "2026-09-23", "lag1")) +} +} diff --git a/man/ts_run.Rd b/man/ts_run.Rd new file mode 100644 index 0000000..7a699a8 --- /dev/null +++ b/man/ts_run.Rd @@ -0,0 +1,53 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/run.R +\name{ts_run} +\alias{ts_run} +\title{Run TreeScan on a count file} +\usage{ +ts_run( + counts, + tree, + dir = tempfile("treescanr_"), + prm = ts_prm_template(), + not_evaluated = NULL, + processes = 2L, + binary = ts_binary() +) +} +\arguments{ +\item{counts}{Output of \code{\link[=ts_counts]{ts_counts()}}.} + +\item{tree}{Path to the TreeScan tree file (long format, e.g. +\code{Tree_File_2027.csv}).} + +\item{dir}{Output directory. Defaults to a temporary directory; for routine +use pass a persistent location such as +\code{file.path(tools::R_user_dir("treescanr", "data"), Sys.Date(), "lag1")}.} + +\item{prm}{A \code{ts_prm} object used as template (see \code{\link[=ts_prm_template]{ts_prm_template()}}).} + +\item{not_evaluated}{Optional path to a file of nodes not to evaluate +(e.g. \code{Do_not_evaluate_nodes.csv}).} + +\item{processes}{Number of parallel processes used by TreeScan.} + +\item{binary}{Path to the TreeScan binary (see \code{\link[=ts_binary]{ts_binary()}}).} +} +\value{ +A \code{ts_result} object (see \code{\link[=ts_results]{ts_results()}}). +} +\description{ +Writes the count file and a parameter file into \code{dir}, runs the TreeScan +binary, and reads the results. The data time range and temporal windows +are set from the \code{end_date} and \code{study_days} stored in \code{counts}. +} +\examples{ +\dontrun{ +dir <- tools::R_user_dir("treescanr", "data") +res <- read.csv("visits.csv") |> + ts_visits() |> + ts_counts(end_date = Sys.Date() - 1, tree_wide = "Tree_File_2026_wide_format.txt") |> + ts_run(tree = "Tree_File_2027.csv", dir = file.path(dir, Sys.Date(), "lag1")) +res +} +} diff --git a/man/ts_visits.Rd b/man/ts_visits.Rd new file mode 100644 index 0000000..8f5b9c7 --- /dev/null +++ b/man/ts_visits.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visits.R +\name{ts_visits} +\alias{ts_visits} +\alias{ts_visits_nssp} +\title{Standardize visit-level data} +\usage{ +ts_visits( + data, + key = "key", + date = "date", + codes = "diagnosis_codes", + admitted = "severity" +) + +ts_visits_nssp(data) +} +\arguments{ +\item{data}{A \code{data.frame} with one row per visit.} + +\item{key, date, codes, admitted}{Names of the columns in \code{data} holding the +patient identifier, visit date (or date-time), diagnosis codes (separated +by spaces, commas, or semicolons), and admission status (logical, 0/1, or +\code{"A"}/\code{"V"}). Missing admission status is treated as not admitted.} +} +\value{ +A \code{data.table}. +} +\description{ +Turns visit-level emergency department data (one row per visit) into the +input expected by \code{\link[=ts_counts]{ts_counts()}}: a \code{data.table} with columns \code{key} +(patient identifier), \code{date}, \code{diagnosis_codes} (space-separated ICD-10-CM +codes), and \code{severity} (\code{"A"} = admitted, \code{"V"} = visit only). +} +\details{ +\code{ts_visits_nssp()} is a shortcut for NSSP ESSENCE DataDetails +extracts (columns \code{C_Unique_Patient_ID}, \code{C_Visit_Date_Time}, +\code{DischargeDiagnosis}, and \code{HasBeenAdmitted}). +} +\examples{ +visits <- read.csv(system.file("extdata", "toy_visits.csv", package = "treescanr")) +ts_visits(visits) |> head() +} diff --git a/r-package-port.md b/r-package-port.md new file mode 100644 index 0000000..34d2a18 --- /dev/null +++ b/r-package-port.md @@ -0,0 +1,63 @@ +# How the TreeScan scripts were ported to `treescanr` + +This note maps each file of the original `treescan_project/` onto the R package +at the repository root. The original scripts are still in `treescan_project/`, +unchanged. The package does not use them. + +In short, the global variables (`parent_dir`, `final_date`, `initial_lags`, +`server`, ...) became