v0.7 dev

.github/workflows/R-CMD-check.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
     branches: [main, master]
 

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: swfscDAS
 Title: Processing DAS Data Files
-Version: 0.6.4
+Version: 0.7.0.9000
 Authors@R: 
     person("Sam", "Woodman", email = "sam.woodman@noaa.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6071-8186"))
 Description: Process and summarize DAS data files. 
     These files are typically, but do not have to be 
-    DAS <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data
+    DAS <https://repository.library.noaa.gov/view/noaa/3174> data
     produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'.
     This package standardizes and streamlines basic DAS data processing,
     and includes a PDF with the DAS data format requirements expected by the package.
@@ -31,5 +31,6 @@ Suggests:
     testthat (>= 2.1.0)
 License: Apache License (== 2)
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -23,6 +23,8 @@ S3method(das_comments,das_dfr)
 S3method(das_comments,data.frame)
 S3method(das_effort,das_df)
 S3method(das_effort,data.frame)
+S3method(das_effort_strata,das_df)
+S3method(das_effort_strata,data.frame)
 S3method(das_intersects_strata,data.frame)
 S3method(das_intersects_strata,list)
 S3method(das_process,character)
@@ -54,6 +56,7 @@ export(das_process)
 export(das_read)
 export(das_segdata)
 export(das_sight)
+export(das_spcodes_read)
 export(distance_greatcircle)
 export(randpicks_convert)
 importFrom(dplyr,add_row)
@@ -97,6 +100,7 @@ importFrom(purrr,pmap_int)
 importFrom(purrr,pmap_lgl)
 importFrom(readr,col_character)
 importFrom(readr,cols)
+importFrom(readr,fwf_cols)
 importFrom(readr,fwf_positions)
 importFrom(readr,read_fwf)
 importFrom(rlang,"!!")

NEWS.md

@@ -1,3 +1,20 @@
+# swfscDAS 0.7.0.9000
+
+* Fix bug in `das_process` of incorrect OffsetGMT values, stemming from `as.Date` using 'UTC' tz by default (#16)
+
+* Added an exported function `das_spcodes_read` for consistent reading of shipboard SpCode files
+
+* Changed the argument name in `das_check` of the user-provided SpCodes file from `sp.codes` to `sp.codes.file`. Also added a `sp.codes.skip` argument to pass to `das_spcodes_read`
+
+* Moved example data files to an 'extdata' folder within 'inst'
+
+* Update link to NOAA Tech Memo describing DAS data; now (https://repository.library.noaa.gov/view/noaa/3174)[https://repository.library.noaa.gov/view/noaa/3174](#17)
+
+* Update roxygen to use markdown, fix documentation issues related to upgrade to roxygen2 v8.0
+
+* Added the SpCodes.dat file from [`CruzPlot`](https://github.com/SWFSC/CruzPlot) to 'inst' to have available as a default
+
+
 # swfscDAS 0.6.4
 
 * The DateTime column in `das_read` output now has a timezone of `""` (#13)

R/das_check.R

@@ -6,9 +6,12 @@
 #' @param skip integer: see \code{\link[readr]{read_fwf}}. Default is 0
 #' @param file.out filename to which to write the error log;
 #'   default is \code{NULL}
-#' @param sp.codes character; filename of .dat file from which to read
-#'   accepted species codes. If \code{NULL}, species codes will not be checked.
-#'   Default is \code{NULL}
+#' @param sp.codes.file character; default is `NULL`.
+#'   Filename of the SpCodes file from which to read the species codes.
+#'   If `NULL`, the default (internal) file will be used.
+#'   The SpCodes file will be read by [das_spcodes_read()]
+#' @param sp.codes.skip integer; default is 0.
+#'   Passed directly to `skip` argument of [das_spcodes_read()]
 #' @param print.cruise.nums logical; indicates if a table with all the
 #'   cruise numbers in the \code{x} should be printed using
 #'   \code{\link[base]{table}}. Default is \code{TRUE}
@@ -90,12 +93,22 @@
 #' A warning is printed if any events are r events; see \code{\link{das_process}} for details about r events
 #'
 #' @examples
-#' y <- system.file("das_sample.das", package = "swfscDAS")
+#' y <- system.file("extdata", "das_sample.das", package = "swfscDAS")
 #' if (interactive()) das_check(y)
 #'
+#' # Using your own SpCodes file
+#' sp.codes.file <- system.file("extdata", "SpCodes.dat", package = "swfscDAS")
+#' if (interactive()) das_check(y, sp.codes.file = sp.codes.file)
+#'
 #' @export
-das_check <- function(file, skip = 0, file.out = NULL, sp.codes = NULL,
-                      print.cruise.nums = TRUE) {
+das_check <- function(
+    file,
+    skip = 0,
+    file.out = NULL,
+    sp.codes.file = NULL,
+    sp.codes.skip = 0,
+    print.cruise.nums = TRUE
+    ) {
 
   if (length(unique(file)) != length(file))
     warning("Not all files are unique - this likely will cause an error in ",
@@ -133,10 +146,10 @@ das_check <- function(file, skip = 0, file.out = NULL, sp.codes = NULL,
 
