NMreadParsText() supports OMEGA blocks
valued SAME. This is needed for generation of parameter
tables for models with between-occasion variability.
NMdataConf() gains a quiet argument. If
, an overview of the configuration changes is summarixfzed in a printed
table. This is useful for transparency when sourcing a file with
configuration. Default is .
Improved printing of tables for messages with
message_dt(). This gives a cleaner and more consistent look
of console outputs from several functions in the package.
NMreadExt() would in some situations with multiple
estimation steps not be able to read the .ext file. This
has been fixed.
NMscanTables() - and hence NMscanData()
would fail on some output formats - especially it would not always
detect if tabulators were used as separators. More checks have been
included to detect this.
NMreadCov() adds proper support for
.cov files with multiple tables. The function has been
re-written for added flexibility. Thanks to Brian Reilly for reporting
this important gap.
Better identification of delimitors in output tables. Especially, this helps identifying when tabulator characters er used as delimtors. Until this fix, this would fail in some cases. It may still not be bulletproof but it should now support most cases.
Generally, tabulator characters are now supported in control
streams. Tabulator characters would create issues in processing of
various sections of the control stream leading to issues in functions
such as NMscanInput() and NMreadParText() and
others.
Summary of NMscanData() results has improved text to
more clearly describe the summary numbers shown.
NMwriteInits, NMwriteFilters(), and
NMwriteSizes() are no longer in NMdata. They are from now
on distributed with NMsim package because NMsim functions depend on it,
and NMdata functions do not.NMreadInits()) and write
(NMwriteInits()) initial values, boundaries and fix or
“unfix” parameters included. NMreadInits() may be useful
for inclusion of these values in parameter tables.
NMwriteInits can update those values or any subset of them
through a concise interface, likeNMwriteInits(file.mod,
"theta(2)"=list(init=1.4,lower=.1),
"THETA(3)"=list(FIX=1),
"omega(2,2)"=list(init=0.1,fix=0)
)where file.mod is a path to a control stream.
Functions to read (NMreadFilters()) and write
(NMwriteFilters()) data filter
(ACCEPT/IGNORE) statements in a control stream
have been included. NMreadFilters() run on a path to a
control stream returns a structured data.frame with the
filter statements. NMwriteFilters() can take such a
data.frame or just a string with filters and replace the
data filters in a control stream with those.
Functions to read (NMreadSizes()) and write
(NMwriteSizes()) the $SIZES section of NONMEM
control streams. NMwriteSizes() can either write the
section from scratch (wipe=TRUE) or merge the new sizes
values in with exisiting values.
NMscanInput() was not able to generate copied
columns (i.e. AFRLT=TIME should return in both columns
AFRLT and TIME) when
recover.cols=FALSE. Fixed. Thanks to Brian Reilly for
reporting.
NMrelate() now supports models with non-strict capital
case reference to parameters. This means theta(1) or
Eta(1) will also be recognized. Thanks to Chris Banker for
reporting.When data.frames were printed to the console, they
could be followed by a lines of weird code. This has been cleaned
up.
NMreadInits() is a new function adding the ability
to read the parameter structure as specified in a control stream,
including initial values, lower/upper bounds and FIX information. It
automatically allocates these values to parameter indexes, like
THETA(i) and OMEGA(i,j). It by default returns
a table of parameters and values in a format similar to
NMreadExt(), and if requested it can return detailed
information about the text lines and each element read in the control
stream to derive this parameter table. These details can be used to edit
the values and write back the information in a control stream with
consistent formatting. NMsim::NMwriteInits() does this
allowing NMsim() to edit the $THETA,
$OMEGA and $SIGMA sections.
NMreadParsText() now by default uses
NMreadInits() to index parameters. You can still override
this by specifying an index column (the old default) for all or some of
the parameter sections.
NMwriteSection() gains two new options for the
location argument: “first” and “last”.
NMgenText() can now be run on a data file.
