NMreadSection handling of OMEGA, OMEGAP etc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.6.923
+Version: 0.1.6.931
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

R/NMextractText.R

@@ -104,9 +104,10 @@ NMextractText <- function(file, lines, text, section, char.section,
         type <- "all"
     }
     if(type=="lst") type <- "res"
-
-    if(!match.exactly){
-        section <- substring(section,1,3)
+
+
+    if(!match.exactly && section!="."){
+        section <- paste0(substring(section,1,min(nchar(section),3)),"[A-Z]*")
     }
 
 
@@ -136,7 +137,7 @@ NMextractText <- function(file, lines, text, section, char.section,
                     )
 
     ## Find all the lines that start with the $section
-    idx.starts <- grep(paste0("^ *",char.section,section),lines)
+    idx.starts <- grep(paste0("^ *",char.section,section," *"),lines)
     idx.ends <- grep(paste0("^ *",char.end),lines)
 
     ## get the sections

R/NMreadExt.R

@@ -78,25 +78,29 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m
 
 #### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####
 
+    . <- NULL
+    blocksize <- NULL
+    cond <- NULL
+    eigCor <- NULL
+    est <- NULL
+    FIX <- NULL
+    i <- NULL
+    iblock <- NULL
+    imin <- NULL
+    j <- NULL
     ITERATION <- NULL
-    variable <- NULL
     NMREP <- NULL
     model <- NULL
     par.type <- NULL
     parameter <- NULL
-    i <- NULL
-    j <- NULL
     TABLENO <- NULL
     table.step <- NULL
-    FIX <- NULL
-    est <- NULL
-    cond <- NULL
-    eigCor <- NULL
     partLik <- NULL
     se <- NULL
     seStdDevCor <- NULL
     stdDevCor <- NULL
     value <- NULL
+    variable <- NULL    
 
 ### Section end: Dummy variables, only not to get NOTE's in pacakge checks
 

R/NMreadSection.R

@@ -40,7 +40,6 @@
 ##' @param keepEmpty Deprecated. See keep.empty.
 ##' @param keepName Deprecated. See keep.name.
 ##' @param asOne Deprecated. See as.one.
-##' @param cleanSpaces Deprecated. See clean.spaces.
 ##' @return character vector with extracted lines.
 ##' @param ... Additional arguments passed to NMextractText
 ##' @return character vector with extracted lines.
@@ -57,12 +56,13 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex
                           ## deprecated arguments
                           keepEmpty, keepName,
                           keepComments, asOne,
-                          cleanSpaces, ...){
+                          ...){
 
     ## args <- getArgs()
     args <- getArgs(sys.call(),parent.frame())
     as.one <- deprecatedArg("asOne","as.one",args=args)
-    clean.spaces <- deprecatedArg("cleanSpaces","clean.spaces",args=args)
+    ## clean.spaces <- deprecatedArg("cleanSpaces","clean.spaces",args=args)
+    ## if(!missing(cleanSpaces)) rm(cleanSpaces)
     keep.empty <- deprecatedArg("keepEmpty","keep.empty",args=args)
     keep.name <- deprecatedArg("keepName","keep.name",args=args)
     keep.comments <- deprecatedArg("keepComments","keep.comments",args=args)
@@ -78,6 +78,13 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex
         section <- toupper(section)
     }
 
+    match.exactly <- FALSE
+    if(section!="."){
+
+        string.start <- substring(sub("^\\$","",cleanSpaces(section)),1,3)
+        match.exactly <- !string.start%in%c("COV","EST","SIM")
+    }
+
     res <- NMextractText(file=file, lines=lines, text=text, section=section,
                          ## this wrapper is especially made for "$" sections
                          char.section="\\$",
@@ -90,7 +97,8 @@ NMreadSection <- function(file=NULL, lines=NULL, text=NULL, section, return="tex
                          clean.spaces=clean.spaces,
                          ## we only consider the model definition, not results.
                          type="mod",
-                         match.exactly=FALSE,
+                         ## match.exactly=FALSE,
+                         match.exactly=match.exactly,
                          ## deprecated args
                          ## keepEmpty=keepEmpty,
                          ## keepName=keepName,

R/NMrelateOne.R

@@ -44,7 +44,7 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO
                        ,SIGMA="(SIGMA|ERR|EPS)"
                         )
     str.regex.find <- paste0("[^[:alnum:]]",str.regex)
-
+    
 
     lines.list <- NMreadSection(lines=lines,keep.comments=FALSE)
     lines.list <- lines.list[names(lines.list)%in%sections]
@@ -65,7 +65,11 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO
 
     ## determine found variable type?
 
-    dt.code <- dt.code[,.(varname=regmatches(line2, gregexpr(paste0(str.regex.find,"\\(([0-9]+(,[0-9]+)*)\\)"),line2)) |> unlist()),by=.(line.var,line2)]
+    dt.code <- dt.code[,.(varname=unlist(
+                              regmatches(line2,
+                                         gregexpr(paste0(str.regex.find,"\\(([0-9]+(,[0-9]+)*)\\)"),line2))
+                          )),
+                       by=.(line.var,line2)]
     dt.code[,varname:=sub("^[^[:alnum:]]","",varname)]
     dt.code[,var.type:=sub(sprintf("(%s).*",str.regex),"\\1",varname)][,lineno:=.I]
 

R/NMscanInput.R

@@ -101,6 +101,7 @@ NMscanInput <- function(file, formats.read, file.mod, dir.data=NULL,
 #### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####
 
     datafile <- NULL
+    info <- NULL
     nid <- NULL
     input <- NULL
     result <- NULL
@@ -167,8 +168,12 @@ NMscanInput <- function(file, formats.read, file.mod, dir.data=NULL,
             break
         }
     }
-    if(is.null(type.file)) stop("None of the allowed file formats found.")
-    path.data.input <- info.datafile[[paste0("path.",type.file)]]
+    if(is.null(type.file)){
+        message(paste0("$DATA section extracted\n",info$datafile$DATA))
+        message("Based on that, data files related to this file were expected:\n",info$datafile$string)
+        stop("None of the allowed file formats found.")
+    }
+        path.data.input <- info.datafile[[paste0("path.",type.file)]]
 
     data.input <- NMreadCsv(path.data.input,as.fun="data.table",args.fread=args.fread,args.fst=args.fst,format=type.file)
 

R/NMwriteSectionOne.R

@@ -63,7 +63,7 @@ NMwriteSectionOne <- function(file0,lines,section,location="replace",
                                     keep.name=TRUE,keep.comments=TRUE,as.one=TRUE,
                                     clean.spaces=FALSE)
 
-        if(length(idx.dlines)==0&location%in%cc(replace,before,after)) {
+        if(length(idx.dlines)==0 && location%in%cc(replace,before,after)) {
             if(!quiet) message("Section not found. Nothing to be done.")
             return(lines)
         }