   #----------------------------------------------------------------------------
   ### Process sp.codes file
-  if (!is.null(sp.codes)) {
+  if (!is.null(sp.codes.file)) {
     message("Reading and processing SpCodes file")
     sp.acc.df <- read_fwf(
-      sp.codes,
+      sp.codes.file,
       col_positions = fwf_positions(start = c(1, 6, 18, 58), end = c(4, 15, 57, NA)),
       col_types = cols(.default = col_character()),
       trim_ws = TRUE, skip = 0, skip_empty_rows = FALSE
@@ -146,7 +159,7 @@ das_check <- function(file, skip = 0, file.out = NULL, sp.codes = NULL,
     sp.acc.all <- c(sp.acc, tolower(sp.acc))
 
     if (!all(nchar(sp.acc) %in% 2:3))
-      warning("Some species codes from sp.codes are not two or three charcters. ",
+      warning("Some species codes from sp.codes.file are not two or three charcters. ",
               "Did you load the correct species code .dat file?",
               immediate. = TRUE)
   }
@@ -485,8 +498,8 @@ das_check <- function(file, skip = 0, file.out = NULL, sp.codes = NULL,
   idx.a.4 <- .check_character(x, "A", "Data4", c("N", "Y", "n", "y", NA))
   txt.a.4 <- "Birds (Data4 of A events) is not one of N, Y, n, y, or NA"
 
-  txt.a.spcode <- "Species code(s) were not one of the accepted codes provided via sp.codes"
-  idx.a.spcode <- if (is.null(sp.codes)) {
+  txt.a.spcode <- "Species code(s) were not one of the accepted codes provided via sp.codes.file"
+  idx.a.spcode <- if (is.null(sp.codes.file)) {
     integer(0)
   } else {
     .check_character(x, "A", paste0("Data", 5:8), c(sp.acc.all, NA))
@@ -500,8 +513,8 @@ das_check <- function(file, skip = 0, file.out = NULL, sp.codes = NULL,
   )
 
   # Turtle
-  txt.t.spcode <- "Turtle species code was not one of the accepted codes provided via sp.codes"
-  idx.t.spcode <- if (is.null(sp.codes)) {
+  txt.t.spcode <- "Turtle species code was not one of the accepted codes provided via sp.codes.file"
+  idx.t.spcode <- if (is.null(sp.codes.file)) {
     integer(0)
   } else {
     .check_character(x, "t", paste0("Data", 2), c(sp.acc.all, NA))

R/das_chop_equallength.R

@@ -74,8 +74,8 @@
 #'   \code{x} (i.e., using the same DAS data) in the future. Note that when
 #'   saving with \code{\link[utils:read.table]{write.csv}}, users must specify
 #'   \code{row.names = FALSE} so that the CSV file only has two columns. For an
-#'   example randpicks file, see \code{system.file("das_sample_randpicks.csv",
-#'   package = "swfscDAS")}
+#'   example randpicks file, see
+#'   `system.file("extdata", "das_sample_randpicks.csv", package = "swfscDAS")`
 #'
 #'   If the column \code{dist_from_prev} does not exist, the distance between
 #'   subsequent events is calculated as described in \code{\link{das_effort}}

R/das_chop_section.R

@@ -23,10 +23,10 @@
 #'   See the Examples section for an example where the two methods give the same output.
 #'   Note that the longest continuous effort section in the sample data is ~22km.
 #'
-#' @return See \code{\link{das_chop_equallength}}. The randpicks values will all be \code{NA}
+#' @return See [das_chop_equallength()]. The randpicks values will all be `NA`
 #'
 #' @examples
-#' y <- system.file("das_sample.das", package = "swfscDAS")
+#' y <- system.file("extdata", "das_sample.das", package = "swfscDAS")
 #' y.proc <- das_process(y)
 #'
 #' y.eff1 <- das_effort(y.proc, method = "equallength", seg.km = 25, num.cores = 1)

