Merge remote-tracking branch 'origin/main' into testthat3

NAMESPACE

@@ -93,6 +93,7 @@ S3method(nmObjGetControl,fo)
 S3method(nmObjGetControl,foce)
 S3method(nmObjGetControl,focei)
 S3method(nmObjGetControl,foi)
+S3method(nmObjGetControl,posthoc)
 S3method(nmObjGetControl,saem)
 S3method(nmObjGetEstimationModel,default)
 S3method(nmObjGetEstimationModel,saem)

R/bootstrap.R

@@ -346,7 +346,7 @@ bootstrapFit <- function(fit,
     assign(".bootPlotData", .dataList, envir = fit$env)
   }
   ## Update covariance estimate
-  .nm <- names(fit$theta)[!fit$skipCov[seq_along(fit$theta)]]
+  .nm <- names(fit$theta)[!fit$foceiSkipCov[seq_along(fit$theta)]]
   .cov <- fit$bootSummary$omega$covMatrixCombined[.nm, .nm]
   .setCov(fit, covMethod = .cov)
   assign("covMethod", paste0("boot", fit$bootSummary$nboot), fit$env)

R/broom.R

@@ -79,16 +79,16 @@ confint.nlmixr2FitCoreSilent <- confint.nlmixr2FitCore
   if (!.shrink) {
     .df <- .df[, names(.df) != "shrink"]
   }
-  .ini <- x$uif$ini$err[!is.na(x$uif$ini$ntheta)]
+  .ini <- x$ui$iniDf$err[!is.na(x$ui$iniDf$ntheta)]
   ## effect   group   term            estimate std.error statistic
   .df <- data.frame(
     effect = "fixed",
     term = row.names(.df), .df, stringsAsFactors = FALSE
   )
   if (!.ranpar) {
-    .df <- .df[is.na(x$uif$ini$err[!is.na(x$uif$ini$ntheta)]), ]
+    .df <- .df[is.na(x$ui$iniDf$err[!is.na(x$ui$iniDf$ntheta)]), ]
   } else {
-    .tmp <- x$uif$ini$err[!is.na(x$uif$ini$ntheta)]
+    .tmp <- x$ui$iniDf$err[!is.na(x$ui$iniDf$ntheta)]
     .df <- .df[!is.na(.tmp), ]
     .tmp <- .tmp[!is.na(.tmp)]
     .df$group <- paste0("Residual(", .tmp, ")")

R/focei.R

@@ -2346,7 +2346,7 @@ attr(rxUiGet.foceiOptEnv, "desc") <- "Get focei optimization environment"
   assign("est", est, envir=.ret)
   assign("skipCov", .env$skipCov, envir=.ret)
   nmObjHandleModelObject(.ret$model, .ret)
-  nmObjHandleControlObject(.ret$control, .ret)
+  nmObjHandleControlObject(get("control", envir=.ret), .ret)
   if (.control$calcTables) {
     .ret <- addTable(.ret, updateObject="no", keep=.ret$table$keep, drop=.ret$table$drop,
                      table=.ret$table)

R/nmObjHandle.R

@@ -110,6 +110,10 @@ nmObjGetControl.foi <- nmObjGetControl.focei
 #' @export
 nmObjGetControl.fo <- nmObjGetControl.focei
 
+#' @rdname nmObjGetControl
+#' @export
+nmObjGetControl.posthoc <- nmObjGetControl.focei
+
 #' @rdname nmObjGetControl
 #' @export
 nmObjGetControl.saem <- function(x, ...) {

README.Rmd

@@ -66,13 +66,17 @@ We recommend you have a look at [`rxode2`](https://nlmixr2.github.io/rxode2/arti
 
 When on CRAN, you can install the released version of nlmixr from [CRAN](https://CRAN.R-project.org) with:
 
-``` r
+```{r eval=FALSE, echo=TRUE}
 install.packages("nlmixr2")
 ```
 
-And the development version from [GitHub](https://github.com/) with:
+### Installing the Development Version
 
-``` r
-# install.packages("devtools")
+First, install [rxode2](https://github.com/nlmixr2/rxode2#installation).  If not on Windows, you will also need to follow the instructions to install [symengine](https://github.com/symengine/symengine.R#installation).
+
+And then install the development version of nlmixr2 from [GitHub](https://github.com/) with:
+
+```{r eval=FALSE, echo=TRUE}
+if (!requireNamespace("devtools")) install.packages("devtools")
 devtools::install_github("nlmixr2/nlmixr2")
 ```

