submission 1 of 0.1.7

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.6.961
+Version: 0.1.7
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

NEWS.md

@@ -1,5 +1,5 @@
 
-# 0.1.7
+# NMdata 0.1.7
 
 ## New features
 * `NMreadPartab()` has been generalized to support comment formats very
@@ -9,7 +9,7 @@
   any structure should be supported as long as delimitors are not
   alphabetic or numeric (so any special characters should
   work). Notice, delimitors can change between fields . Example:
-  "$THETA 1.4 ; 3 - CL (Clearance) [L/h]" would be matched by
+  `"$THETA 1.4 ; 3 - CL (Clearance) [L/h]"` would be matched by
   `NMreadPartab(...,format="%init ;%idx-%symbol(%label)[%unit]")`
   which would then return a table including columns init, idx, symbol,
   label, and unit. The comments must be systematic within say `$THETA`
@@ -37,28 +37,25 @@
   data sets. The `common.cols` argument replaces `fun.commoncols` with
   added functionality.
 
-
-\itemize{ 
-
-\item `common.cols="merge.by"` to include them in by, even
+  - `common.cols="merge.by"` to include them in by, even
 if they are not provided in the `by` argument.
 
-\item `common.cols="drop.x"` to drop the columns on the `x` and
+  - `common.cols="drop.x"` to drop the columns on the `x` and
 overwrite with columns in y
 
-\item `common.cols="drop.y"` to preserve in `x`
+  - `common.cols="drop.y"` to preserve in `x`
 
 
-\item `base::stop` The default value. Throw an error if common.columns
+  - `base::stop` The default value. Throw an error if common.columns
 are not included in merge `by` options.
 
-\item `common.cols=NULL` disabled handling and return columns as ".x"
+  - `common.cols=NULL` disabled handling and return columns as ".x"
 and ".y".
 
-\item Any function. `common.cols=warning` will issue a warning instead
+  - Any function. `common.cols=warning` will issue a warning instead
 of throwing an error.
 
-}
+
 
 * `NMreadExt()` separates objective function values into a separate list
   element. The `return` argument is used to control what data to
@@ -98,7 +95,9 @@ of throwing an error.
 * `NMreadExt()` would mess up iterations and parameter estimates if
   `as.fun` was set to returning something else than `data.table`s. Fixed.
 
-# 0.1.6
+
+
+# NMdata 0.1.6
 
 ## New features
 
@@ -124,7 +123,7 @@ of throwing an error.
   `ADDL` and `II`) followed by other doses. Fixed. Thanks to Simone
   Cassani for catching it.
 
-# 0.1.5
+# NMdata 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
@@ -158,7 +157,9 @@ of throwing an error.
   so). Now `NMdataConf(reset=TRUE)` makes sure to wipe all such
   configuration if exists.
 
-# 0.1.4
+
+
+# NMdata 0.1.4
 
 ## New functions
 * `NMreadParsText()` is a new function to extract comments to
@@ -194,7 +195,7 @@ tables.
 * `NMreadText` would fail to disregard some comment lines when
   `keep.comments=FALSE`. Fixed.
 
-# 0.1.3
+# NMdata 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
@@ -204,7 +205,7 @@ tables.
 * Improved support for reading multiple models with NMreadExt and
 NMreadPhi. 
 
-# 0.1.2
+# NMdata 0.1.2
 ## New features
 * NMreadExt is a new function that reads parameter estimates,
   uncertainties if available, estimation iterations and other
@@ -223,7 +224,7 @@ NMreadPhi.
   arguments.
 
 
-# 0.1.1
+# NMdata 0.1.1
 ## New features
 * NMwriteSection can now handle functions to perform control stream
   editing. NMwriteSection provides methods to edit control
@@ -239,7 +240,7 @@ NMreadPhi.
   with a directory (`dir`) only.
 * Minor bugfix in compareCols in case input is an unnamed list
 
-# 0.1.0
+# NMdata 0.1.0
 
 ## New features
 * The super fast `fst` format is now supported. Data sets can be
@@ -308,7 +309,7 @@ This release provides a few bugfixes, nothing major.
   cumulative number and it aligns with col.doscuma which is the
   cumulative amount.
 