NMgenText() suggest $DATA and
$INPUT sections based on a data set. Previously a data
object had to be passed to the function. Now also just a path to the
data set on file can be used.
fnAppend() can now append to strings that do not
have a file name extension. fnAppend() is mainly intended
for editing file names with file name extensions but for programming
purposes, this generalization is useful.
addCor() is a new function, deprecating
addOmegaCorr(). addCor() works similarly and
adds correlations for both OMEGA and SIGMA
elements, as found in provided parameter table.
NMreadExt() was incorrectly calculating blocksize
for some OMEGAs. Thanks to Brian Reilly for proposing a bugfix!
mat2dt() was doing the opposite to what was
specified by the triangle argument and returned the upper
triangle when triangle=lower and vice versa.
NMwriteSection() would fail if the first section in
a control stream was modified.
NMrelate() was ignoring the par.type
argument.
dt2mat() would only work on
data.tables. Support for other data.frames
added.
addTAPD() has a few improvements on documentations
and the following improvements on code. Together they imply that
by defaults to NMdataConf()$col.id.
col.id and col.time now respect
NMdataConf() defaults.
by defaults to value of
col.id.
NMcheckData() did not check for missing (NA) values
on dose events. Checks now capture this.
NMgenText() now looks up col.flagn
using NMdataConf() for default value.
NMwriteData() can now control stamping using
args.stamp even if no script is provided.
Also, it now only runs NMgenText() if writing csv
files.
If truncating/dropping columns in the csv file,
NMwriteData() accepts data with commas in values, even when
writing to csv files. The way NMwriteData() writes csv
files, commas in character columns are a problem. But the
trunc.csv.as.nm=TRUE argument means that columns not used
by NONMEM (i.e. including most character columns) are not written to
csv. Instead of rejecting these data sets right away,
NMwriteData() will now only return an error ifcharacter
variables with commas in values are attempted written to csv
file.
NMscanTables() includes model name in meta data
table. Useful for generation of overviews of output tables from multiple
models.
NMscanMultiple() would sometimes print a bit of a
messy overview of the results. That has been fixed without implications
on the results returned.
dt2mat() now returns actual matrix objects. This
provides compatibility with the simpar package.
NMreadPartab() has been generalized to support
comment formats very generally. NMreadPartab() reads the
comments in $THETA, $OMEGA and
$SIGMA sections, splits them into variables, and organizes
those variables in a parameter table. With this upgrade, pretty much any
structure should be supported as long as delimitors are not alphabetic
or numeric (so any special characters should work). Notice, delimitors
can change between fields . Example:
"$THETA 1.4 ; 3 - CL (Clearance) [L/h]" would be matched by
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 but the format can be different for
$OMEGA and $SIGMA. See examples in
?NMreadParTab.
NMrelate() is a new automated approach to label
parameters. It interprets NONMEM code and provides labels used in the
control stream. If the line TVCL=THETA(1) is the only line
in the code that references THETA(1), NMrelate() will
return a label TVCL.
Improved support for character-coded TIME and
DATE arguments. The default behavior is to allow (not
require) TIME and DATE columns to be
non-numeric. This is to support the NONMEM character format of DATE and
TIME. It affects sorting of columns (NMorderColumn()) and
the auto-generated $INPUT section suggestions. Where
applicable, the allow.char.TIME argument controls this
behavior. Set to allow.char.TIME=FALSE to require
TIME and DATE columns be numeric. Thanks to
Sanaya Shroff for the request, enabling NMsim to simulate
using data sets with one or more of these columns coded as
character.
mergeCheck(x,y) has new options for handling common
columns in data sets. The common.cols argument replaces
fun.commoncols with added functionality.
common.cols="merge.by" to include them in by, even
if they are not provided in the by argument.
common.cols="drop.x" to drop the columns on the
x and overwrite with columns in y
common.cols="drop.y" to preserve in
x
base::stop The default value. Throw an error if
common.columns are not included in merge by
options.
common.cols=NULL disabled handling and return
columns as “.x” and “.y”.
