NMreadExt reports only last table by default

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.3.911
+Version: 0.1.3.912
 Authors@R: c(person("Philip", "Delff", email = "philip@delff.dk", role = c("aut", "cre")))
 Maintainer: Philip Delff <philip@delff.dk>
 Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.

NEWS.md

@@ -23,6 +23,10 @@ tables.
   options or function arguments but it will now work either way. An
   error will be thrown if both should be found.
 
+* `NMreadExt` will by default only return parameters and iterations
+  from the last table available. This can be controlled by the
+  `tableno` argument.
+
 * `fnAppend` will now throw an error in case the file name extension
   cannot be identified.
 

R/NMreadExt.R

@@ -13,6 +13,21 @@
 ##'     something else. If data.tables are wanted, use
 ##'     as.fun="data.table". The default can be configured using
 ##'     NMdataConf.
+##' @param tableno In case the ext file contains multiple tables, this argument controls which one to choose. The options are
+##' \itemize{
+##' 
+##' \item "max" (default) Pick the table with the highest table
+##' number. This typically means the results from the last
+##' `$ESTIMATION` step are used.
+##' 
+##' \item "min" Pick results from the first table available.
+##'
+##' \item "all" Keep all results. The tables can be distinguished by
+##' the `tableno` column.
+##'
+##' \item an integer greater than 0, in which case the table with this
+##' table number will be picked.
+##' }
 ##' @param modelname See ?NMscanData
 ##' @param col.model See ?NMscanData
 ##' @param auto.ext If TRUE (default) the extension will automatically
@@ -25,7 +40,7 @@
 ##' @import data.table
 ##' @export
 
-NMreadExt <- function(file,return="pars",as.fun,modelname,col.model,auto.ext,file.ext){
+NMreadExt <- function(file,return="pars",as.fun,modelname,col.model,auto.ext,tableno="max",file.ext){
 
 #### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####
 
@@ -50,6 +65,13 @@ NMreadExt <- function(file,return="pars",as.fun,modelname,col.model,auto.ext,fil
     modelname <- NMdataDecideOption("modelname",modelname)
     if(missing(auto.ext) || is.null(auto.ext)) auto.ext <- TRUE
 
+    if(is.null(tableno)) tableno <- "max"
+
+    if(! (is.character(tableno)&&tableno%in%c("min","max","all") ) ||
+       (is.numeric(tableno) && tableno>0 && tableno%%1==0) ){
+        stop("tableno must be either one of the character strings min, max, all or an integer greater than zero.")
+    }
+
     args <- getArgs()
     if(missing(file.ext)) file.ext <- NULL
     file <- deprecatedArg("file.ext","file",args=args)
@@ -84,6 +106,19 @@ NMreadExt <- function(file,return="pars",as.fun,modelname,col.model,auto.ext,fil
         this.model <- modelname(file)
         NMreadTab(file,as.fun="data.table",quiet=TRUE,col.table.name=TRUE)[,(col.model):=this.model]
     })
+
+    if(tableno=="min"){
+        res.NMdat <- lapply(res.NMdat,function(x)x[TABLENO==min(TABLENO)])
+    }
+    if(tableno=="max"){
+        res.NMdat <- lapply(res.NMdat,function(x)x[TABLENO==max(TABLENO)])
+    }
+    if(is.numeric(tableno)){
+        res.NMdat <- lapply(res.NMdat,function(x)x[TABLENO==tableno])
+    }
+
+
+
     res.NMdat <- rbindlist(res.NMdat,fill=TRUE)
 
     ## NONMEM USERS GUIDE

_pkgdown.yml

@@ -63,6 +63,7 @@ reference:
   - NMstamp
   - NMwriteSection
   - NMreplaceDataFile
+  - colLabels
 - title: Retrieve NONMEM data
   desc: Functions for retrieving NONMEM input and output data
   contents:
@@ -75,6 +76,7 @@ reference:
   - NMreadExt
   - NMreadPhi
   - NMreadTab
+  - NMreadParsText
   - NMinfo
 - title: Checking and Debugging
   desc: Functions for checking data and input control streams