Dev (#396)

* Update DESCRIPTION * Update DESCRIPTION * Update R-CMD-check.yml * Update R-CMD-check.yml * try removing ThorsonUtilities * Update R-CMD-check.yml * try to make Actions happy * try at getting INLA dependency to work in Actions * Update test-zeroinfl-against-pscl.R * another attempt at making R_CMD_check happy * another attempt * another attempt * another attempt * another attempt * another attempt * remove Linux from github Actions * update NEWS * Update test-multi-species-examples.R --------- Co-authored-by: Jim Thorson <James.T.Thorson@gmail.com>
James-Thorson-NOAA · Jan 17, 2025 · 431621f · 431621f
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diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
@@ -17,22 +17,20 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -41,14 +39,6 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
       - name: Install system dependencies for Linux
         if: runner.os == 'Linux'
         run: |
@@ -85,6 +75,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           devtools::install_local()
+          devtools::install_deps(dependencies=TRUE)
           out <- devtools::test(stop_on_failure=TRUE)
           print(getwd())
           print(ls())

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: VAST
 Type: Package
 Title: Vector-Autoregressive Spatio-Temporal (VAST) Model
-Version: 3.11.2
-Date: 2024-07-15
+Version: 3.11.3
+Date: 2025-01-16
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
@@ -23,14 +23,13 @@ Imports:
     abind,
     effects,
     stats,
-    ThorsonUtilities,
     utils,
     fmesher,
     remotes,
     devtools
 Depends:
     TMB (>= 1.8.0),
-    FishStatsUtils (>= 2.13.1),
+    FishStatsUtils (>= 2.13.2),
     R (>= 3.5.0)
 Suggests:
     testthat,
@@ -42,11 +41,10 @@ Suggests:
     lme4,
 Remotes:
     james-thorson-NOAA/FishStatsUtils,
-    james-thorson/utilities
 License: file LICENSE
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 ByteCompile: true
 URL: http://github.com/James-Thorson-NOAA/VAST
 BugReports: http://github.com/James-Thorson-NOAA/VAST/issues

diff --git a/R/list_parameters.R b/R/list_parameters.R
@@ -0,0 +1,35 @@
+
+
+#' List fixed and random effects
+#'
+#' \code{list_parameters} lists all fixed and random effects
+#'
+#' @param Obj Compiled TMB object
+#' @return Return Tagged-list of fixed and random effects (returned invisibly)
+
+#' @export
+list_parameters = function( Obj, verbose=TRUE ){
+  Return = list()
+  Table = data.frame()
+  if( length(Obj$env$random)>0 ){
+    Return[["Fixed_effects"]] = names(Obj$env$last.par[-Obj$env$random])
+    Return[["Random_effects"]] = names(Obj$env$last.par[Obj$env$random])
+    Table = data.frame( "Coefficient_name"=names(table(Return[["Fixed_effects"]])),
+                        "Number_of_coefficients"=as.numeric(table(Return[["Fixed_effects"]])),
+                        "Type"="Fixed")
+    Table = rbind( Table,
+                   data.frame("Coefficient_name"=names(table(Return[["Random_effects"]])),
+                              "Number_of_coefficients"=as.numeric(table(Return[["Random_effects"]])),
+                              "Type"="Random"))
+  }else{
+    Return[["Fixed_effects"]] = names(Obj$env$last.par)
+    Table = data.frame( "Coefficient_name"=names(table(Return[["Fixed_effects"]])),
+                        "Number_of_coefficients"=as.numeric(table(Return[["Fixed_effects"]])),
+                        "Type"="Fixed")
+  }
+  if( verbose==TRUE ){
+    message("List of estimated fixed and random effects:")
+    print(Table)
+  }
+  return( invisible(Table) )
+}
diff --git a/R/make_model.R b/R/make_model.R
@@ -265,7 +265,7 @@ function( TmbData,
   Obj$env$inner.control$grad.tol <- c(1e-8,1e-12,1e-15)[ConvergeTol] # # Default : 1e-8  # Maximum gradient limit inner optimization
 
   # Print number of parameters
-  ThorsonUtilities::list_parameters( Obj )
+  list_parameters( Obj )
 
   # Return stuff
   Return = list("Obj"=Obj, "Upper"=Bounds[,'Upper'], "Lower"=Bounds[,'Lower'], "Parameters"=Parameters, "Map"=Map, "Random"=Random)

diff --git a/R/project_model.R b/R/project_model.R
@@ -6,9 +6,10 @@
 #'
 #' The function specifically simulates new values for random effects occurring
 #'      during forecasted years.  This includes some combination of intercepts
-#'      {beta1/beta2} and spatio-temporal terms {epsilon1/epsilon2} depending on which
+#'      \code{beta1} or \code{beta2} and spatio-temporal terms
+#'      \code{epsilon1} or \code{epsilon2} depending on which
 #'      are treated as random during estimation.  It does *not* generate new values of
-#'      covariates or random-effects that are not indexed by time {omega1/omega2}
+#'      covariates or random-effects that are not indexed by time \code{omega1} or \code{omega2}
 #'
 #' Note that the model may behave poorly when \code{historical_uncertainty="both"}
 #'      and the estimation model includes an AR1 process for any component.

