Merge branch 'master' of github.com:philipdelff/NMdata

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.2.913
+Version: 0.1.5.902
 Authors@R: c(person("Philip", "Delff", email = "[email protected]", role = c("aut", "cre")))
 Maintainer: Philip Delff <[email protected]>
 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'.

NAMESPACE

@@ -20,6 +20,7 @@ export(NMorderColumns)
 export(NMreadCov)
 export(NMreadCsv)
 export(NMreadExt)
+export(NMreadParsText)
 export(NMreadPhi)
 export(NMreadSection)
 export(NMreadTab)
@@ -31,11 +32,14 @@ export(NMscanTables)
 export(NMstamp)
 export(NMwriteData)
 export(NMwriteSection)
+export(addOmegaCorr)
 export(addTAPD)
 export(cc)
 export(cl)
+export(colLabels)
 export(compareCols)
 export(dims)
+export(dt2mat)
 export(editCharCols)
 export(egdt)
 export(findCovs)
@@ -46,6 +50,7 @@ export(fnAppend)
 export(fnExtension)
 export(is.NMdata)
 export(listMissings)
+export(mat2dt)
 export(mergeCheck)
 export(renameByContents)
 export(tmpcol)
@@ -56,6 +61,7 @@ importFrom(data.table,fwrite)
 importFrom(data.table,setattr)
 importFrom(fst,read_fst)
 importFrom(fst,write_fst)
+importFrom(stats,cov2cor)
 importFrom(stats,reorder)
 importFrom(stats,setNames)
 importFrom(utils,capture.output)

NEWS.md

@@ -1,8 +1,96 @@
-# 0.1.2
-* Improved support for reading multiple models with NMreadExt and
-NMreadPhi. 
+# 0.1.6
+
+## New features
+* Functions `mat2dt()` and `dt2mat()` included to convert between
+  matrices and data.frame format of matrix data.
+
+* Function `addOmegaCorr` adds estimated correlation between ETAs to
+  parameter tables, as obtained using `NMreadExt()`.
+
+## Bugfixes
+* `NMcheckData` now respects `NMdataConf()` setting of `col.time` and
+  `col.id`. When using the `file` argument `col.id` was not respected
+  at all. This is fixed.
+
+# 0.1.5
+## New features
+* `countFlags` no longer needs a table of flags. By default it will
+  summarize the ones found in data. If additional flags wanted in
+  summary table (with no findings), the flag table is still needed.
+
+* If a flag table is provided, `countFlags` will throw an error if the
+  flags found in data are not covered by the provided flag table.
+
+* `NMorderColumns` now includes arguments `col.id` and
+  `col.time`. These can now also be controlled using `NMdataConf()`.
+
+* `NMreadParText` includes argument `modelname`, `col.model`, and
+  `as.fun` and defaults to what is defined in `NMdataConf()` like
+  other `NMdata` functions. It also includes a `parameter` column for
+  easier merge with data from e.g. `ext` files `NMreadExt()`.
+
+* `NMreadParText` accepts function (with the control stream path as
+  argument) to define how to read the parameter information. This is
+  useful if one defines the tabulated information in a comment in the
+  control stream. NMreadParText basically allows for a full automation
+  of flexible parameter table generation.
 
+* `NMdataConf()` is configured to handle `NMsim`'s `dir.sims` and
+  `dir.res`.
 
+* `NMdataConf(reset=TRUE)` wipes all settings. In recent versions,
+  `NMdataConf` accepts the `allow.unknown` argument which means
+  settings that are unknown to `NMdata` can be stored. This is
+  relevant for other packages that want to make use of `NMdata`'s
+  configuration system (`NMsim` is an example of a package that does
+  so). Now `NMdataConf(reset=TRUE)` makes sure to wipe all such
+  configuration if exists.
+
+# 0.1.4
+
+## New functions
+* `NMreadParsText()` is a new function to extract comments to
+  `$THETA`, `$OMEGA` and `$SIGMA` sections. As long as the comments
+  are structured in a table-like manner, `NMreadParsText()` should be
+  able to fetch them almost no matter what delimiters you used. Use
+  say `fields="%init;num)symbol/transform/label(unit)"` if you have
+  lines like
+`(0,1) ; 1) CL / log / This is clearance (L/h)`
+  All comment lines don't have to be completed, and you can specify
+separate formats for `$THETA`, `$OMEGA` and `$SIGMA`. Together with
+`NMreadExt()` this is a very flexible basis for generating parameter
+tables.
+
+* `colLabels()` is a simple wrapper of `compareCols()` that extracts
+  the SAS column labels on data sets.
+
+## New features
+* NMdata functions will now by default look for input control streams
+  with file name extensions either `.mod` or `.ctl`. The user
+  previously had to tell NMdata to look for `.ctl` using configuration
+  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.
+
+## Bugfixes
+* `NMreadText` would fail to disregard some comment lines when
+  `keep.comments=FALSE`. Fixed.
+
+# 0.1.3
+* Better support for models with multiple estimation
+  steps. Particularly reading output tables now better distinguishes
+  between Nonmem table numbers and repetitions (like
+  SUBPROBLEMS). Also, functions that read parameter estimates clearly
+  separates Nonmem table numbers.
+
+* Improved support for reading multiple models with NMreadExt and
+NMreadPhi. 
 