README.md

@@ -86,9 +86,17 @@ When on CRAN, you can install the released version of nlmixr from
 install.packages("nlmixr2")
 ```
 
-And the development version from [GitHub](https://github.com/) with:
+### Installing the Development Version
+
+First, install [rxode2](https://github.com/nlmixr2/rxode2#installation).
+If not on Windows, you will also need to follow the instructions to
+install
+[symengine](https://github.com/symengine/symengine.R#installation).
+
+And then install the development version of nlmixr2 from
+[GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
+if (!requireNamespace("devtools")) install.packages("devtools")
 devtools::install_github("nlmixr2/nlmixr2")
 ```

build/nsis.R

@@ -210,8 +210,8 @@ DeleteRegKey HKCU \"Software\\R-core\\Rtools\\<%=rtoolsver%>\"
 SectionEnd"
 
 buildInstaller <- function(name="nlmixr"){
-    rtools <- gsub("/", "\\", RxODE:::.rxRtoolsBaseWin(), fixed=TRUE);
-    python <- gsub("/", "\\", RxODE:::.rxPythonBaseWin(), fixed=TRUE);
+    rtools <- gsub("/", "\\", rxode2:::.rxRtoolsBaseWin(), fixed=TRUE);
+    python <- gsub("/", "\\", rxode2:::.rxPythonBaseWin(), fixed=TRUE);
     R <- gsub("/", "\\", Sys.getenv("R_HOME"), fixed=TRUE);
     lic <- gsub("/", "\\", devtools::package_file("LICENSE"), fixed=TRUE);
     readme <- gsub("/", "\\", devtools::package_file("build/installation-notes.rtf"), fixed=TRUE);
@@ -220,7 +220,7 @@ buildInstaller <- function(name="nlmixr"){
     icon <- gsub("/", "\\", devtools::package_file("build/icon_red.ico"), fixed=TRUE)
     rver <- paste(R.version$major,R.version$minor,sep=".");
     ## rtools.curr <- utils::readRegistry("SOFTWARE\\R-core\\Rtools", hive = "HLM", view = "32-bit", maxdepth = 2);
-    full.ver <- gsub("Rtools version ", "", readLines(file.path(RxODE:::.rxRtoolsBaseWin(), "VERSION.txt")))
+    full.ver <- gsub("Rtools version ", "", readLines(file.path(rxode2:::.rxRtoolsBaseWin(), "VERSION.txt")))
     min.rver <- gsub("([0-9]+[.][0-9]+).*", "\\1", full.ver);
     rtools.curr <- min.rver;
     rtools.cur.ver <- rtools.curr

tests/testthat/test-autocovar.R

@@ -1,6 +1,11 @@
 nlmixr2Test(
   {
-    RxODE::.rxWithWd(tempdir(), {
+<<<<<<< HEAD
+    rxode2::.rxWithWd(tempdir(), {
+=======
+    context("autocovar")
+    rxode2::.rxWithWd(tempdir(), {
+>>>>>>> origin/main
 
       # === addCovariate
       testthat::test_that("adding non-categorical covariate to funstring with log-transformation", {

tests/testthat/test-bootstrap.R

@@ -11,6 +11,7 @@ nlmixr2Test(
 
 
     test_that("resuming the fit should not return the same datasets as before", {
+
       one.cmt <- function() {
         ini({
           ## You may label each parameter with a comment
@@ -47,7 +48,7 @@ nlmixr2Test(
       fit2 <- nlmixr2:::bootstrapFit(fit, nboot = 4, restart = FALSE)
 
       output_dir <-
-        paste0("nlmixrBootstrapCache_", "fit", "_", fit$bootstrapMd5)
+        paste0("nlmixr2BootstrapCache_", "fit", "_", fit$bootstrapMd5)
 
       fnameBootDataPattern <- paste0("boot_data",
         "_", "[0-9]+", ".rds",
@@ -73,6 +74,7 @@ nlmixr2Test(
     })
 
     testthat::test_that("different confidence levels should result in different bands", {
+
       one.cmt <- function() {
         ini({
           ## You may label each parameter with a comment
@@ -96,7 +98,7 @@ nlmixr2Test(
         })
       }
 
-      fit <- suppressWarnings(nlmixr(
+      fit <- suppressWarnings(nlmixr2(
         one.cmt,
         samp_dat,
         est = "focei",
@@ -119,6 +121,7 @@ nlmixr2Test(
     })
 
     testthat::test_that("expected columns in fit$parFixedDf object should match", {
+
       one.cmt <- function() {
         ini({
           ## You may label each parameter with a comment
@@ -142,7 +145,7 @@ nlmixr2Test(
         })
       }
 
-      fit <- suppressWarnings(nlmixr(
+      fit <- suppressWarnings(nlmixr2(
         one.cmt,
         samp_dat,
         est = "focei",
@@ -160,7 +163,7 @@ nlmixr2Test(
       testthat::expect_equal(colsAfter, colsBefore)
 
       lapply(
-        list.files("./", pattern = "nlmixrBootstrapCache_.*"),
+        list.files("./", pattern = "nlmixr2BootstrapCache_.*"),
         function(x) {
           unlink(x, recursive = TRUE, force = TRUE)
         }