diff --git a/man/list_parameters.Rd b/man/list_parameters.Rd
diff --git a/manual/NEWS.docx b/manual/NEWS.docx
diff --git a/manual/NEWS.pdf b/manual/NEWS.pdf
diff --git a/tests/testthat/test-EOF.R b/tests/testthat/test-EOF.R
@@ -9,6 +9,10 @@ test_that("EOF is working ", {
   # Previously worked with CI, but not anymore
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
 
   test_path = file.path(multispecies_example_path,"EOF")
   load( file.path(test_path,"parameter_estimates.RData") )

diff --git a/tests/testthat/test-Tweedie-against-mgcv.R b/tests/testthat/test-Tweedie-against-mgcv.R
@@ -8,6 +8,10 @@ test_that("Tweedie gives identical results to mgcv::gam(.) ", {
   # Previously worked with CI, but not anymore
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
   library(mgcv)
 
   #library(tweedie)  # Installed from locally from tweedie_2.3.2.tar.gz here: https://cran.r-project.org/web/packages/tweedie/index.html
@@ -64,6 +68,10 @@ test_that("Tweedie gives identical results to mgcv::gam(.) ", {
 test_that("Covariate effects when using a smoother gives identical results to mgcv::gam(.) ", {
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
   library(mgcv)
 
   # Simulate

diff --git a/tests/testthat/test-catchability_against_glm.R b/tests/testthat/test-catchability_against_glm.R
@@ -20,6 +20,10 @@ test_that("Catchability covariates give identical results to glm(.) ", {
   # Previously worked with CI, but not anymore
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
 
   # load data set
   example = load_example( data_set="covariate_example" )

diff --git a/tests/testthat/test-condition-and-density.R b/tests/testthat/test-condition-and-density.R
@@ -5,6 +5,7 @@ context("Testing examples")
 test_that("Condition-and-density example is working ", {
   skip_on_ci()
   skip_if(skip_local)
+
   # Prepping
   test_path = file.path(multispecies_example_path,"Condition_and_density")
   load( file.path(test_path,"saved_estimates.RData") )

diff --git a/tests/testthat/test-covariates_against_glm.R b/tests/testthat/test-covariates_against_glm.R
@@ -20,6 +20,10 @@ test_that("Density covariates give identical results to glm(.) ", {
   # Previously worked with CI, but not anymore
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
 
   # load data set
   example = load_example( data_set="covariate_example" )

diff --git a/tests/testthat/test-multi-species-examples.R b/tests/testthat/test-multi-species-examples.R
@@ -23,7 +23,7 @@ test_that("Eastern Bering Sea 3-species is working ", {
   TmbData = make_data("Version"=Version_VAST, "OverdispersionConfig"=rep(VesselConfig[2],2), "FieldConfig"=FieldConfig, "RhoConfig"=RhoConfig, "ObsModel"=ObsModel, "c_i"=Data_Geostat[,'spp']-1, "b_i"=Data_Geostat[,'Catch_KG'], "a_i"=Data_Geostat[,'AreaSwept_km2'], "v_i"=as.numeric(factor(paste(Data_Geostat[,'Vessel'],Data_Geostat[,'Year'])))-1, "t_i"=Data_Geostat[,'Year'], "spatial_list"=Spatial_List )
   TmbList = make_model("build_model"=TRUE, "TmbData"=TmbData, "RunDir"=test_path, "Version"=Version_VAST, "RhoConfig"=RhoConfig, "loc_x"=Spatial_List$loc_x)
   #on.exit( dyn.unload(paste0(system.file("executables", package = "VAST"),"/",TMB::dynlib(Version_VAST))), add=TRUE )
-  Opt = TMBhelper::fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )
+  Opt = fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )
   # Comparisons
   expect_equal( abs(Opt$par)[-which(names(Opt$par)%in%c("beta1_tf","beta2_tf","beta1_ct","beta2_ct","beta1_ft","beta2_ft"))], abs(opt$par)[-which(names(opt$par)%in%c("beta1_tf","beta2_tf","beta1_ct","beta2_ct","beta1_ft","beta2_ft"))], tolerance=1e-3 )
   expect_equal( Opt$objective, opt$objective, tolerance=1e-3 )
@@ -33,6 +33,7 @@ test_that("Eastern Bering Sea 3-species is working ", {
 test_that("Eastern Bering Sea 5-species is working ", {
   skip_on_ci()
   skip_if(skip_local)
+
   # Prepping
   test_path = file.path(multispecies_example_path,"EBS_5species")
   load( file.path(test_path,"opt.RData") )
@@ -48,7 +49,7 @@ test_that("Eastern Bering Sea 5-species is working ", {
   TmbData = make_data("Version"=Version_VAST, "OverdispersionConfig"=rep(VesselConfig[2],2), "FieldConfig"=FieldConfig, "RhoConfig"=RhoConfig, "ObsModel"=ObsModel, "c_i"=Data_Geostat[,'spp']-1, "b_i"=Data_Geostat[,'Catch_KG'], "a_i"=Data_Geostat[,'AreaSwept_km2'], "v_i"=as.numeric(factor(paste(Data_Geostat[,'Vessel'],Data_Geostat[,'Year'])))-1, "t_i"=Data_Geostat[,'Year'], "spatial_list"=Spatial_List )
   TmbList = make_model("TmbData"=TmbData, "RunDir"=test_path, "Version"=Version_VAST, "RhoConfig"=RhoConfig, "loc_x"=Spatial_List$loc_x)
   #on.exit( dyn.unload(paste0(system.file("executables", package = "VAST"),"/",TMB::dynlib(Version_VAST))), add=TRUE )
-  Opt = TMBhelper::fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )
+  Opt = fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )
   # Comparisons
   expect_equal( abs(Opt$par)[-which(names(Opt$par)%in%c("beta1_tf","beta2_tf","beta1_ct","beta2_ct","beta1_ft","beta2_ft"))], abs(opt$par)[-which(names(opt$par)%in%c("beta1_tf","beta2_tf","beta1_ct","beta2_ct","beta1_ft","beta2_ft"))], tolerance=1e-3 )
   expect_equal( Opt$objective, opt$objective, tolerance=1e-3 )

