add offset option for ENV Q #97
Workflow file for this run
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| # Build SS3 and run models with estimation and hessian | |
| name: run-ss3-bootstrap-files | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| pull_request: | |
| types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review'] | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| # run fast running SS3 models with estimation | |
| jobs: | |
| run-ss3-bootstrap-files: | |
| if: github.event.pull_request.draft == false | |
| runs-on: ubuntu-latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - name: Checkout ss3 repo | |
| uses: actions/checkout@v4 | |
| - name: Checkout models repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'nmfs-ost/ss3-test-models' | |
| path: test-models-repo | |
| - name: install libcurl | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| # - name: Get admb and put in path, linux | |
| # run: | | |
| # wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip | |
| # sudo unzip admb-13.1-linux.zip -d /usr/local/bin | |
| # sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb | |
| # echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH | |
| # - name: Build stock synthesis | |
| # run: | | |
| # rm -rf SS330 | |
| # mkdir SS330 | |
| # /bin/bash ./Make_SS_330_new.sh -b SS330 | |
| - name: Build stock synthesis with admb docker image | |
| run: | | |
| rm -rf SS330 | |
| rm -rf ss3_osx.tar | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 | |
| - name: move exes, scripts to needed locations | |
| run: | | |
| mv test-models-repo/models test-models-repo/model_runs | |
| mv SS330/ss3 test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3 | |
| - name: change permissions on ss3 exes | |
| run: sudo chmod a+x test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3 | |
| - name: download R packages | |
| run: Rscript -e 'install.packages(c("remotes", "purrr", "arsenal", "utils"))' | |
| - name: install r4ss | |
| run: Rscript -e 'remotes::install_github("r4ss/r4ss")' | |
| - name: does ss3 produce bootstrap files | |
| run: | | |
| # Use Simple_with_DM_sizefreq model to test bootstrap files | |
| boot_mod_dir <- grep("Simple_with_DM_sizefreq", list.dirs(file.path("test-models-repo", "model_runs"), full.names = TRUE, recursive = FALSE), value = TRUE) | |
| # Change to have model output 8 bootstrap files | |
| boot_files <- r4ss::SS_read(dir = boot_mod_dir) | |
| boot_files$start$N_bootstraps <- 10 | |
| r4ss::SS_write(boot_files, dir = boot_mod_dir, overwrite = TRUE) | |
| r4ss::run(dir = boot_mod_dir, exe = file.path(getwd(), "test-models-repo", "model_runs", "Simple_with_DM_sizefreq", "ss3")) | |
| bootstrap_length <- length(list.files(boot_mod_dir, pattern = "data_boot")) | |
| if(bootstrap_length != (boot_files$start$N_bootstraps - 2)){ | |
| stop("Did not produce the amount of bootstrap files specified.") | |
| } else { | |
| message("All bootstrap files produced.") | |
| } | |
| # Make sure values in echo and bootstrap files are different | |
| dat <- r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_echo.ss_new")) | |
| boot1 <- r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_boot_001.ss")) | |
| boot2 <- r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_boot_002.ss")) | |
| # unlist sizefreq data | |
| dat_sizefreq <- purrr::map_df(dat$sizefreq_data_list, ~.x) | |
| boot1_sizefreq <- purrr::map_df(boot1$sizefreq_data_list, ~.x) | |
| boot2_sizefreq <- purrr::map_df(boot2$sizefreq_data_list, ~.x) | |
| df <- data.frame( | |
| var = c("lencomp", "lencomp","catch","catch","CPUE","CPUE", "agecomp","agecomp","sizefreq","sizefreq"), | |
| data_compare = rep(c("dat_boot1", "boot1_boot2"), 5), | |
| n_diff = c( | |
| sum(summary(arsenal::comparedf(dat$lencomp, boot1$lencomp))$diffs.byvar.table$n), | |
| sum(summary(arsenal::comparedf(boot1$lencomp, boot2$lencomp))$diffs.byvar.table$n), | |
| length(summary(arsenal::comparedf(dat$catch, boot1$catch, int.as.num = TRUE))$diffs.table$row.x), | |
| length(summary(arsenal::comparedf(dat$catch, boot1$catch, int.as.num = TRUE))$diffs.table$row.x), | |
| length(summary(arsenal::comparedf(dat$CPUE, boot1$CPUE, int.as.num = TRUE))$diffs.table$row.x), | |
| length(summary(arsenal::comparedf(boot1$CPUE, boot2$CPUE, int.as.num = TRUE))$diffs.table$row.x), | |
| sum(summary(arsenal::comparedf(dat$agecomp, boot1$agecomp))$diffs.byvar.table$n), | |
| sum(summary(arsenal::comparedf(boot1$agecomp, boot2$agecomp))$diffs.byvar.table$n), | |
| sum(summary(arsenal::comparedf(dat_sizefreq, boot1_sizefreq))$diffs.byvar.table$n), | |
| sum(summary(arsenal::comparedf(boot1_sizefreq, boot2_sizefreq))$diffs.byvar.table$n) | |
| ) | |
| ) | |
| df_error <- df |> | |
| dplyr::filter(dplyr::if_any(dplyr::where(is.numeric), ~ .x < 20)) | |
| print_and_capture <- function(x){ | |
| paste(utils::capture.output(print(x)), collapse = "\n") | |
| } | |
| if(length(df_error > 0)){ | |
| stop("Bootstrap data produced less than 20 changes in a data type, see printed table below.\n", print_and_capture(df_error)) | |
| } else { | |
| message("Bootstrap data types all have > 20 changes") | |
| } | |
| # Check that the model produced all .ss_new files and that they have content in them | |
| ss_new_files <- list.files(boot_mod_dir, pattern = ".ss_new") | |
| ss_new_validate <- c("control.ss_new", "data_echo.ss_new", "forecast.ss_new", "starter.ss_new", "wtatage.ss_new") | |
| new_dif <- setdiff(ss_new_files, ss_new_validate) | |
| if(length(new_dif) > 0){ | |
| stop("Not all .ss_new files were produced") | |
| } else { | |
| message("All .ss_new files produced") | |
| } | |
| ss_new_length <- purrr::map(ss_new_files, ~length(readLines(file.path(boot_mod_dir, .x)))) | |
| ss_new_too_short <- any(ss_new_length |> purrr::map_lgl(~.x < 10)) | |
| if(ss_new_too_short == TRUE){ | |
| stop("Error producing all lines in one or more .ss_new files") | |
| } else { | |
| message("All .ss_new files seem to be appropriate length") | |
| } | |
| shell: Rscript {0} |