Remove fit_tmb, add codecov and fix yaml files for Actions (#10)

* removing fit_tmb

* fix small issue

* adding codecov

* Update README.md

* try adding Matrix as DEPENDS to trigger update

* expand R-CMD-check Action

* expand R-CMD-check to build Matrix/TMB from source

* test change to R-CMD-check

* test fix for Matrix/TMB inconsistency in codecov

* Update test-coverage.yaml

* another experiment

* Update test-coverage.yaml

* strip out codecov

* trigger check

* add manual codecov script

* try adding installs for R-CMD-check

* fix bug and move codecov.yml to scratch

* removing Matrix from Depends

* add test-coverage.yaml

* improving codecov

* small fix

* add codecov badge

* updating NEWS and DESCRIPTION

* small updates

* adding build-from-source for TMB/Matrix in pkgdown yaml

* adding build-from-source for test-coverage.yaml

* compiled Rd files

---------

Co-authored-by: Jim Thorson <James.T.Thorson@gmail.com>

.Rbuildignore

@@ -8,3 +8,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^codecov\.yml$

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

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, remove-fit_tmb]
   pull_request:
-    branches: [main, master]
+    branches: [main, remove-fit_tmb]
 
 name: R-CMD-check
 
@@ -21,9 +21,21 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -30,6 +30,18 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, dev, remove-fit_tmb]
+  pull_request:
+    branches: [main, dev, remove-fit_tmb]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          install.packages('remotes')
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("knitr")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("rcmdcheck")
+          install.packages("Matrix", type = "source")
+          install.packages("TMB", type = "source")
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: phylosem
 Type: Package
 Title: Phylogenetic Structural Equation Model
-Version: 1.1.2
-Date: 2023-12-19
+Version: 1.1.3
+Date: 2024-01-31
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
@@ -19,10 +19,11 @@ Imports:
     sem,
     ape,
     phylobase,
-    phylopath
+    phylopath,
+    methods
 Depends:
     TMB,
-    R (>= 4.0.0)
+    R (>= 4.0.0),
 Suggests:
     semPlot,
     TreeTools,
@@ -54,3 +55,5 @@ Encoding: UTF-8
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 URL: https://james-thorson-noaa.github.io/phylosem/
+BugReports: https://github.com/James-Thorson-NOAA/phylosem/issues
+

NAMESPACE

@@ -8,7 +8,6 @@ S3method(logLik,phylosem)
 S3method(print,phylosem)
 S3method(summary,phylosem)
 S3method(vcov,phylosem)
-export(TMBAIC)
 export(as_fitted_DAG)
 export(as_phylo4d)
 export(as_sem)
@@ -17,16 +16,17 @@ export(best)
 export(checkDepPackageVersion)
 export(choice)
 export(compare_phylosem)
-export(fit_tmb)
 export(list_parameters)
 export(phylosem)
+export(phylosem_control)
 importFrom(TMB,MakeADFun)
 importFrom(TMB,compile)
 importFrom(TMB,dynlib)
 importFrom(TMB,sdreport)
 importFrom(ape,Ntip)
 importFrom(ape,node.depth.edgelength)
 importFrom(ape,rtree)
+importFrom(methods,is)
 importFrom(phylobase,phylo4d)
 importFrom(phylopath,average_DAGs)
 importFrom(phylopath,coef_plot)

NEWS.md

@@ -1,3 +1,8 @@
+# phylosem 1.1.3
+* Removing fit_tmb to simplify code and remove unnecessary warnings
+* Adding codecov and extra tests
+* Fixing R-CMD-check to force build Matrix/TMB from source
+
 # phylosem 1.1.2
 * Adding new functions to provide warning if Matrix version doesn't match
   what's expected by TMB

R/coerce_methods.R

@@ -13,7 +13,7 @@ function( object ){
   # extract and name identical to output from est_DAG
   out = list(
     coef = t(object$report$Rho_jj),
-    se = t(as.list(object$opt$SD, what="Std. Error", report=TRUE)$Rho_jj)
+    se = t(as.list(object$sdrep, what="Std. Error", report=TRUE)$Rho_jj)
   )
   dimnames(out$coef) = dimnames(out$se) = list( colnames(object$data), colnames(object$data) )
 
@@ -64,7 +64,7 @@ function( object,
 
   #
   what = match.arg(what)
-  traits = as.list( object$opt$SD, what=what )$x_vj
+  traits = as.list( object$sdrep, what=what )$x_vj
   colnames(traits) = colnames(object$data)
   out = phylo4d( x=object$tree, all.data=traits )
 

R/compare_phylosem.R

@@ -22,6 +22,7 @@ function( sem_set,
           estimate_ou = FALSE,
           estimate_lambda = FALSE,
           estimate_kappa = FALSE,
+          control = phylosem_control(),
           ... ){
 
   # Initialize object of results
@@ -31,16 +32,18 @@ function( sem_set,
   # Loop through models
   for( modelI in seq_along(sem_set) ){
     fit = tryCatch( phylosem( sem = sem_set[[modelI]],
+    #fit = phylosem( sem = sem_set[[modelI]],
                               tree = tree,
                               data = data,
                               family = family,
                               covs = covs,
                               estimate_ou = estimate_ou,
                               estimate_lambda = estimate_lambda,
                               estimate_kappa = estimate_kappa,
+                              control = control,
                               ... ),
                     error = function(e) e )
-    if( "phylosem" %in% class(fit) ){
+    if( isTRUE(is(fit, "phylosem")) ){
       out[[modelI]] = fit
     }
   }

R/data.R

@@ -4,7 +4,7 @@
 #' Data used to demonstrate phylogenetic comparative methods for fisheries science. 
 #' Specifically a copy of the Then et al. database \doi{10.1093/icesjms/fsu136} 
 #' using file "Mlifehist_ver1.0.csv" accessed from 
-#' \url{https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php}
+#' \url{https://www.vims.edu/research/departments/fisheries/programs/mort_db/}
 #'
 #' @name Mlifehist_ver1_0
 #' @docType data