diff --git a/tests/testthat/test-single-species-examples.R b/tests/testthat/test-single-species-examples.R
@@ -20,6 +20,10 @@ test_that("Eastern Bering Sea pollock is working ", {
   # Previously worked with CI, but not anymore
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
 
   # Prepping
   test_path = file.path(singlespecies_example_path,"EBS_pollock")
@@ -36,7 +40,7 @@ test_that("Eastern Bering Sea pollock is working ", {
   TmbData = make_data("Version"=Version_VAST, "OverdispersionConfig"=rep(VesselConfig[2],2), "FieldConfig"=FieldConfig, "RhoConfig"=RhoConfig, "ObsModel"=c(ObsModel,0), "c_i"=rep(0,nrow(Data_Geostat)), "b_i"=Data_Geostat[,'Catch_KG'], "a_i"=Data_Geostat[,'AreaSwept_km2'], "v_i"=as.numeric(factor(paste(Data_Geostat[,'Vessel'],Data_Geostat[,'Year'])))-1, "t_i"=Data_Geostat[,'Year'], "spatial_list"=Spatial_List )
   TmbList = make_model("TmbData"=TmbData, "build_model"=TRUE, "RunDir"=test_path, "Version"=Version_VAST, "RhoConfig"=RhoConfig, "loc_x"=Spatial_List$loc_x ) #, "Parameters"=Params)
   #on.exit( dyn.unload(paste0(system.file("executables", package = "VAST"),"/",TMB::dynlib(Version_VAST))), add=TRUE )
-  Opt = TMBhelper::fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )  # , rel.tol=1e-20
+  Opt = fit_tmb( obj=TmbList[["Obj"]], getsd=FALSE, lower=TmbList[["Lower"]], upper=TmbList[["Upper"]] )  # , rel.tol=1e-20
   # Comparisons
   Par1 = Opt$par[names(Opt$par)%in%c("ln_H_input","beta1_ct","beta1_ft","logkappa1","beta2_ct","beta2_ft","logkappa1","logSigmaM")]
   Par2 = opt$par[names(opt$par)%in%c("ln_H_input","beta1_t","logkappa1","beta2_t","logkappa1","logSigmaM")]

diff --git a/tests/testthat/test-spatially-varying-coefficient.R b/tests/testthat/test-spatially-varying-coefficient.R
@@ -6,7 +6,6 @@ test_that("Spatially varying coefficient example is working ", {
   skip_on_ci()
   skip_if(skip_local)
 
-
   # Prepping
   test_path = file.path(multispecies_example_path,"Spatially_varying_coefficient")
   load( file=file.path(test_path,"Data.RData") )

diff --git a/tests/testthat/test-zeroinfl-against-pscl.R b/tests/testthat/test-zeroinfl-against-pscl.R
@@ -7,6 +7,10 @@ context("Testing examples")
 test_that("Zero-inflated Poisson gives identical results to pscl::zeroinfl(.) ", {
   #skip_on_ci()
   skip_if(skip_local)
+  if(!require("INLA")){
+    install.packages("INLA", dep=TRUE, repos=c( CRAN="https://cloud.r-project.org",
+                                                INLA="https://inla.r-inla-download.org/R/stable") )
+  }
 
   ## Simulate
   set.seed(101)

diff --git a/tests/testthat/testthat-problems.rds b/tests/testthat/testthat-problems.rds