example fix and more Rdevel data.table fixes

Author: philipdelff

R/NMcheckData.R

@@ -896,10 +896,11 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
 
 ######## End Default columns
 
-
+    
     ## ID-level checks
 ### Warning if the same ID is in non-consequtive rows
-    data[,ID.jump:=c(0,diff(get(rowint))),by=col.id]
+    ##data[,ID.jump:=c(0,diff(get(rowint))),by=col.id]
+    data[,ID.jump:=c(0,diff(.SD[[rowint]])),by=col.id]
     findings <- listEvents("ID.jump",colname=col.id,name="ID disjoint",fun=function(x) x<=1,events=findings,debug=FALSE)
 
 

R/NMgenText.R

@@ -231,8 +231,11 @@ NMgenText <- function(data,
         warning("No columns to use in Nonmem. Did you forget to order or drop columns")
         return(NULL)
     }
+
 
-    dt.num.ok[include==TRUE,occ.cum:=1:.N,by=name.nm]
+    ## dt.num.ok[include==TRUE,occ.cum:=1:.N,by=name.nm]
+    dt.num.ok[,occ.cum:=1:.N,by=name.nm]
+    dt.num.ok[include!=TRUE,occ.cum:=NA_real_]
     if(dt.num.ok[occ.cum>1,.N]>0) {
         warning(paste("Duplicated column name(s) in data for Nonmem:\n",
                       paste0(dt.num.ok[occ.cum>1,unique(name.nm)],collapse=", "),"\n",

R/NMrelateOne.R

@@ -50,7 +50,7 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO
     lines.list <- lines.list[names(lines.list)%in%sections]
     ## lines <- do.call(c,lines.list)
     lines <- unlist(lines.list)
-       
+    
     dt.code <- data.table(line.var = lines[grepl(str.regex.find,lines,ignore.case=TRUE)])
 
     if(is.null(dt.code) || nrow(dt.code)==0) return(NULL)
@@ -73,7 +73,7 @@ NMrelateOne <- function(file,lines,par.type="OMEGA",sections=c("PRED","PK","ERRO
 
 
     dt.code[var.type%in%c("ETA","THETA","ERR","EPS"),
-            i:=as.numeric(sub(paste0(".*",var.type,"\\(([1-9][0-9]*)\\)"),"\\1",x=var.name,ignore.case=TRUE)),
+            i:=as.numeric(sub(paste0(".*",first(var.type),"\\(([1-9][0-9]*)\\)"),"\\1",x=var.name,ignore.case=TRUE)),
             by=lineno]
 
     dt.code[,j:=NA_integer_]

R/lapplydt.R

@@ -20,9 +20,9 @@
 ##' @import data.table
 ##' @examples
 ##' pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata"))
-##' lapplydt(pk,by="DOSE",fun=function(x) {
+##' lapplydt(pk,by="DOSE",fun=function(x,.nm) {
 ##'     message("this is subset",.nm)
-##'     nrow(x) 
+##'     message(paste("Result:",nrow(x)))
 ##' })
 ##' @return a list 
 ##' @export