From f1590d359914d8105ba15fe2ae110878d95f4a58 Mon Sep 17 00:00:00 2001
From: Philip Delff <philip@delff.dk>
Date: Thu, 12 Oct 2023 10:26:24 -0400
Subject: [PATCH] NMreadExt introduced

---
 NEWS.md        | 5 +++++
 R/NMscanData.R | 1 +
 R/addTAPD.R    | 6 ------
 devel/todo.org | 3 +++
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 1ca87e3d..afcfc12c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,9 @@
 # 0.1.2
+## New features
+* NMreadExt is a new function that reads parameter estimates,
+  uncertainties if available, estimation iterations and other
+  information from .ext files. 
+
 ## Other improvements
 * NMreadCsv supports multiple prioritized formats in the `format`
   arguments.
diff --git a/R/NMscanData.R b/R/NMscanData.R
index 511a891a..f952508a 100644
--- a/R/NMscanData.R
+++ b/R/NMscanData.R
@@ -218,6 +218,7 @@ NMscanData <- function(file, col.row, use.input, merge.by.row,
     if(missing(check.time)) check.time <- NULL
     if(missing(tz.lst)) tz.lst <- NULL
     if(missing(as.fun)) as.fun <- NULL
+    ### why is this not needed?
     ## if(missing(modelname)) modelname <- NULL
     if(missing(quiet)) quiet <- NULL
     if(missing(formats.read)) formats.read <- NULL
diff --git a/R/addTAPD.R b/R/addTAPD.R
index d382fdc1..a8bf7bcb 100644
--- a/R/addTAPD.R
+++ b/R/addTAPD.R
@@ -85,12 +85,6 @@ addTAPD <- function(data,col.time="TIME",col.evid="EVID",col.amt="AMT",col.tpdos
     
 ### Section end: Dummy variables, only not to get NOTE's in pacakge checks
 
-    ## if(!missing(col.ndoses)){
-    ##     if(col.doscumn!="DOSCUMN"){
-    ##         stop("col.ndoses is deprecated. Use col.doscumn instead.")
-    ##     }
-    ##     warning("col.ndoses is deprecated. Use col.doscumn instead.")
-    ## }
     args <- getArgs()
     deprecatedArg("col.ndoses","col.doscumn",args=args)
     
diff --git a/devel/todo.org b/devel/todo.org
index abc719e9..98d77190 100644
--- a/devel/todo.org
+++ b/devel/todo.org
@@ -79,6 +79,7 @@ if(any(nmdat[,sapply(.SD,function(x)any(grepl(",",x))),.SDcols=cnames.fac])) sto
     Export to parent. Not sure check allows though...
 ** Function improvements
 *** addTAPD
+**** TODO [#A] Add subset.data arg like in flags functions
 **** DONE Rename NDOSES to DOSCUMN
 It aligns with DOSCUMA and it is clearer from DOSCUMN that its
 cumulative number of doses.
@@ -119,6 +120,8 @@ pdosamt, doscuma
 **** Bad name, what could we call it?
 *** cc - create character vector function
 *** NMgenText
+**** TODO Test variables given in until arg exist
+Or only use those that do exist. Right now a strange error is returned
 **** TODO Handle until values not matching column names
 **** DONE Add a until argument to specify the last column to use in nonmem
 **** TODO [#B] checks: duplicate column names