function arguments. `setwd()` and the fixed folder tree +became a single `dir` argument. The package now covers steps 0 and 2–5. The +other steps are planned (see [Not ported yet](#not-ported-yet)). + +## Pipeline scripts (`treescan_project/code/`) + +| Original | Package | Notes | +|---|---|---| +| `run_full_pipeline.R` | `ts_visits() \|> ts_counts() \|> ts_run()` | The settings at the top of the script are now function arguments. There are no interactive prompts, and no scripts edit their own source to store lags. Several lags are run with `lapply()` (see the vignette). | +| `0_locate_treescan.R` | `ts_binary()` (`R/binary.R`) | The `server` flag is replaced by an explicit path taken from `options(treescanr.binary)`, `TREESCAN_BIN`, or the `PATH`. | +| `1_download_data.R` | — | Not ported yet. Its daily CSVs can be read and passed to `ts_visits_nssp()`. | +| `1.1_subset_downloaded_data.R` | — | Not ported. Filter the data by `Region` before calling `ts_visits_nssp()`. | +| `2_clean_downloaded_data.R` | `ts_visits()`, `ts_visits_nssp()` (`R/visits.R`) | Builds the same `key, date, diagnosis_codes, severity` table from any data source. The lag-assessment subset it also saved is not ported. | +| `2.1_assess_lag.R`, `2.2_pick_lags.R`, `2.3_quick_lag_check.R` | — | Not ported yet. The lag is simply `end_date = run_date - lag` in `ts_counts()`. | +| `2.4_data_artifact_check.R` | — | Not ported yet. | +| `3_create_count_file.R` | `ts_counts()` (`R/counts.R`) | Line-by-line port of the algorithm. `process_patient_faster()` became `.incident()`. The unused `process_patient()` was dropped. The rarest-code tie-break can be seeded (`seed`). The `v2/lag*.csv` table is returned as `attr(counts, "incident")`. A test checks that the output matches this script exactly on the toy data. | +| `4_update_parameter_file.R` | `ts_prm_*()` (`R/prm.R`), and `ts_run()` fills in the values | `update_prm_file()` became generic helpers that set any parameter by name. `ts_run()` fills in the paths, date ranges, processes (2 by default), and not-evaluated nodes. | +| `5_run_treescan.R` | `ts_run()` (`R/run.R`) | A single `system2()` call writes a log. If TreeScan fails, R stops with the end of the log. | +| `6_create_signal_linelist.R`, `6.1_download_background_for_interpretation.R` | — | Not ported yet. Results are available as `ts_results()$results`. | +| `7_create_signal_report.R`, `7.1_create_signal_report_standalone.R` | — | Not ported yet. | +| `8_WC_signal_review.R` | — | Specific to the World Cup. Planned as an example script rather than package code. | + +## Data and parameters + +| Original | Package | Notes | +|---|---|---| +| `params/Parameter_File_lag1.prm` (v2.4.1) | `inst/extdata/Parameter_File_template.prm`, `ts_prm_template()` | Same settings, but the paths and dates are blank (`ts_run()` fills them in) and `parallel-processes=2`. | +| `params/Parameter_File*.prm`, `params (v2.4.0)/` | — | Replaced by the single template. | +| `data/Tree_File_2027.csv` | `tree` argument of `ts_run()` | Not bundled (50 MB). Users pass the path. | +| `data/Tree_File_2026_wide_format.txt` | `tree_wide` argument of `ts_counts()` | Not bundled (20 MB). Users pass the path. | +| `data/Do_not_evaluate_nodes.csv` | `not_evaluated` argument of `ts_run()` | Not bundled. Users pass the path. | +| `data/Common_cause.csv` | — | Used only by steps 6 and 7 (not ported yet). | +| Output folders (`raw_data/`, `results/`, `lag/`, ...) | `dir` argument of `ts_run()` | One folder per run: `counts.txt`, `parameters.prm`, `results.