fixing curly braces

R/NMcheckData.R

@@ -110,7 +110,7 @@
 ##'
 ##' \item col.time (TIME) must be non-negative
 ##'
-##' \item EVID must be in {0,1,2,3,4}.
+##' \item EVID must be in \{0,1,2,3,4\}.
 ##'
 ##' \item CMT must be positive integers. However, can be missing or zero for EVID==3.
 ##'
@@ -123,7 +123,7 @@
 ##'
 ##' \item DV must be numeric
 ##'
-##' \item DV must be missing for EVID in {1,4}.
+##' \item DV must be missing for EVID in \{1,4\}.
 ##'
 ##' \item If found, RATE must be a numeric, equaling -2 or non-negative for dosing events.
 ##'
@@ -141,9 +141,9 @@
 ##'     error. Use a second ID column if you deliberately want to
 ##'     soften this check)
 ##'
-##' \item TIME cannot be decreasing within ID, unless EVID in {3,4}.
+##' \item TIME cannot be decreasing within ID, unless EVID in \{3,4\}.
 ##'
-##' \item all ID's must have doses (EVID in {1,4})
+##' \item all ID's must have doses (EVID in \{1,4\})
 ##'
 ##' \item all ID's must have observations (EVID==0)
 ##'

R/NMorderColumns.R

@@ -56,7 +56,7 @@
 ##'     following steps, each step depending on corresponding
 ##'     argument.
 ##'
-##' \itemize{
+##' \describe{
 ##'  \item{"col.row - "}{Row id if argument row is non-NULL}
 ##'  \item{"not editable - "}{ID (if a column is called ID)}
 ##'  \item{"col.nomtime - "}{Nominal time.}

R/NMreadCsv.R

@@ -21,7 +21,7 @@
 ##'     format is used, the extension can very well be different from
 ##'     "csv" (say file name is
 ##'     "input.tab")". This will work for any delimited format supported by fread.
-##' @param args.fst Optional arguments to pass to \code{read_fst} if code{format="fst"} is used.
+##' @param args.fst Optional arguments to pass to \code{read_fst} if \code{format="fst"} is used.
 ##' @details This is almost just a shortcut to fread so you don't have to remember how to read the data that was exported for Nonmem. The only added feature is that meta data as written by NMwriteData is read and attached as NMdata metadata before data is returned.
 ##' @return A data set of class as defined by as.fun.
 ##' @importFrom data.table fread

R/NMscanData.R

@@ -6,7 +6,8 @@
 ##'  \item{Read and combine output tables,}
 ##'  \item{If wanted, read input data and restore variables that were not output from the Nonmem model}
 ##'  \item{If wanted, also restore rows from input data that were disregarded in
-##' Nonmem (e.g. observations or subjects that are not part of the analysis)}
+##' Nonmem (e.g. observations or subjects that are not part of the analysis)
+##' }
 ##' }
 ##' 
 ##' @param file Path to a Nonmem control stream or output file from
@@ -293,7 +294,7 @@ NMscanData <- function(file, col.row, use.input, merge.by.row,
     ## For now, searching for a row identifier is disabled. This may belong in a separate function. 
     search.col.row <- FALSE
 ### notice, this can't be evaluated if merge.by.row=="ifAvailable"
-    if(is.null(merge.by.row.arg) && is.character(merge.by.row) && merge.by.row=="ifAvailable"){
+    if(!quiet && is.null(merge.by.row.arg) && is.character(merge.by.row) && merge.by.row=="ifAvailable"){
         search.col.row <- TRUE
     }
 

tests/testthat/test_NMscanData.R

@@ -616,7 +616,7 @@ test_that("Modifying row identifier",{
 
 test_that("merge.by.row=ifAvailable when available",{
     NMdataConf(reset=TRUE)
-    fileRef <- "testReference/NMscanData21.rds"
+    fileRef <- "testReference/NMscanData_21.rds"
 
     file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
 

tests/testthat/test_NMscanMultiple.R

@@ -28,17 +28,25 @@ fix.time <- function(x){
     invisible(x)
 }
 
+
+
 NMdataConf(reset=TRUE)
 test_that("basic",{
 
-    fileRef <- "testReference/NMscanMultiple1.rds"
+    fileRef <- "testReference/NMscanMultiple_01.rds"
     resRef <- if(file.exists(fileRef)) readRDS(fileRef) else NULL
-
-    res <- NMscanMultiple(dir=system.file("examples/nonmem",package="NMdata"),file.pattern="xgxr.*\\.lst", check.time = FALSE,quiet=TRUE)
+
+### we do this in two steps because not all systems will find the files in same order apparently
+    lsts <- list.files(path="testData/nonmem/",pattern="xgxr00[1-9]\\.lst",full.names=TRUE)
+    lsts <- sort(lsts)
+    res <- NMscanMultiple(lsts, check.time = FALSE,quiet=TRUE)
     ## dim(res)
 
-    res <- lapply(res,fix.time)
-
+    ## res <- lapply(res,fix.time)
+    res <- as.data.frame(res)
+    unNMdata(res)
+    ## res[,.N,by=.(model)]
+
     expect_equal_to_reference(res,fileRef,version=2)
     ## without meta
     ##    expect_equal(unNMdata(res1),unNMdata(readRDS(fileRef)))