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 retrieve. Use one of “pars” (default, parameter
estimates), “iterations” (parameter estimates for each iteration), “obj”
for objective funtion value, or “all” for a list with all of
those.
NMreadExt() adds block information to
OMEGA and SIGMA elements based on off-diagonal
values. iblock identifies which block the element is in.
blocksize is the size of the block the element is in. Thank
you Brian Reilly for contributing to this.
NMreadExt() adds a par.name column
which is provides consistent parameter naming. Instead of NONMEM’s
THETA1 which is found in the parameter column,
the par.name column will contain THETA(1)
consistent with the OMEGA and SIGMA naming
like OMEGA(1,1)
NMreadExt() recognizes Laplacian estimation steps in
addition to the already supported FO, FOCE(i), SAEM, and IMP.
A new option nc can be controlled with NMdataConf().
This is to serve NMsim. Please see
NMsim::NMexec. NMsim::NMsim() does not adhere
to this setting because it does not parallellize by default.
NMscanInput() and NMreadCsv() could
fail if file names had no extensions. Fixed.
NMreplaceDataFile() now works on directories and
regular expressions to find models to update.
Some internal functions would make some functions including
NMscanData() fail if used within lapply().
Fixed.
NMexpandDoses() would give a warning if
length(cols.id)>1. Fixed.
NMreadExt() would mess up iterations and parameter
estimates if as.fun was set to returning something else
than data.tables. Fixed.
Function NMreadShk() to read and format
.shk (shrinkage) files.
Functions mat2dt() and dt2mat()
included to convert between matrices and data.frame format
of matrix data - especially for symmetric matrices.
Function addOmegaCorr() adds estimated correlation
between ETAs to parameter tables, as obtained using
NMreadExt().
fnAppend() can now handle multiple strings to
append. Allows for more easily readable code.
NMcheckData now respects NMdataConf()
setting of col.time and col.id. When using the
file argument col.id was not respected at all.
Fixed.
addTAPD would get cumulative counting of number of
doses and cumulative dose amount wrong in case of repeated dosing (using
ADDL and II) followed by other doses. Fixed.
Thanks to Simone Cassani for catching it.
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.
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.
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.
NMreadText would fail to disregard some comment lines
when keep.comments=FALSE. Fixed.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.
translate and
recover.cols.format arguments.type.data which allows
switching between estimation and simulation type data.dir) only.The super fast fst format is now supported. Data
sets can be written to this format, and NMscanData() and related
functions can read it. It can be used instead of rds which
is the default full-featured data format used in the package.
New function NMreplaceDataFile to replace the input data file in a control stream. A simple wrapper of NMwriteSection but useful for this specific purpose.
New function editCharCols that allows for editing character columns in a dataset based on regular expressions or strings. This allows for instance for removal of special characters that are not allowed in the selected data format (like a comma can make trouble in a csv file).
NMcheckData has a new argument, cols.dup, to include
additional columns (to col.id, col.cmt, col.evid, and col.time) in
search for duplicated events. This is useful for different assays run on
the same compartment (say a DVID column) or maybe stacked datasets. If
col.cmt is of length>1, this search is repeated for each cmt column.
Thanks to Eric Anderson for suggesting and testing this.
NMcheckData has improved checks of II and ADDL columns.
NMwriteData now uses the formats
argument to specify the requested file formats. This replaces arguments
like write.csv and write.rds. To get those
two, do formats=c("csv","rds") (which is default). The
argument save is used to control whether outputs are
written altogether.
Argument name format has been cleaned and aligned to follow the an.arg format rather than camel toe which was also used in some functions before. All deprecated arguments have been soft deprecated meaning they still work.