 # 0.1.2
 ## New features
@@ -212,7 +300,7 @@ chaned to ensure consistent test results once data.table 1.14.7 is
 
 ## New data
 * A new data set called mad is included. It is based on the
-  mad_missing_duplicates from the xgxr package. Doses are implemented
+  mad_missing_duplicates from the `xgxr` package. Doses are implemented
   using ADDL and II (so only one dosing row per subject). It is
   included for testing the new NMexpandDoses and addTAPD functions.
 
@@ -247,12 +335,12 @@ chaned to ensure consistent test results once data.table 1.14.7 is
   set using the tz.lst argument or using NMdataConf - at least for
   now.
 
-* Checks of unique subject identifier (usubjid) included in
+* Checks of unique subject identifier (`usubjid`) included in
   NMcheckData. This is mostly to detect the potential issue that the
   subject IDs generated for analysis are not unique across actual
-  subjects. If a usubjid (e.g. from clinical data sets) is included in
+  subjects. If a `usubjid` (e.g. from clinical data sets) is included in
   data, NMcheckData can check this for basic properties and check the
-  analysis subject ID and the usubjid against each other.
+  analysis subject ID and the `usubjid` against each other.
 
 * New function: cl - creates factors, ordered by the appearance of the
   elements when created. cl("b","a") results in a factor with levels

R/NMcheckData.R

@@ -168,10 +168,10 @@
 ##'     subject and occasion.
 ##'
 ##' \item Columns specified in cols.num must be present, numeric
-##'     and non-NA.
+##'     and non-`NA`.
 ##'
-##' \item If a unique subject identifier column (col.usubjid) is
-##' provided, col.id must be unique within values of col.usubjid and
+##' \item If a unique subject identifier column (`col.usubjid`) is
+##' provided, `col.id` must be unique within values of `col.usubjid` and
 ##' vice versa.
 ##'
 ##' \item Events should not be duplicated. For all rows, the
@@ -213,10 +213,10 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
     ADDL <- NULL
     AMT <- NULL
     CMT <- NULL
-    DV <- NULL
+    ## DV <- NULL
     EVID <- NULL
     ID.jump <- NULL
-    ID <- NULL
+    ## ID <- NULL
     II <- NULL
     MDVDV <- NULL
     MDV <- NULL
@@ -266,9 +266,16 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
     if(missing(as.fun)) as.fun <- NULL
     as.fun <- NMdataDecideOption("as.fun",as.fun)
 
+    if(missing(col.id)) col.id <- NULL
+    col.id <- NMdataDecideOption("col.id",col.id)
+
     if(missing(col.flagn)) col.flagn <- NULL
     col.flagn.orig <- col.flagn
     col.flagn <- NMdataDecideOption("col.flagn",col.flagn)
+
+    if(missing(col.time)) col.time <- NULL
+    col.time <- NMdataDecideOption("col.time",col.time)
+
     if(missing(file)) file <- NULL
 
     if(!is.null(covs) && !is.character(covs)) {
@@ -304,7 +311,7 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
         }
     }
 
-
+    
     if(!(is.character(col.dv)&&length(col.dv)==1)){
         stop("col.dv must be a character and vector of length 1.")
     }
@@ -330,7 +337,7 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
 ### file mode
     if(!is.null(file)){
         if(!is.null(col.flagn.orig)){warning("col.flagn is not used when file is specified.")}
-        col.id <- "ID"
+        ## col.id <- "ID"
         ## use.rds <- FALSE
         formats.read="csv"
         file.mod <- NULL