Merge pull request #175 from nlmixr2/174-omegap-should-be-ignored-at-this-point

ignore omegap records

Author: mattfidler

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

@@ -50,7 +50,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 3
+          cache-version: 4
           pak-version: devel
           extra-packages: |
             any::rcmdcheck

.github/workflows/test-coverage.yaml

@@ -23,7 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
+          cache-version: 3
           pak-version: devel
           extra-packages: |
             any::covr

NEWS.md

@@ -1,5 +1,7 @@
 # nonmem2rx (development version)
 
+* Omega and Sigma prior estimates are currently ignored
+
 * Read all NONMEM files using latin1 encoding to allow single byte
   parser to work
 

R/records.R

@@ -14,11 +14,15 @@
     sub="sub", # $subroutines
     abb="abb", # $abbrevited
     pre="pre", # $pred
-    the="the", # $theta
+    the="the", # $heta
     thetap="thetap", #thetap
     thetapv="thetapv", # thetapv
     ome="ome", # $omega
+    omegap="omegap", #omegap
+    omegapd="omegapd", # omegapd
     sig="sig", # $sigma
+    sigmap="sigmap", #sigmap
+    sigmapd="sigmapd", # sigmapd
     msf="msf", # $msfi
     sim="sim", # $simulation
     est="est", # $estimation
@@ -47,11 +51,15 @@
     sub="$SUBROUTINES", # $subroutines
     abb="$ABBREVITED", # $abbrevited
     pre="$PRED", # $pred
-    the="$THETA", # $theta
+    the="$gTHETA", # $theta
     thetap="$THETAP", # $thetap
     thetapv="$THETAPV", # $thetapv
     ome="$OMEGA", # $omega
+    omegap="$OMEGAP", # $omegap
+    omegapd="$OMEGAPD", # $omegapd
     sig="$SIGMA", # $sigma
+    sigmap="$SIGMAP", # $sigmap
+    sigmapd="$SIGMAPD", # $sigmapd
     msf="$MSFI", # $msfi
     mix="$MIX",
     sim="$SIMULATION", # $simulation
@@ -87,9 +95,9 @@
   .rec <- tolower(rec)
   .ret <- .transRecords[.rec]
   if (is.na(.ret)) {
-    if (.rec == "thetap") {
-      .ret <- .transRecords[.rec]
-    } else if (.rec == "thetapv") {
+    if (.rec %in% c("thetap", "thetapv",
+                    "omegap", "omegapd",
+                    "sigmap", "sigmapd")) {
       .ret <- .transRecords[.rec]
     } else {
       .rec0 <- substr(.rec, 1, 3)

tests/testthat/test-bauer-2019.R

@@ -37,5 +37,13 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
                              })
                            })
 
+  withr::with_options(list(nonmem2rx.save=FALSE, nonmem2rx.load=FALSE, nonmem2rx.overwrite=FALSE,
+                           nonmem2rx.extended=FALSE), {
+                             rx <- nonmem2rx(system.file("mods/bauer_2019_cptpsp_tutorial_2/supp2/504_nuts.ctl",
+                                                         package="nonmem2rx"))
+
+                             expect_true(dim(rx$omega)[1] == 2)
+                           })
+
 
 }