support for data file names containing IGN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.7
+Version: 0.1.7.901
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

NEWS.md

@@ -1,3 +1,11 @@
+# NMdata 0.1.8
+
+## Bugfixes
+
+Support for data file names including substrings "ACCEPT" and "IGN" is
+added. Before, such data set file names could lead to failure if
+interpreting data subsetting filters (ACCEPT and IGN(ORE)) in Nonmem
+control streams. 
 
 # NMdata 0.1.7
 
@@ -104,7 +112,7 @@ of throwing an error.
 * Function `NMreadShk()` to read and format `.shk` (shrinkage) files.
 
 * Functions `mat2dt()` and `dt2mat()` included to convert between
-  matrices and data.frame format of matrix data - especially for
+  matrices and `data.frame` format of matrix data - especially for
   symmetric matrices.
 
 * Function `addOmegaCorr()` adds estimated correlation between ETAs to

R/NMapplyFilters.R

@@ -31,7 +31,7 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
     value <- NULL
 
 ### Section end: Dummy variables, only not to get NOTE's in pacakge checks
-
+    
 
     if(missing(quiet)) quiet <- NULL
     quiet <- NMdataDecideOption("quiet",quiet)
@@ -71,11 +71,19 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
     ## simplifying so IGNORE/IGN is always IGN
     text3 <- gsub("IGNORE","IGN",text3)
 
-    conds.sc <- regmatches(text3, gregexpr("(?:IGN) *=* *[^ (+=]",text3))
+
+    ## ^(.* )* : if anything before IGN, there must be a space in between
+    ## conds.sc <- regmatches(text3, gregexpr("^(.* )*(?:IGN) *=* *[^ (+=]",text3))
+    conds.sc <- regmatches(text3, gregexpr("(?<![[:alnum:]])IGN *=* *[^ (+=]",text3,perl=T))
+    conds.sc
     conds.sc <- do.call(c,conds.sc)
 ### getting rid of single char conditions
-    text3 <- gsub(paste0("IGN"," *=* *[^ (+=]"),"",text3)
-
+
+    ## text3 <- gsub(paste0("^(\\(.* \\)*)IGN"," *=* *[^ (+=]"),"\\1",text3)
+    ## gsub("^((.* )*)IGN *=* *[^ (+=](.*)","\\1\\2",text3)
+    ## gsub("((.* )*)IGN *=* *[^ (+=](.*)","\\1\\2",text3)
+    text3 <- gsub("(?<![[:alnum:]])IGN *=* *[^ (+=]","",perl=TRUE,text3)
+
     ## check if IGNORE or ACCEPT are found. If both found, it is an error. 
     any.accepts <- any(grepl("ACCEPT",text3))
     any.ignores <- any(grepl("IGN",text3))
@@ -89,7 +97,7 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
         type.condition <- "ACCEPT"
     }
 
-
+    
 ### expression-style ones
     ## this is not entirely correct.
 ### 1. A comma-separated list of expressions can be inside the ()s.
@@ -101,6 +109,7 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
 
 
 
+
     ## translating single-charaters
     name.c1 <- colnames(data)[1]
     scs <- sub(paste0("IGN"," *=* *(.+)"),"\\1",conds.sc)
@@ -165,8 +174,11 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
 
     cond.combine <- "|"
     ## remember to negate everything if the type is ignore
+
     if(type.condition=="IGN") {
-        expressions.list <- paste0("!",expressions.list)
+        if(length(expressions.list)){
+            expressions.list <- paste0("!",expressions.list)
+        }
         cond.combine <- "&"
     }
 
@@ -175,11 +187,13 @@ NMapplyFilters <- function(data,file,text,lines,invert=FALSE,as.fun,quiet) {
     } else {
         conditions.all.sc <- "TRUE"
     }
+
 
     expressions.all <- NULL
     if(length(expressions.list)) {
         expressions.all <- paste0("(",paste(expressions.list,collapse=cond.combine),")")
     }
+
 
     if(invert) {