Fix pkTrans()

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

@@ -53,7 +53,11 @@ jobs:
           pak-version: devel
           extra-packages: |
             any::rcmdcheck
+            nlmixr2/dparser-R
+            nlmixr2/lbfgsb3c
             nlmixr2/lotri
+            nlmixr2/PreciseSums
+            nlmixr2/n1qn1c
             nlmixr2/rxode2ll
             nlmixr2/rxode2
             nlmixr2/nlmixr2est

.github/workflows/pkgdown.yaml

@@ -34,7 +34,11 @@ jobs:
           pak-version: devel
           extra-packages: |
             any::pkgdown
+            nlmixr2/dparser-R
+            nlmixr2/lbfgsb3c
             nlmixr2/lotri
+            nlmixr2/PreciseSums
+            nlmixr2/n1qn1c
             nlmixr2/rxode2ll
             nlmixr2/rxode2
             nlmixr2/nlmixr2est

.github/workflows/test-coverage.yaml

@@ -27,7 +27,11 @@ jobs:
           pak-version: devel
           extra-packages: |
             any::covr
+            nlmixr2/dparser-R
+            nlmixr2/lbfgsb3c
             nlmixr2/lotri
+            nlmixr2/PreciseSums
+            nlmixr2/n1qn1c
             nlmixr2/rxode2ll
             nlmixr2/rxode2
             nlmixr2/nlmixr2est

R/modeldb.R

@@ -123,16 +123,18 @@ addFileToModelDb <- function(dir, file, modeldb) {
   dosing <- NULL
   dosing_meta <- mod$meta$dosing
   if(!is.null(dosing_meta)){
-    dosing = paste(dosing_meta, collapse=",")
+    dosing <- paste(dosing_meta, collapse=",")
   }else {
-    if("depot" %in% mod$params$cmt){
-      dosing = c(dosing, "depot") }
-    if("central" %in% mod$params$cmt){
-      dosing = c(dosing, "central") }
-    if(!is.null(dosing)){
-      dosing = paste(dosing, collapse=",")
+    if("depot" %in% mod$props$cmt) {
+      dosing <- c(dosing, "depot")
+    }
+    if("central" %in% mod$props$cmt) {
+      dosing <- c(dosing, "central")
+    }
+    if(!is.null(dosing)) {
+      dosing <- paste(dosing, collapse=",")
     } else {
-      dosing = NA_character_ 
+      dosing <- NA_character_
     }
   }
 
@@ -143,7 +145,7 @@ addFileToModelDb <- function(dir, file, modeldb) {
     depends = paste(depends_meta, collapse=",")
   }
   if(is.null(depends)){
-    depends = NA_character_ 
+    depends = NA_character_
   }
 
   # Extract the parameter names
@@ -166,22 +168,22 @@ addFileToModelDb <- function(dir, file, modeldb) {
   if (is.null(paramErr)) {
     paramErr <- ""
   }
-  
-  
-  if(!mod$params$linCmt && (length(mod$params$cmt)  == 0)){
+
+
+  if(!mod$props$linCmt && (length(mod$props$cmt)  == 0)){
     algebraic = TRUE
   } else {
     algebraic = FALSE
   }
-   
+
 
   ret <-
     data.frame(
       name        = modelName,
       description = description,
       parameters  = paste(modParamFixed, collapse = ","),
       DV          = paramErr,
-      linCmt      = mod$params$linCmt,
+      linCmt      = mod$props$linCmt,
       algebraic   = algebraic,
       dosing      = dosing,
       depends     = depends,

R/transPk.R

@@ -160,6 +160,7 @@ addLogEstimates <- function(ui, vars,
       .tmp$pre,
       .extra,
       extraLines,
+      .tmp$w,
       .tmp$post
     )
   }

tests/testthat/test-transPk.R

@@ -4,6 +4,10 @@ test_that("transPk -- k", {
     pkTrans("k")
   expect_true(all(c("lkel", "lk12", "lk21", "lk13", "lk31") %in% names(p3k$theta)))
 
+  # Issue #87 -- Make sure depot is not dropped
+  expect_equal(rxode2::modelExtract(p3k, "d/dt(depot)"),
+               "d/dt(depot) <- -ka * depot")
+
   p2k <- readModelDb("PK_2cmt_des") |>
     pkTrans("k")
   expect_true(all(c("lkel", "lk12", "lk21") %in% names(p2k$theta)))