From 786f2f24d360a3ab53dc4ece50c66e813e797024 Mon Sep 17 00:00:00 2001
From: Philip Delff <philip@delff.dk>
Date: Sat, 18 Jan 2025 15:06:45 -0500
Subject: [PATCH] documentation

---
 R/NMcheckData.R                   | 25 +++++++++++++------------
 R/compareCols.R                   |  6 +++---
 man/NMreadInits.Rd                |  9 ++++++++-
 man/NMreadSection.Rd              |  4 ++--
 man/NMwriteData.Rd                |  6 +++---
 tests/testthat/test_compareCols.R | 17 +++++++++++++++++
 6 files changed, 46 insertions(+), 21 deletions(-)

diff --git a/R/NMcheckData.R b/R/NMcheckData.R
index 1edf864e..c10455ec 100644
--- a/R/NMcheckData.R
+++ b/R/NMcheckData.R
@@ -219,30 +219,31 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
     ADDL <- NULL
     AMT <- NULL
     CMT <- NULL
+    column <- NULL
+    check <- NULL
+    checkTimeInc <- NULL
+    cov <- NULL
     ## DV <- NULL
     EVID <- NULL
     ID.jump <- NULL
     ## ID <- NULL
     II <- NULL
+    isnewID <- NULL
+    level <- NULL
     MDVDV <- NULL
     MDV <- NULL
-    N <- NULL
+    newID <- NULL
+    NidByUID <- NULL
+    Nids <- NULL
     Nrep <- NULL
+    Nrows <- NULL
+    NUID <- NULL
+    occ <- NULL
     RATE <- NULL
+    reset <- NULL
     ROW <- NULL
     SS <- NULL
-    column <- NULL
-    check <- NULL
-    checkTimeInc <- NULL
-    cov <- NULL
-    newID <- NULL
-    isnewID <- NULL
-    level <- NULL
-    occ <- NULL
-    reset <- NULL
     variable <- NULL
-    NUID <- NULL
-    NidByUID <- NULL
     usubjNotUnique <- NULL
     
 ### Section end: Dummy variables, only not to get NOTE's in pacakge checks
diff --git a/R/compareCols.R b/R/compareCols.R
index 12f1eabd..374e2702 100644
--- a/R/compareCols.R
+++ b/R/compareCols.R
@@ -183,7 +183,7 @@ compareCols <- function(...,list.data,keep.names=TRUE,test.equal=FALSE,diff.only
 
             res.dims <- dims(list.data=dots)
             message("Dimensions:")
-            print(as.fun(res.dims))
+            message(print(as.fun(res.dims)))
         }
 
         if(nrow(dt.cols)==0&&ndots==1){
@@ -193,12 +193,12 @@ compareCols <- function(...,list.data,keep.names=TRUE,test.equal=FALSE,diff.only
         } else {
             if(diff.only){
                 message("\nColumns that differ:")
-                print(as.fun(dt.cols))
+                message(print(as.fun(dt.cols)))
                 message()
                 messageWrap(paste0("\nColumns where no differences were found: ",paste(dt.cols.full[nu==1&n==ndots,column],collapse=", "),"."),fun.msg=message)
             } else {
                 message("\nOverview of all columns:")
-                print(as.fun(dt.cols))
+                message(print(as.fun(dt.cols)))
             }
         }
         return(invisible(as.fun(dt.cols)))
diff --git a/man/NMreadInits.Rd b/man/NMreadInits.Rd
index 9f2fdc09..e2eb47c1 100644
--- a/man/NMreadInits.Rd
+++ b/man/NMreadInits.Rd
@@ -16,7 +16,14 @@ or "sigma". Default is those three.}
 
 \item{as.fun}{See ?NMscanData}
 }
+\value{
+By default (when \code{return="pars"}, a parameter table
+    with initial values, FIX, lower and upper bounds etc. In most
+    cases, that is what is needed to derive information about
+    parameter definitions. If \code{return="all"}, two additional
+    tables are returned which can be used if the aim is to modify
+    and write the resulting parameters to a control stream.
+}
 \description{
 Tabulate information from parameter sections in control streams
 }
-\keyword{internal}
diff --git a/man/NMreadSection.Rd b/man/NMreadSection.Rd
index 8ff211cb..be38cc48 100644
--- a/man/NMreadSection.Rd
+++ b/man/NMreadSection.Rd
@@ -94,9 +94,9 @@ suitable for the results part too.
 }
 \section{Functions}{
 \itemize{
-\item \code{NMgetSection}: Deprecated function name. Use NMreadSection.
-}}
+\item \code{NMgetSection()}: Deprecated function name. Use NMreadSection.
 
+}}
 \examples{
 NMreadSection(system.file("examples/nonmem/xgxr001.lst", package="NMdata"),section="DATA")
 
diff --git a/man/NMwriteData.Rd b/man/NMwriteData.Rd
index 742ed98d..906d4d81 100644
--- a/man/NMwriteData.Rd
+++ b/man/NMwriteData.Rd
@@ -17,7 +17,7 @@ NMwriteData(
   quiet,
   args.NMgenText,
   csv.trunc.as.nm = FALSE,
-  genText = TRUE,
+  genText,
   save = TRUE,
   write.csv,
   write.rds,
@@ -88,8 +88,8 @@ columns of non-numeric class like character and factor for
 post-processing.}
 
 \item{genText}{Run and report results of NMgenText? Default is
-TRUE. You may want to disable this if data set is not for
-Nonmem.}
+`TRUE` if a csv file is written, otherwise `FALSE`. You may
+want to disable this if data set is not for Nonmem.}
 
 \item{save}{Save defined files? Default is TRUE. If a variable is
 used to control whether a script generates outputs (say
diff --git a/tests/testthat/test_compareCols.R b/tests/testthat/test_compareCols.R
index 4adc20bd..ac1c2ca9 100644
--- a/tests/testthat/test_compareCols.R
+++ b/tests/testthat/test_compareCols.R
@@ -120,3 +120,20 @@ test_that("list.data",{
     expect_equal(res1,res2)
 
 })
+
+test_that("basic - not quiet",{
+
+    fileRef <- "testReference/compareCols_06.rds"
+
+    pk <- readRDS(file=system.file("examples/data/xgxr2.rds",package="NMdata"))
+
+    pk.reduced <- pk[1:(.N%/%2)]
+    pk.reduced[,CYCLE:=NULL]
+    pk.reduced[,AMT:=as.character(AMT)]
+
+
+    suppressMessages(res1 <- compareCols(pk,pk.reduced,quiet=FALSE))
+
+    expect_equal_to_reference(res1,fileRef)
+
+})