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NMautoverse · Oct 30, 2024 · d39b364 · d39b364
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.7.911
+Version: 0.1.7.912
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

diff --git a/R/NMreadParsText.R b/R/NMreadParsText.R
@@ -42,6 +42,7 @@
 ##' @param fields Deprecated. Use `format`.
 ##' @param fields.omega Deprecated. Use `format.omega`.
 ##' @param fields.sigma Deprecated. Use `format.sigma`.
+##' @return data.frame with parameter names and fields read from comments
 ##' @details Off-diagonal omega and sigma elements will only be
 ##'     correctly treated if their num field specifies say 1-2 to
 ##'     specify it is covariance between 1 and 2.

diff --git a/R/NMrelate.R b/R/NMrelate.R
@@ -23,6 +23,7 @@
 ##'     gain information but only extracts what it can from the model
 ##'     code. You can then merge with information from functions such
 ##'     as `NMreadExt()` and `NMreadParText()`.
+##' @return data.frame relating parameters to variable names
 ##' @export
 
 NMrelate <- function(file,lines,modelname,par.type,col.model,sections,as.fun){

diff --git a/R/colLabels.R b/R/colLabels.R
@@ -1,5 +1,6 @@
 ##' Extract column labels as defined in SAS
 ##' @param ... See `?compareCols`
+##' @return A data.frame with variable and their labels
 ##' @seealso compareCols NMinfo 
 ##' @export 
 

diff --git a/R/editCharCols.R b/R/editCharCols.R
@@ -17,6 +17,7 @@
 ##' @param ... Additional arguments passed to `gsub()`. Especially,
 ##'     notice fixed=TRUE will disable interpretation of `pattern` and
 ##'     `replace` as regular expressions.
+##' @return a data.frame
 ##' @examples
 ##' ### remove commas from character columns 
 ##' dat <- data.frame(A=1:3,text=cc(a,"a,d","g"))

diff --git a/R/uniquePresent.R b/R/uniquePresent.R
@@ -12,7 +12,8 @@
 ##'     variables. \code{uniquePresent} with `req.n1=TRUE` makes sure the
 ##'     result is a single unique value (e.g., within subjects). A
 ##'     typical use is carrying subject-level covariates from one data
-##'     set to another in a longitudinal analysis. 
+##'     set to another in a longitudinal analysis.
+##' @param a vector of same class as `x`
 ##' @export
 uniquePresent <- function(x,req.n1=TRUE,na.pattern){
     if(missing(na.pattern)) na.pattern <- "^ *$"

diff --git a/README.Rmd b/README.Rmd
@@ -153,15 +153,16 @@ explicitly select CRAN for the installation. Or if you should want a
 version that has not yet reached CRAN, installing from Github is easy
 too. 
 
-```
+```{r,eval=FALSE}
+## Option 1: Install from your default repository
+install.packages("NMdata")
+
 ## Option 2: Install explicitly from CRAN
 install.packages("NMdata",repos="https://cloud.r-project.org")
-library(NMdata)
 
 ## Option 3: Install from github
 library(remotes)
 install_github("nmautoverse/NMdata")
-library(NMdata)
 ```
 If you use the Github version, you may want to see the
 [FAQ](https://nmautoverse.github.io/NMdata/articles/NMdata-FAQ.html)

diff --git a/README.md b/README.md
@@ -185,14 +185,17 @@ that case you have two other options. You can explicitly select CRAN for
 the installation. Or if you should want a version that has not yet
 reached CRAN, installing from Github is easy too.
 
-    ## Option 2: Install explicitly from CRAN
-    install.packages("NMdata",repos="https://cloud.r-project.org")
-    library(NMdata)
-
-    ## Option 3: Install from github
-    library(remotes)
-    install_github("nmautoverse/NMdata")
-    library(NMdata)
+``` r
+## Option 1: Install from your default repository
+install.packages("NMdata")
+
+## Option 2: Install explicitly from CRAN
+install.packages("NMdata",repos="https://cloud.r-project.org")
+
+## Option 3: Install from github
+library(remotes)
+install_github("nmautoverse/NMdata")
+```
 
 If you use the Github version, you may want to see the
 [FAQ](https://nmautoverse.github.io/NMdata/articles/NMdata-FAQ.html) for

diff --git a/devel/scripts/dsCreate_1.R b/devel/scripts/dsCreate_1.R
@@ -316,7 +316,11 @@ NMwriteSection(file.nm("xgxr001dir/input.txt"),section="DATA",newlines=sec.data.
 ### xgxgr002: CYCLE=DROP, BBW for WEIGHTB
 pk2 <- copy(pk)
 pk2[,AMT:=AMT*1000]
-nmcode <- NMwriteData(pk2,file=file.data.test("xgxr12.csv"),script=script.1,args.stamp = list(description="AMT in micrograms"))
+nmcode <- NMwriteData(pk2,
+                      file=file.data.test("xgxr12.csv"),
+                      script=script.1,
+                      args.stamp = list(description="AMT in micrograms"),
+                      args.rds=list(version=2))
 
 
 ### Section end: Version with AMT in microgram

diff --git a/man/NMreadParsText.Rd b/man/NMreadParsText.Rd
diff --git a/man/NMrelate.Rd b/man/NMrelate.Rd
diff --git a/man/colLabels.Rd b/man/colLabels.Rd
diff --git a/man/editCharCols.Rd b/man/editCharCols.Rd
diff --git a/man/uniquePresent.Rd b/man/uniquePresent.Rd
diff --git a/tests/testthat/test_NMdataConf.R b/tests/testthat/test_NMdataConf.R
@@ -159,6 +159,7 @@ test_that("use.rds - deprecated",{
     NMdataConf(reset=TRUE)
     NMdataConf(use.rds=F)
     res <- NMdataConf()
+    res <- dropFuns(res)
 
     expect_equal_to_reference(res,fileRef)