0.0.13 released

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.0.12.908
+Version: 0.0.13
 Authors@R: person("Philip", "Delff", email = "[email protected]",
                   role = c("aut", "cre"))
 Maintainer: Philip Delff <[email protected]>

NEWS.md

@@ -1,4 +1,4 @@
-# Post 0.0.12
+# 0.0.13
 
 ## New functions
 * NMexpandDoses - Transform repeated dosing events (ADDL/II) to
@@ -10,15 +10,16 @@
   has long been part of NMdata but has not been exported until now.
 
 ## 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
-using ADDL and II (so only one dosing row per subject). It is included
-for testing the new NMexpandDoses and coming addTAD functions.
+* A new data set called mad is included. It is based on the
+  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 coming addTAD
+  functions.
 
 ## Bugfixes
-Non-critical bugfix in mergeCheck dimensions overview printed to
-console. One column too many was reported in input and result data. No
-implications on results from mergeCheck.
+* Non-critical bugfix in mergeCheck dimensions overview printed to
+  console. One column too many was reported in input and result
+  data. No implications on results from mergeCheck.
 
 # NMdata 0.0.12
 

R/NMextractText.R

@@ -15,8 +15,8 @@
 ##'     "PK", "TABLE", etc. It can also be result sections like
 ##'     "MINIMIZATION".
 ##' @param char.section The section denoted as a string compatible
-##'     with regular expressions. "\\$" for sections in .mod files,
-##'     "0" for results in .lst files.
+##'     with regular expressions. "$" (remember to escape properly)
+##'     for sections in .mod files, "0" for results in .lst files.
 ##' @param char.end A regular expression to capture the end of the
 ##'     section. The default is to look for the next occurrence of
 ##'     char.section.

R/addTAPD.R

@@ -44,23 +44,30 @@
 ##'     subjects. Typically if using nominal time, it may be important
 ##'     to specify whether samples at dosing times are pre-dose
 ##'     samples. The default is c(3,0,4,1,2) - i.e. samples and
-##'     simulations are pre-dose.
+##'     simulations are pre-dose. See details.
 ##' @param by Columns to do calculations within. Default is ID.
 ##' @param as.fun The default is to return data as a data.frame. Pass
 ##'     a function (say tibble::as_tibble) in as.fun to convert to
 ##'     something else. If data.tables are wanted, use
 ##'     as.fun="data.table". The default can be configured using
 ##'     NMdataConf.
+##' @details addTAPD does not require the data to be ordered, and it
+##'     will not order it. This means you can run addTAPD before
+##'     ordering data (which may be one of the final steps) in data
+##'     set prepation. The argument called order.evid is important
+##'     because of this. If a dosing event and a sample occur at the
+##'     same time, when which dose was the previous for that sample?
+##'     Default is to assume the sample is a pre-dose sample, and
+##'     hence output will be calculated in relation to the dose
+##'     before. If no dose event is found before, NA's will be
+##'     assigned.
 ##' @import data.table
 ##' @export
+##' @family DataCreate
 
 
 addTAPD <- function(data,col.time="TIME",col.evid="EVID",col.amt="AMT",col.tpdos="TPDOS",col.tapd="TAPD",col.ndoses="NDOSES",col.pdosamt="PDOSAMT",col.doscuma="DOSCUMA",subset.dos,subset.is.complete,order.evid = c(3,0,2,4,1),by="ID",as.fun){
 
-#### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####
-
-### Section end: Dummy variables, only not to get NOTE's in pacakge checks
-
 
     if(missing(as.fun)) as.fun <- NULL
     as.fun <- NMdataDecideOption("as.fun",as.fun)
@@ -99,8 +106,7 @@ addTAPD <- function(data,col.time="TIME",col.evid="EVID",col.amt="AMT",col.tpdos
     data[,(col.event):=FALSE]
     data[eval(parse(text=subset.event)),(col.event):=TRUE]
 
-### quit if no doses found etc
-
+
     ## expand doses if necessary
     data2 <- NMexpandDoses(data=data,col.id=by,quiet=TRUE,as.fun="data.table",col.time=col.time,col.evid=col.evid)
 

devel/scripts/dsCreate_2_MAD.R

@@ -31,6 +31,5 @@ ggIndProfs(mad.all.exp,amt="AMT")
 
 mad.all <- NMorderColumns(mad.all)
 
-NMwriteData(mad.all,file="~/wdirs/NMdata/inst/examples/data/mad.rds",write.csv=FALSE,write.rds=TRUE)
+NMwriteData(mad.all,file="~/wdirs/NMdata/inst/examples/data/mad.rds",write.csv=FALSE,write.rds=TRUE,args.rds=list(version=2))
 file.copy("~/wdirs/NMdata/inst/examples/data/mad.rds","~/wdirs/NMdata/tests/testthat/testData/data",overwrite=T)
-

devel/todo.org

@@ -49,17 +49,20 @@ With load_all():
     Risk now is that arguments are set to NULL
     Export to parent. Not sure check allows though...
 ** Function improvements
+*** addTAPD
+**** TODO Quit if no doses found etc
 *** cl
 *** dims
 **** DONE Check if objects are data.frames
 *** DONE fnAppend
 **** TODO Support strings without extensions
 Example: fnAppend("run",".lst")
-**** TODO Make internal in tracee
+fnAppend("run",".lst",sep="")
+**** DONE Make internal in tracee
 *** NMcheckColNames
 **** return input column names and Nonmem interpretation for user to spot errors
 **** Bad name, what could we call it?
-*** cc - create character vector function
+*** cc - create character vector function*
 *** NMgenText
 **** TODO Handle until values not matching column names
 **** DONE Add a until argument to specify the last column to use in nonmem
@@ -114,7 +117,7 @@ Error if not convertible and not NA or ""? "b" should be an error right?
 *** TODO [#B] NMcreateDoses Generate dosing schedule with loading, ADDL etc :newFunction:
     This is available as a suitcase function
 *** TODO [#B] Function for complex dosing regimens              :newFunction:
-*** TODO [#B] Function to unfold ADDL/II doses to multiple rows :newFunction:
+*** DONE [#B] Function to unfold ADDL/II doses to multiple rows :newFunction:
 *** mergeCheck
 **** TODO [#B] Implement a faster method?
 What if we just check for matches in by columns?