Initial implementation of likelihood profiling

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

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,17 +24,14 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          #- {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      _R_CHECK_FORCE_SUGGESTS_: false
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -44,16 +43,20 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          pak-version: devel
           extra-packages: |
             any::rcmdcheck
             nlmixr2/lotri
             nlmixr2/rxode2ll
             nlmixr2/rxode2
             nlmixr2/nlmixr2est
             nlmixr2/nlmixr2plot
+            nlmixr2/PreciseSums
+            nlmixr2/lbfgsb3c
+            nlmixr2/n1qn1c
+            nlmixr2/dparser-R
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -37,6 +41,10 @@ jobs:
             nlmixr2/rxode2
             nlmixr2/nlmixr2est
             nlmixr2/nlmixr2plot
+            nlmixr2/PreciseSums
+            nlmixr2/lbfgsb3c
+            nlmixr2/n1qn1c
+            nlmixr2/dparser-R
             local::.
           needs: website
 
@@ -46,7 +54,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,7 +17,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -25,32 +27,46 @@ jobs:
         with:
           extra-packages: |
             any::covr
+            any::xml2
             nlmixr2/lotri
             nlmixr2/rxode2ll
             nlmixr2/rxode2
             nlmixr2/nlmixr2est
             nlmixr2/nlmixr2plot
+            nlmixr2/PreciseSums
+            nlmixr2/lbfgsb3c
+            nlmixr2/n1qn1c
+            nlmixr2/dparser-R
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nlmixr2extra
 Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra Support
     Functions
-Version: 2.0.10
+Version: 3.0.0
 Authors@R: c(
     person("Matthew", "Fidler", email="matthew.fidler@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),
@@ -32,6 +32,7 @@ Imports:
     crayon,
     data.table,
     digest,
+    dplyr,
     ggplot2,
     ggtext,
     knitr,
@@ -49,7 +50,6 @@ Suggests:
     nlmixr2data,
     testthat (>= 3.0.0),
     withr,
-    dplyr,
     devtools
 LinkingTo:
     Rcpp,
@@ -59,5 +59,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyData: true

NAMESPACE

@@ -1,9 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(bootplot,nlmixr2FitCore)
+S3method(extractEqHelper,"(")
+S3method(extractEqHelper,"function")
+S3method(extractEqHelper,"{")
+S3method(extractEqHelper,call)
+S3method(extractEqHelper,character)
+S3method(extractEqHelper,default)
+S3method(extractEqHelper,name)
+S3method(extractEqHelper,nlmixr2FitCore)
+S3method(extractEqHelper,numeric)
+S3method(extractEqHelper,rxUi)
 S3method(knit_print,nlmixr2FitCore)
 S3method(knit_print,rxUi)
 S3method(print,nlmixr2BoostrapSummary)
+S3method(profile,nlmixr2FitCore)
+S3method(rxUiDeparse,llpControl)
 export(adaptivelassoCoefficients)
 export(addCatCovariates)
 export(addorremoveCovariate)
@@ -14,21 +26,27 @@ export(bootstrapFit)
 export(buildcovInfo)
 export(buildupatedUI)
 export(covarSearchAuto)
+export(fixedControl)
 export(foldgen)
 export(forwardSearch)
 export(horseshoeSummardf)
 export(ini)
 export(knit_print)
 export(lassoCoefficients)
 export(lassoSummardf)
+export(llpControl)
 export(model)
 export(nlmixr)
 export(nlmixr2)
 export(nlmixrWithTiming)
 export(normalizedData)
 export(optimUnisampling)
 export(preconditionFit)
+export(profileFixed)
+export(profileFixedSingle)
+export(profileLlp)
 export(regularmodel)
+export(rxUiDeparse)
 import(lotri)
 import(utils)
 importFrom(Rcpp,evalCpp)
@@ -40,6 +58,7 @@ importFrom(nlmixr2est,nlmixrWithTiming)
 importFrom(nlmixr2est,setCov)
 importFrom(rxode2,ini)
 importFrom(rxode2,model)
+importFrom(rxode2,rxUiDeparse)
 importFrom(stats,AIC)
 importFrom(stats,approxfun)
 importFrom(stats,cov)

NEWS.md

@@ -1,3 +1,7 @@
+# nlmixr2extra development version
+
+* New `profile()` method for likelihood profiling (Issue #1)
+
 # nlmixr2extra 2.0.10
 
 * `bootstrapFit()` fixes `se` option (Issue #66)

R/computingutil.R

@@ -958,11 +958,7 @@ modelBootstrap <- function(fit,
   }
 
   # get control settings for the 'fit' object and save computation effort by not computing the tables
-  .ctl <- fit$control
-  .ctl$print <- 0L
-  .ctl$covMethod <- 0L
-  .ctl$calcTables <- FALSE
-  .ctl$compress <- FALSE
+  .ctl <- setQuietFastControl(fit$control)
 
   modelsEnsemble <-
     lapply(bootData[.env$mod_idx:nboot], function(boot_data) {

R/knit_printEquation.R

@@ -69,22 +69,27 @@ extractEqHelperLhsRhs <- function(x, ..., inModel, prefix = "", middle, suffix =
   paste0(prefix, lhs, middle, rhs, suffix)
 }
 
+#' @export
 extractEqHelper.nlmixr2FitCore <- function(x, ..., inModel) {
   extractEqHelper(as.function(x), ..., inModel=FALSE)
 }
 
+#' @export
 extractEqHelper.rxUi <- function(x, ..., inModel, name) {
   extractEqHelper(as.function(x), ..., inModel=FALSE)
 }
 
+#' @export
 extractEqHelper.function <- function(x, ..., inModel, name) {
   extractEqHelper(methods::functionBody(x), ..., inModel=FALSE)
 }
 
+#' @export
 "extractEqHelper.{" <- function(x, ..., inModel, name) {
   extractEqHelperSeqDrop(x, ..., inModel = inModel)
 }
 
+#' @export
 "extractEqHelper.(" <- function(x, ..., inModel, dropParen = FALSE, name) {
   stopifnot(length(x) == 2)
   if (dropParen) {
@@ -178,6 +183,7 @@ latexOpMap <-
     "!"="{\\lnot}"
   )
 
+#' @export
 extractEqHelper.call <- function(x, ..., inModel, name) {
   if (inModel) {
     if (is.name(x[[1]])) {
@@ -270,6 +276,7 @@ extractEqHelper.call <- function(x, ..., inModel, name) {
   ret
 }
 
+#' @export
 extractEqHelper.name <- function(x, ..., inModel, underscoreToSubscript = FALSE, name) {
   if (inModel) {
     ret <- as.character(x)
@@ -292,6 +299,7 @@ extractEqHelper.name <- function(x, ..., inModel, underscoreToSubscript = FALSE,
   ret
 }
 
+#' @export
 extractEqHelper.numeric <- function(x, ..., inModel, name = NULL) {
   if (inModel) {
     ret <- format(x)
@@ -329,6 +337,7 @@ escapeLatex <- function (x, newlines = FALSE, spaces = FALSE) {
   x
 }
 
+#' @export
 extractEqHelper.character <- function(x, ..., inModel, name = NULL) {
   if (inModel) {
     ret <- sprintf('\\text{"%s"}', escapeLatex(x))
@@ -394,6 +403,7 @@ extractEqHelper.if <- function(x, ..., inModel, alignment, indent = 0L, firstIf
   ret
 }
 
+#' @export
 extractEqHelper.default <- function(x, ..., inModel) {
   if (inherits(x, "<-") | inherits(x, "=")) {
     # The assignment classes go via extractEqHelper.default to fix an R CMD