R/das_comments.R

@@ -13,7 +13,7 @@
 #'   comment_str containing the concatenated comment strings
 #'
 #' @examples
-#' y <- system.file("das_sample.das", package = "swfscDAS")
+#' y <- system.file("extdata", "das_sample.das", package = "swfscDAS")
 #' y.proc <- das_process(y)
 #'
 #' das_comments(y.proc)

R/das_effort.R

@@ -39,65 +39,66 @@
 #' @param ... arguments passed to the specified chopping function, such as
 #'   \code{seg.km} or \code{seg.min.km}
 #'
-#' @details This is the top-level function for chopping processed DAS data into
-#'   modeling segments (henceforth 'segments'), and assigning sightings and
-#'   related information (e.g., weather conditions) to each segment. This
-#'   function returns data frames with all relevant information for the effort
-#'   segments and associated sightings ('segdata' and 'sightinfo',
-#'   respectively). Before chopping, the DAS data is filtered for events (rows)
-#'   where either the 'OnEffort' column is \code{TRUE} or the 'Event' column
-#'   "E". In other words, the data is filtered for continuous effort sections
-#'   (henceforth 'effort sections'), where effort sections run from "R" to "E"
-#'   events (inclusive), and then passed to the chopping function specified
-#'   using \code{method}. Note that while B events immediately preceding an R
-#'   are on effort, they are ignored during effort chopping. In addition, all on
-#'   effort events (other than ? and numeric events) with \code{NA} DateTime,
-#'   Lat, or Lon values are verbosely removed.
+#' @details
+#' This is the top-level function for chopping processed DAS data into modeling
+#' segments (henceforth 'segments'), and assigning sightings and related
+#' information (e.g., weather conditions) to each segment. This function returns
+#' data frames with all relevant information for the effort segments and
+#' associated sightings ('segdata' and 'sightinfo', respectively). Before
+#' chopping, the DAS data is filtered for events (rows) where either the
+#' 'OnEffort' column is \code{TRUE} or the 'Event' column "E". In other words,
+#' the data is filtered for continuous effort sections (henceforth 'effort
+#' sections'), where effort sections run from "R" to "E" events (inclusive), and
+#' then passed to the chopping function specified using \code{method}. Note that
+#' while B events immediately preceding an R are on effort, they are ignored
+#' during effort chopping. In addition, all on effort events (other than ? and
+#' numeric events) with \code{NA} DateTime, Lat, or Lon values are verbosely
+#' removed.
 #'
-#'   If \code{strata.files} is not \code{NULL}, then the effort lines will be
-#'   split by the user-provided stratum (strata). In this case, a column
-#'   'stratum' will be added to the end of the segdata data frame with the
-#'   user-provided name of the stratum that the segment was in, or \code{NA} if
-#'   the segment was not in any of the strata. If no name was provided for the
-#'   stratum in \code{strata.files}, then the value will be "Stratum#", where
-#'   "#" is the index of the applicable stratum in \code{strata.files}. While
-#'   the user can provide as many strata as they want, these strata can share
-#'   boundaries but they cannot overlap. See \code{\link{das_effort_strata}} for
-#'   more details.
+#' If \code{strata.files} is not \code{NULL}, then the effort lines will be
+#' split by the user-provided stratum (strata). In this case, a column 'stratum'
+#' will be added to the end of the segdata data frame with the user-provided
+#' name of the stratum that the segment was in, or \code{NA} if the segment was
+#' not in any of the strata. If no name was provided for the stratum in
+#' \code{strata.files}, then the value will be "Stratum#", where "#" is the
+#' index of the applicable stratum in \code{strata.files}. While the user can
+#' provide as many strata as they want, these strata can share boundaries but
+#' they cannot overlap. See \code{\link{das_effort_strata}} for more details.
 #'
-#'   The following chopping methods are currently available: "condition",
-#'   "equallength", and "section. When using the "condition" method, effort
-#'   sections are chopped into segments every time a condition changes, thereby
-#'   ensuring that the conditions are consistent across the entire segment. See
-#'   \code{\link{das_chop_condition}} for more details about this method,
-#'   including arguments that must be passed to it via the argument \code{...}
+#' The following chopping methods are currently available: "condition",
+#' "equallength", and "section. When using the "condition" method, effort
+#' sections are chopped into segments every time a condition changes, thereby
+#' ensuring that the conditions are consistent across the entire segment. See
