diff --git a/.DS_Store b/.DS_Store deleted file mode 100755 index 4bb8cab..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/atlantis/.DS_Store b/atlantis/.DS_Store deleted file mode 100755 index 7934a4b..0000000 Binary files a/atlantis/.DS_Store and /dev/null differ diff --git a/atlantis/atecology/.DS_Store b/atlantis/atecology/.DS_Store deleted file mode 100755 index b0fcd99..0000000 Binary files a/atlantis/atecology/.DS_Store and /dev/null differ diff --git a/atlantis/ateconomic/.DS_Store b/atlantis/ateconomic/.DS_Store deleted file mode 100755 index 5008ddf..0000000 Binary files a/atlantis/ateconomic/.DS_Store and /dev/null differ diff --git a/atlantis/atlantismain/.DS_Store b/atlantis/atlantismain/.DS_Store deleted file mode 100755 index 7e078aa..0000000 Binary files a/atlantis/atlantismain/.DS_Store and /dev/null differ diff --git a/atlantis/atmanage/.DS_Store b/atlantis/atmanage/.DS_Store deleted file mode 100755 index f216377..0000000 Binary files a/atlantis/atmanage/.DS_Store and /dev/null differ diff --git a/atlantis/atmanage/atManageSetup.c b/atlantis/atmanage/atManageSetup.c index e12625f..5bc8bc5 100755 --- a/atlantis/atmanage/atManageSetup.c +++ b/atlantis/atmanage/atManageSetup.c @@ -1193,7 +1193,7 @@ void Allocate_Arrays_Pre_Load(MSEBoxModel *bm) { /* These are always allocated even if the management option is off */ bm->reg_season = (int *) i_alloc1d(bm->K_num_reg); bm->phased_out = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 1.0); - bm->BiTAC_sp = (double ****) alloc4d(2, bm->K_num_tot_sp, totalreg_id + 1, 6); + bm->BiTAC_sp = Util_Alloc_Init_4D_Double(2, bm->K_num_tot_sp, totalreg_id + 1, 6, 0.0);; bm->BiTACamt = Util_Alloc_Init_4D_Double(2, nfleets, bm->K_num_tot_sp, 6, 0.0); bm->TACamt = Util_Alloc_Init_3D_Double(K_num_TAC_entries, nfleets, bm->K_num_tot_sp, 0.0); bm->TripCatch = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 0.0); diff --git a/atlantis/externalLibs/win32_vs_dll_4.0.1-beta3.tar/.DS_Store b/atlantis/externalLibs/win32_vs_dll_4.0.1-beta3.tar/.DS_Store deleted file mode 100755 index 5008ddf..0000000 Binary files a/atlantis/externalLibs/win32_vs_dll_4.0.1-beta3.tar/.DS_Store and /dev/null differ diff --git a/example/.DS_Store b/example/.DS_Store deleted file mode 100755 index c37caae..0000000 Binary files a/example/.DS_Store and /dev/null differ diff --git a/example/.Rhistory b/example/.Rhistory deleted file mode 100755 index 348f3f6..0000000 --- a/example/.Rhistory +++ /dev/null @@ -1,119 +0,0 @@ -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -####### Compare outputs and Biomass visualization ####### -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder2/outputSETAS.nc' -nc.old <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/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) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -####### Predation analysis from the Atlantis output ####### -biom <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASBiomIndx.txt' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -bio.age <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASAgeBiomIndx.txt' ## optional file. just if you want to check the predation by age -grp.csv <- '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) -####### Exploring predator-prey interactions from the initial conditions ####### -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -nc.initial <- 'INIT_VMPA_Jan2015.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 -feeding.mat(prm.file, grp.file, nc.initial, bgm.file, cum.depths) -####### Atlantis food web and trophic level composition ####### -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/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) -## diet.file.bypol Detailed diet check file, this can be obtained as an extra output from Atlantis "DetailedDietCheck.txt". To get this file from Atlantis turn on the option "flagdietcheck" on the Run.prm file. -####### Growth of primary producers and limiting factors ####### -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -####### Analysis of recruitment and primary production ####### -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -yoy.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASYOY.txt' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -recruitment.cal(nc.initial, nc.current, yoy.file, grp.csv, prm.file) -####### Harvest outputs and model skill assessment ####### -catch.nc <- 'outputSETASCATCH.nc' -ext.catch <- 'external_catch_time_series.csv' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -fsh.csv <- 'SETasFisheries.csv' -bgm.file <- 'VMPA_setas.bgm' -grp.csv <- 'SETasGroupsDem.csv' -catch(grp.csv, fsh.csv, catch.nc, ext.catch) -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -devtools::install_github('Atlantis-Ecosystem-Model/ReactiveAtlantis', force=TRUE, dependencies=TRUE) -devtools::install_github("Atlantis-Ecosystem-Model/shinyrAtlantis", force=TRUE, dependencies=TRUE) -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder2/outputSETAS.nc' -nc.old <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/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) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -biom <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASBiomIndx.txt' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -bio.age <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASAgeBiomIndx.txt' ## optional file. just if you want to check the predation by age -grp.csv <- 'SETasGroupsDem.csv' -## Predation by Age -## 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 <- 'VMPA_setas_biol_fishing_Trunk.prm' -nc.initial <- 'INIT_VMPA_Jan2015.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 -feeding.mat(prm.file, grp.file, nc.initial, bgm.file, cum.depths) -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -food.web(diet.file, grp.csv) -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -yoy.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASYOY.txt' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -recruitment.cal(nc.initial, nc.current, yoy.file, grp.csv, prm.file) -catch.nc <- 'outputSETASCATCH.nc' -ext.catch <- 'external_catch_time_series.csv' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -fsh.csv <- 'SETasFisheries.csv' -bgm.file <- 'VMPA_setas.bgm' -grp.csv <- 'SETasGroupsDem.csv' -catch(grp.csv, fsh.csv, catch.nc, ext.catch) diff --git a/example/inputs/.DS_Store b/example/inputs/.DS_Store deleted file mode 100755 index 58317d4..0000000 Binary files a/example/inputs/.DS_Store and /dev/null differ diff --git a/example/inputs/._.DS_Store b/example/inputs/._.DS_Store deleted file mode 100644 index 338bd7b..0000000 Binary files a/example/inputs/._.DS_Store and /dev/null differ diff --git a/example/outputFolderPristine/.DS_Store b/example/outputFolderPristine/.DS_Store deleted file mode 100755 index 5008ddf..0000000 Binary files a/example/outputFolderPristine/.DS_Store and /dev/null differ