*`, `treescan.log`. The vignette suggests the layout `//lag/`. | +| `TS_linux/`, `TS_windows/` | Private devcontainer image | TreeScan is bundled in `ghcr.io/epiforesite/treescanr-dev` (`.devcontainer/`), which is used by CI. | +| — | `inst/extdata/toy_*` | A small subset of the 2026/2027 trees plus synthetic visits, for examples and tests (`data-raw/toy_data.R`). | + +## Behavior kept as is (to review) + +`ts_counts()` deliberately reproduces some behavior of `3_create_count_file.R` +that the original team may want to review: + +- When deciding if a diagnosis is incident, "prior visit" means an earlier + *row*. Rows are ordered by code (after the tree merge), not by date. +- `search2[i]` is indexed by the admission counter `i` instead of the row + (`this_row`) (marked with a `NOTE` in `R/counts.R`). +- The TreeScan data time range is `[end_date - 90, end_date]` (91 days), while + the counts cover 90 days. + +Step 3 also used the 2026 wide tree while step 4 used the 2027 tree. In the +package, both are explicit arguments. + +## Not ported yet + +In order of priority: NSSP download (1, 1.1), lag assessment (2.1–2.3), +artifact scores (2.4), signal linelist and background data (6, 6.1), and +reports (7, 7.1). diff --git a/tests/tinytest.R b/tests/tinytest.R new file mode 100644 index 0000000..61bb851 --- /dev/null +++ b/tests/tinytest.R @@ -0,0 +1,3 @@ +if (requireNamespace("tinytest", quietly = TRUE)) { + tinytest::test_package("treescanr") +} diff --git a/treescan_project/README.md b/treescan_project/README.md new file mode 100644 index 0000000..bcd6216 --- /dev/null +++ b/treescan_project/README.md @@ -0,0 +1,104 @@ +## TreeScan for the World Cup +# 🌳 TreeScan Implementation + +A full pipeline for running TreeScan-based analyses using R and the TreeScan software. + +This project provides a structured workflow to prepare data, run TreeScan, and process results using an R-based pipeline. + +
+ +## 📦 Installation +### 1. Download this Repository +* Click the green **Code** button on GitHub +* Select **Download ZIP** +* Extract the ZIP file +* Locate the `treescan_project` subfolder +* Move `treescan_project` to your desired working directory + +
+ +### 2. Install RStudio + +Download and install RStudio: +https://posit.co/download/rstudio-desktop/ + +
+ +### 3. Install TreeScan + +Download TreeScan from: +https://www.treescan.org/download_treescan.html + +**⚠️ Important setup details:** + +* You must create an account before downloading +* Choose version based on your environment: + * **Windows** → if running locally + * **Linux** → if running on a server +* Select the **NON-graphical version** + * The standard (graphical) version may cause IT/access issues + +
+ +### 4. Place TreeScan in Project Folder + +After downloading: + +Move the TreeScan files into the correct subfolder inside `treescan_project`: +| Environment | Folder | +| ----------- | ------ | +| Windows | TS_windows/ | +| Linux | TS_linux/ | + +
+ +## 🚀 Running the Pipeline +### 1. Open the Project in RStudio + +* Launch RStudio +* In the bottom-right file explorer: + * Navigate to: `treescan_project/code/` + * Open: `run_full_pipeline.R` + +
+ +### 2. Configure the Script + +Before running, update the following: + +**Set Working Directory** + +Update line 4 to match your local path: + +```r +setwd("~/TreeScan-implementation/treescan_project") +``` + +Replace with wherever you saved treescan_project. + +**Set Execution Mode** + +Modify these variables depending on your setup: + +```r +server <- FALSE # Set to TRUE if running on a server +first_time <- TRUE # Set to FALSE after first run +``` + +
+ +### 3. Run the Pipeline + +* Run the script in RStudio + +The pipeline will: +* Execute TreeScan +* Process outputs +* Complete the full analysis workflow + +
