From 11ef963548b1907a4434b879dda8fcf7fc970cad Mon Sep 17 00:00:00 2001 From: Hem Nalini Morzaria-Luna Date: Tue, 22 Sep 2026 16:45:10 -0700 Subject: [PATCH] Delete .Rhistory --- .Rhistory | 136 ------------------------------------------------------ 1 file changed, 136 deletions(-) delete mode 100644 .Rhistory diff --git a/.Rhistory b/.Rhistory deleted file mode 100644 index 198e635..0000000 --- a/.Rhistory +++ /dev/null @@ -1,136 +0,0 @@ -rm(list = ls()) # clear memory -library("devtools") -library("ReactiveAtlantis") -library("proj4") -library("here") -####### Compare outputs and Biomass visualization ####### -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -nc.old <- here::here("example","outputFolder_mum","outputSETAS.nc") -grp.csv <- 'SETasGroupsDem.csv' -bgm.file <- 'VMPA_setas.bgm' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -biom <- here::here("example","outputFolder_original","outputSETASBiomIndx.txt") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -bio.age <- here::here("example","outputFolder_original","outputSETASAgeBiomIndx.txt") ## optional file. just if you want to check the predation by age -grp.csv <- here::here("example","SETasGroupsDem.csv") -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -## No predation by Age -predation(biom, grp.csv, diet.file, bio.age = NULL) -prm.file <- here::here("example","outputFolder_original","VMPA_setas_biol_fishing_Trunk.prm") -nc.initial <- here::here("example","outputFolder_original","INIT_VMPA_Jan2015.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -nc.initial <- here::here("example","INIT_VMPA_Jan2015.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -food.web(diet.file, grp.csv) -## optional you can explore the food web by polygon -food.web(diet.file, grp.file, diet.file.bypol) -food.web(diet.file, grp.csv) -nc.initial <- here::here("example","INIT_VMPA_Jan2015.nc") -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -rm(list = ls()) # clear memory -library("devtools") -library("ReactiveAtlantis") -library("proj4") -library("here") -####### Compare outputs and Biomass visualization ####### -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -nc.old <- here::here("example","outputFolder_mum","outputSETAS.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -####### Predation analysis from the Atlantis output ####### -biom <- here::here("example","outputFolder_original","outputSETASBiomIndx.txt") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -bio.age <- here::here("example","outputFolder_original","outputSETASAgeBiomIndx.txt") ## optional file. just if you want to check the predation by age -grp.csv <- here::here("example","SETasGroupsDem.csv") -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -## No predation by Age -predation(biom, grp.csv, diet.file, bio.age = NULL) -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -nc.initial <- here::here("example","INIT_VMPA_Jan2015.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -food.web(diet.file, grp.csv) -nc.initial <- here::here("example","INIT_VMPA_Jan2015.nc") -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -# -nc.initial <- here::here("example","INIT_VMPA_Jan2015.nc") -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -yoy.file <- here::here("example","outputFolder_original","outputSETASYOY.txt") -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -recruitment.cal(nc.initial, nc.current, yoy.file, grp.csv, prm.file) -rm(list = ls()) # clear memory -rm(list = ls()) # clear memory -library("devtools") -library("ReactiveAtlantis") -library("proj4") -library("here") -####### Compare outputs and Biomass visualization ####### -nc.current <- here::here("example","outputFolder_original","outputSETAS.nc") -nc.old <- here::here("example","outputFolder_mum","outputSETAS.nc") -grp.csv <- here::here("example","SETasGroupsDem.csv") -bgm.file <- here::here("example","VMPA_setas.bgm") -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -biom <- here::here("example","outputFolder_original","outputSETASBiomIndx.txt") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -bio.age <- here::here("example","outputFolder_original","outputSETASAgeBiomIndx.txt") ## optional file. just if you want to check the predation by age -grp.csv <- here::here("example","SETasGroupsDem.csv") -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -####### Atlantis food web and trophic level composition ####### -grp.csv <- here::here("example","SETasGroupsDem.csv") -prm.file <- here::here("example","VMPA_setas_biol_fishing_Trunk.prm") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -food.web(diet.file, grp.csv) -biom <- here::here("example","outputFolder_original","outputSETASBiomIndx.txt") -diet.file <- here::here("example","outputFolder_original","outputSETASDietCheck.txt") -bio.age <- here::here("example","outputFolder_original","outputSETASAgeBiomIndx.txt") ## optional file. just if you want to check the predation by age -grp.csv <- here::here("example","SETasGroupsDem.csv") -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -claude -1850/365 -source("~/psatlantismodel/PS_runs_PCBs.R") -source("~/psatlantismodel/PS_runs_PCBs.R") -source("~/psatlantismodel/PS_runs_PCBs.R")