+#' \code{\link{das_chop_condition}} for more details about this method,
+#' including arguments that must be passed to it via the argument \code{...}
 #'
-#'   The "equallength" method consists of chopping effort sections into
-#'   equal-length segments of length \code{seg.km}, and doing a weighted average
-#'   of the conditions for the length of that segment. See
-#'   \code{\link{das_chop_equallength}} for more details about this method,
-#'   including arguments that must be passed to it via the argument \code{...}
+#' The "equallength" method consists of chopping effort sections into
+#' equal-length segments of length \code{seg.km}, and doing a weighted average
+#' of the conditions for the length of that segment. See
+#' \code{\link{das_chop_equallength}} for more details about this method,
+#' including arguments that must be passed to it via the argument \code{...}
 #'
-#'   The "section" method involves 'chopping' the effort into continuous effort
-#'   sections, i.e. each continuous effort section is a single effort segment.
-#'   See \code{\link{das_chop_section}} for more details about this method.
+#' The "section" method involves 'chopping' the effort into continuous effort
+#' sections, i.e. each continuous effort section is a single effort segment. See
+#' \code{\link{das_chop_section}} for more details about this method.
 #'
-#'   The distance between the lat/lon points of subsequent events is calculated
-#'   using the method specified in \code{distance.method}. If "greatcircle",
-#'   \code{\link{distance_greatcircle}} is used, while
-#'   \code{\link[swfscMisc]{distance}} is used otherwise. See
-#'   \code{\link{das_sight}} for how the sightings are processed.
+#' The distance between the lat/lon points of subsequent events is calculated
+#' using the method specified in \code{distance.method}. If "greatcircle",
+#' \code{\link{distance_greatcircle}} is used, while
+#' \code{\link[swfscMisc]{distance}} is used otherwise. See
+#' \code{\link{das_sight}} for how the sightings are processed.
 #'
-#'   The sightinfo data frame includes the column 'included', which is used in
-#'   \code{\link{das_effort_sight}} when summarizing the number of sightings and
-#'   animals for selected species. \code{\link{das_effort_sight}} is a separate
-#'   function to allow users to personalize the included values as desired for
-#'   their analysis. By default, i.e. in the output of this function, 'included'
-#'   is \code{TRUE} if: the sighting was made when on effort, by a standard
-#'   observer (see \code{\link{das_sight}}), and in a Beaufort sea state less
-#'   than or equal to five.
+#' The sightinfo data frame includes the column 'included', which is used in
+#' \code{\link{das_effort_sight}} when summarizing the number of sightings and
+#' animals for selected species. \code{\link{das_effort_sight}} is a separate
+#' function to allow users to personalize the included values as desired for
+#' their analysis. By default, i.e. in the output of this function, 'included'
+#' is \code{TRUE} if: the sighting was made when on effort, by a standard
+#' observer (see \code{\link{das_sight}}), and in a Beaufort sea state less than
+#' or equal to five.
 #'
-#' @return List of three data frames:
+#' @return
+#' List of three data frames:
 #'   \itemize{
 #'     \item segdata: one row for every segment, and columns for information
 #'     including unique segment number (segnum), the corresponding effort
@@ -123,7 +124,7 @@
 #'   \code{\link{das_chop_section}}, \code{\link{das_segdata}}
 #'
 #' @examples
-#' y <- system.file("das_sample.das", package = "swfscDAS")
+#' y <- system.file("extdata", "das_sample.das", package = "swfscDAS")
 #' y.proc <- das_process(y)
 #'
 #' # Using "condition" method
@@ -137,14 +138,14 @@
 #'
 #' \donttest{
 #' # Using "equallength" method
-#' y.rand <- system.file("das_sample_randpicks.csv", package = "swfscDAS")
+#' y.rand <- system.file("extdata", "das_sample_randpicks.csv", package = "swfscDAS")
 #' das_effort(
 #'   y.proc, method = "equallength", seg.km = 10, randpicks.load = y.rand,
 #'   num.cores = 1
 #' )
 #'
 #' # Using "section" method and chop by strata
-#' stratum.file <- system.file("das_sample_stratum.csv", package = "swfscDAS")
+#' stratum.file <- system.file("extdata", "das_sample_stratum.csv", package = "swfscDAS")
 #' das_effort(
 #'   y.proc, method = "section", strata.files = list(Poly1 = stratum.file),
 #'   num.cores = 1

R/das_effort_sight.R

@@ -44,7 +44,7 @@
 #'   the sightings that were included in the effort segment summaries
 #'
 #' @examples
-#' y <- system.file("das_sample.das", package = "swfscDAS")
+#' y <- system.file("extdata", "das_sample.das", package = "swfscDAS")
 #' y.proc <- das_process(y)
 #' y.eff.cond <- das_effort(
 #'   y.proc, method = "condition", conditions = "Bft", seg.min.km = 0.05,