+ +## ⚠️ Notes +* Ensure the correct TreeScan version is placed in the matching folder (`TS_windows` or `TS_linux`) +* Using the **non-graphical version is required** +* Incorrect working directory paths will cause errors diff --git a/vignettes/treescanr.qmd b/vignettes/treescanr.qmd new file mode 100644 index 0000000..7332e76 --- /dev/null +++ b/vignettes/treescanr.qmd @@ -0,0 +1,146 @@ +--- +title: "Routine TreeScan analyses with treescanr" +vignette: > + %\VignetteIndexEntry{Routine TreeScan analyses with treescanr} + %\VignetteEngine{quarto::html} + %\VignetteEncoding{UTF-8} +knitr: + opts_chunk: + collapse: true + comment: "#>" +--- + +treescanr turns emergency department (ED) visits into a TreeScan analysis in +three steps: standardize the visits, build the count file, and run TreeScan. +Each step takes the output of the previous one, so the whole analysis is a +single `|>` pipeline. + +```{r} +library(treescanr) +ex <- function(f) system.file("extdata", f, package = "treescanr") +``` + +## Where to store things + +treescanr is designed to run routinely (e.g., every day), so it helps to keep +inputs and outputs in a **known, persistent directory**. We recommend the +user data directory, but any path works: + +```{r} +#| eval: false +dir <- tools::R_user_dir("treescanr", "data") +dir.create(dir, recursive = TRUE, showWarnings = FALSE) +``` + +A suggested layout: + +``` +/ + reference/ # tree files and not-evaluated nodes + Tree_File_2027.csv + Tree_File_2026_wide_format.txt + Do_not_evaluate_nodes.csv + 2026-06-30/ # one folder per analysis date... + lag1/ # ...and per lag + counts.txt parameters.prm results.csv results.html treescan.log +``` + +The code in this vignette that writes to disk is not run when the vignette is +built. Chunks that are run use the toy data bundled with the package. + +## 1. Visit-level data + +`ts_visits()` accepts any data with one row per visit and tells it which +columns hold the patient identifier, the visit date, the diagnosis codes, and +whether the patient was admitted: + +```{r} +visits <- read.csv(ex("toy_visits.csv")) |> + ts_visits(key = "key", date = "date", codes = "diagnosis_codes", + admitted = "severity") +head(visits) +``` + +For NSSP ESSENCE DataDetails extracts (e.g., the daily files downloaded by +`treescan_project/code/1_download_data.R`), use `ts_visits_nssp()`: + +```{r} +#| eval: false +files <- list.files(file.path(dir, "raw_data"), pattern = "\\.csv$", full.names = TRUE) +visits <- data.table::rbindlist(lapply(files, data.table::fread)) |> + ts_visits_nssp() +``` + +The data should cover the study period (90 days by default) plus one year of +lookback, which is used to find incident diagnoses. + +## 2. Count file + +`ts_counts()` keeps incident diagnoses and aggregates them into daily counts +per node. `0-` nodes are ED visits and `1-` nodes are admissions. The +`end_date` is usually the analysis date minus a reporting lag: + +```{r} +counts <- visits |> + ts_counts(end_date = "2026-06-30", tree_wide = ex("toy_tree_wide.txt"), seed = 1) +counts[order(-n)] |> head() +``` + +## 3. Parameter file + +The package bundles a parameter template for a tree-temporal scan +(TreeScan 2.4.1). Change any setting by name: + +```{r} +prm <- ts_prm_template() |> + ts_prm_set("monte-carlo-replications" = 999) +ts_prm_get(prm, "monte-carlo-replications") +``` + +`ts_run()` fills in the file paths, the date ranges, and the number of +processes (2 by default). + +## 4. Run TreeScan + +```{r} +#| eval: false +options(treescanr.binary = "~/TreeScan/treescan64") +ref <- file.path(dir, "reference") + +res <- counts |> + ts_run( + tree = file.path(ref, "Tree_File_2027.csv"), + not_evaluated = file.path(ref, "Do_not_evaluate_nodes.csv"), + prm = prm, + dir = file.path(dir, "2026-06-30", "lag1") + ) +res +``` + +## A routine run with several lags + +```{r} +#| eval: false +run_date <- Sys.Date() +ref <- file.path(dir, "reference") + +results <- lapply(c(1, 4), function(lag) { + visits |> + ts_counts( + end_date = run_date - lag, + tree_wide = file.path(ref, "Tree_File_2026_wide_format.txt") + ) |> + ts_run( + tree = file.path(ref, "Tree_File_2027.csv"), + not_evaluated = file.path(ref, "Do_not_evaluate_nodes.csv"), + dir = file.path(dir, run_date, paste0("lag", lag)) + ) +}) +``` + +Results from earlier runs can be reloaded at any time: + +```{r} +#| eval: false +ts_results(file.path(dir, "2026-06-30", "lag1")) +```