This release provides a few bugfixes, nothing major.
skip.absent argument.Filtering by the abbreviated IGN notation in NONMEM control statements would not always work when not using a row identifier for combining input and output data. This should now be fixed. However, it is still recommended to use a row identifier to merge input and output data.
flagsCount now reports NA discards for total and analysis data. It used to report zero but these criteria are not applied at these steps.
NMcheckData has improved checks of some columns related to either observations (like MDV) or doses (like RATE). This will give less findings that NONMEM would not fail on anyway.
addTAPD’s col.ndoses argument has been renamed to col.doscumn and the default value is now “DOSCUMN”. This makes it clear that it is a cumulative number and it aligns with col.doscuma which is the cumulative amount.
NMwriteSection() includes argument
location. In combination with section, this
determines where the new section is inserter. Possible values are
“replace” (default), “before”, “after”, “first”, “last”.
NMreadSection() adds support for partial matching of
section names. Specifically, this means that the first three characters
will be matched only, i.e. allowing say $SIMULATION to
match $SIM or $ESTIMATION to match
$EST.
NMcheckData() did not check columns listed in cols.num
for NA elements. Now it does.
NMcheckData now only checks col.dv to be non-NA for
col.mdv==0 if col.mdv is present.
NMscanInput() would fail if there was no column called
ID in the dataset on file. This has been fixed to support
cases where renaming or a pseudonym is being used to generate an
ID column in $INPUT.
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
fnExtension() has been generalized. It now ignores
leading spaces in new extension, and extensions with zero or one leading
period are treated identically (so asking for xml or
.xml is the same). Also, by providing “” as the new
extension will now remove the extension, and if extension is not
provided, fnExtension will retrieve the extension rather than replace
it.
NMscanData() now supports repeated output tables,
like those created using the SUBPROBLEM option.
NMwriteData() has a new argument
csv.trunc.as.nm. If TRUE, csv file will be
truncated horizontally (columns will be dropped) to match the
$INPUT text generated for NONMEM (genText must
be TRUE for this option to be allowed). This can be a great
advantage when dealing with large datasets that can create problems in
parallellization. Combined with write.rds=TRUE, the full
data set will still be written to an rds file, so this can be used when
combining output and input data when reading model results. This is done
by default by NMscanData(). This means writing a lean
(narrow) csv file for NONMEM while keeping columns of non-numeric class
like character and factor for post-processing.
NMwriteData() has got an arguement ‘genText’ to
control whether text for NONMEM should be generated. Default is to do
so. Also, support is added for script=NULL which now means
the same as not specifying script.
addTAPD() now includes SDOS, a scalar
to be applied when computing last dose amount and cumulative dose amount
from AMT. Sometimes, AMT is in one unit, and
other variables related to doses is in another. Say that dose is in mg
and concentrations are in ng/mL, then AMT should be in mcg.
But you may want everything else related to doses to be in mg. Then use
SDOS=1000.
addTAPD() includes convenient prefix.cols and
suffix.cols arguments that will prepend or append strings to all created
columns. This is useful if dosing more than one drug, and you want to
run addTAPD() for both (different suffixes?), or if you
want to run for nominal and actual time (prefix A and N?).
flagsAssign() now reports that data is empty and
return the data if nothing is left after applying subset. It used to
return an error.
NMgenText() has a new argument, width, passed to
strwrap to control the width of the $INPUT text for NONMEM.
NMapplyFilters (and then NMscanInput and NMscanData) gave an error when multiple filters were applied on the same column. Fixed.
addTAPD() was not respecting subset.dos for all
generated columns.
NMisNumeric() would interpret a NA of class
character or logical as non-numeric. Fixed.
Internally, combination of input and output data without a row identifier is simplified.
NMdata version added to welcome message.