-# 0.0.16
+# NMdata 0.0.16
 ## New features
 * `NMwriteSection()` includes argument `location`. In combination with
   `section`, this determines where the new section is
@@ -332,11 +333,11 @@ on file. This has been fixed to support cases where renaming or a
 pseudonym is being used to generate an `ID` column in `$INPUT`.
 
 
-# 0.0.15
+# NMdata 0.0.15
 This update is of no difference to users. A technicality has been
 chaned to ensure consistent test results once data.table 1.14.7 is
 
-# 0.0.14
+# NMdata 0.0.14
 ## New features
 * `fnExtension()` has been generalized. It now ignores leading spaces in
   new extension, and extensions with zero or one leading period are
@@ -399,9 +400,13 @@ chaned to ensure consistent test results once data.table 1.14.7 is
   identifier is simplified.
 
 * NMdata version added to welcome message.
-# 0.0.13
+
+
+
+# NMdata 0.0.13
 
 ## New functions
+
 * `NMexpandDoses()` - Transform repeated dosing events (`ADDL`/`II`)
   to individual dosing events
 * `addTAPD()` - Add cumulative number of doses, time of last dose,
@@ -411,12 +416,14 @@ chaned to ensure consistent test results once data.table 1.14.7 is
   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 addTAPD 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.

README.md

@@ -157,20 +157,6 @@ read multiple models and compare their predictions.
 ``` r
 res <- NMscanMultiple(dir=system.file("examples/nonmem", package="NMdata"),
 file.pattern="xgxr.*\\.lst",as.fun="data.table",quiet=TRUE)
-#> 
-#> Overview of model scanning results:
-#>                                                                  lst nrows
-#> 1: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr001.lst   905
-#> 2: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr002.lst   905
-#> 3: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr003.lst   905
-#> 4: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr014.lst   905
-#> 5: /data/home/philipde/wdirs/NMdata/inst/examples/nonmem/xgxr018.lst   905
-#>    ncols success warning
-#> 1:    40    TRUE   FALSE
-#> 2:    34    TRUE   FALSE
-#> 3:    34    TRUE   FALSE
-#> 4:    36    TRUE   FALSE
-#> 5:    33    TRUE   FALSE
 gmean <- function(x)exp(mean(log(x)))
 res.mean <- res[,.(gmeanPRED=gmean(PRED)),by=.(model,NOMTIME)]
 obs.all <- unique(res[,.(ID,NOMTIME,TIME,DV)])

devel/scripts/check_NMdata.R

@@ -1,6 +1,17 @@
+
+
 library(devtools)
 
 load_all()
 
 res.test <- test()
 res.chek <- check()
+
+
+devtools::build_readme()
+setwd("~/wdirs/NMdata")
+library(rmarkdown)
+render("NEWS.md")
+
+library(pkgdown)
+pkgdown::build_news()

devel/todo.org

@@ -40,7 +40,7 @@ With load_all():
     function is called from other functions. Possible to distinguish
     somehow?
 ** High level features
-*** TODO [#A] Support for DATE type columns
+*** DONE Support for DATE type columns
 ** New functions
 *** document columns
 **** TODO Check for existence of char column in values
@@ -439,7 +439,7 @@ if return="iterations" only return iterations
 *** NMreadTabSlow
 **** TODO [#A] Only handle Table numbers if "TABLE..." strings found
 *** NMreadParsText
-**** DONE [#A] order columns - created ones to the right
+**** DONE order columns - created ones to the right
 **** DONE change num to idx
 and include a field.idx so user can specify what to use. If idx is not
 taken from fields, it should not come out in the results.
@@ -449,7 +449,7 @@ in which case "; [" is a delimiter
 **** DONE Empty fields make it break
 Like ;1;CL;;;mL/h
 **** TODO [#B] Handle SAME
-***** DONE [#A] Include test so we at least know what happens
+***** DONE Include test so we at least know what happens
 *** NMreadSection
 **** DONE error returned when return="idx" and no section specified     :Bug: 
 **** TODO [#B] return="text"/"idx" should be return.idx=TRUE/FALSE instead