Merge pull request #189 from nlmixr2/188-abbrev-err

Fix the Replace grammar to accept ETA(#) on rhs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nonmem2rx
 Type: Package
 Title: Converts 'NONMEM' Models to 'rxode2'
-Version: 0.1.5
+Version: 0.1.5.9000
 Maintainer: Matthew Fidler <[email protected]>
 Authors@R: c(person("Matthew","Fidler", role = c("aut", "cre"), email = "[email protected]", comment=c(ORCID="0000-0001-8538-6691")),
     person("Philip", "Delff", email = "[email protected]",role = c("ctb")),

NEWS.md

@@ -1,3 +1,9 @@
+# nonmem2rx (development version)
+
+* Add more flexible replacement of ETA and other values #188
+
+* Add ability to use `nonmem2rx` with a NONMEM control stream text input
+
 # nonmem2rx 0.1.5
 
 * Be more forgiving in the validation and remove IDs without

R/nonmem2rx.R

@@ -587,6 +587,12 @@ nonmem2rx <- function(file, inputData=NULL, nonmemOutputDir=NULL,
                       load=getOption("nonmem2rx.load", TRUE),
                       compress=getOption("nonmem2rx.compress", TRUE),
                       keep=getOption("nonmem2rx.keep", c("dfSub", "dfObs", "thetaMat", "sigma"))) {
+  if (any(grepl("[$][Pp][Rr][Oo][Bb][Ll][Ee][Mm]", file))) {
+    .file <- tempfile(fileext=".ctl")
+    writeLines(gsub("[ \t]+[$]", "$", file), .file)
+    file <- .file
+    on.exit(unlink(.file))
+  }
   .pt <- proc.time()
   .ret <- .collectWarn({
     checkmate::assertFileExists(file)

inst/abbrec.g

@@ -46,7 +46,7 @@ seq_nm: decimalint (':' | 'TO' | 'to' | 'To') decimalint
 seq_arg: '(' ','* (seq_nm | decimalint)  (',' (seq_nm | decimalint))* ')';
 
 replace_direct1: var_replace '(' identifier_nm ')' '=' var_replace '(' decimalintNo0 ')';
-replace_direct2: identifier_nm '=' (identifier_nm | constantneg);
+replace_direct2: identifier_nm '=' (identifier_nm | constantneg | var_replace '(' decimalintNo0 ')');
 replace_direct3: identifier_nm '=' string;
 
 replace_data: var_rep2 '(' identifier_nm ')' '=' var_rep2 (seq_arg | dec_arg);
@@ -70,4 +70,3 @@ decimalintNo0: "([1-9][0-9]*)" $term -1;
 decimalint: "0|([1-9][0-9]*)" $term -1;
 float1: "([0-9]+.[0-9]*|[0-9]*.[0-9]+)([eE][\-\+]?[0-9]+)?" $term -2;
 float2: "[0-9]+[eE][\-\+]?[0-9]+" $term -3;
-