NMexpandDoses() - Transform repeated dosing events
(ADDL/II) to individual dosing eventsaddTAPD() - Add cumulative number of doses, time of
last dose, previous dose amount, cumulative dose amount, and time since
previous dose to datatmpcol() provides column names not already used in data
sets. tmpcol() has long been part of NMdata but has not
been exported until now.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.Vignettes are no longer included in R package and can only be read online at https://philipdelff.github.io/NMdata/ They are still being maintained, and the exclusion from the package releases is only due to CRAN’s restrictive requirements to the package size.
New function, NMscanMultiple(), to read multiple
models and stack results in one data set. This is very useful for meta
analysis. NMscanMultiple() is a wrapper of
NMscanData(). It keeps track of warnings and errors for
reading of individual models rather than getting stuck. You can either
specify a vector of model paths or a directory plus a regular expression
(just like for NMwriteSection).
Improved tests of order of age of output control streams and input data in NMscanData. So far, all data were tested on file modification times which is not useful in the common case that data files and/or nonmem control streams are moved around between systems. Now NMscanData can look for a time stamp in the output control stream and if NMwriteData was use to write the input data to file, the creation time is taken from meta data. This will make the warnings about the order of age of files more reliable. Notice however, that for the output control stream, the timezone has to be set using the tz.lst argument or using NMdataConf - at least for now.
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 data, NMcheckData can check this for basic properties and
check the 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 “b” and “a”. This can save quite some typing in data set preparation.
New function: fnAppend - append a string to a file name before the file name extension. fnAppend(“data.csv”,“subset”) results in “data_subset.csv”.
General support for a file.data argument when a specific input data file is to be used instead of finding this information in the control streams. This is very useful if you archive input data together with a nonmem run in a way that the path in the control stream has to be overruled. Like many other of this type of arguments in NMdata, it can be a function that systematically converts the path to the control stream to the input data archive. Running NONMEM this way breaks the link between an input dataset that may change over time and the model runs that become self-contained packages of input and output data.
Support for NOHEADER option in NONMEM
$TABLE blocks. If NMdata is used to read the
results, there is no need to use NOHEADER (which opens the door to
mistakes if manually renaming the columns in results), but NMdata should
now also be able to handle this.
If found in data, CMT is added to the breakdown of
rows when summarizing results from NMscanData. Before, it was broken
down on EVID only. Also, a total line is included with total number of
rows in each of input-only, output, and result.
Support for non-event (say for $PRED) datasets in
NMcheckData.
Support for custom column names for DV
(col.dv) and MDV (col.mdv), ID (col.ID), AMT (col.amt) in
NMcheckData.
Support for file.mod and dir.data arguments in NMcheckData when running on a control stream.
NMgenText now has an argument called until that
specifies the last column(s) to include in $INPUT.
compareCols takes the list.data argument same way as
dims() does. This is often easier to use in programming.
If NMgenText does not find any NONMEM-compatible
columns to report, it now throws a warning and returns NULL.
NMcheckData’s ability to find data files when using
the file argument in NMcheckData. Only affects certain
models.compareCols now by default lists the columns where no differences were found.
NMreadTab throws a message instead of a warning in
case duplicate column names are found and removed.
NMwriteData now runs NMgenText in try,
just in case.
fnExtension now supports adding extensions to
strings without extensions,
i.e. fnExtension("file",".txt").
NMcheckData is a new function that checks data for NONMEM compatibility in numerous ways. It returns a list of all findings making it easy to identify the location of each issue in the data. See the man page of NMcheckData for a complete list of the checks that are done. The function does not modify data in any way, and it is a very simple and easy step to avoid many problems in NONMEM. NMcheckData can check a data object in R, and it can also check how a control stream reads data and then do all the checks. The latter provides an extensive check of potential issues related to data and getting it into NONMEM. Great for both debugging and QC.
NMextractDataFile is a function that identifies the input datafile used by a NONMEM model. It reports the string as in the NONMEM control stream, file path and whether the file exists. It also looks for the corresponding rds files. The function is not new in NMdata but was not exported until 0.0.10.
cc is a function that creates character vectors from arguments without quotes. This is just to be able to skip typing quotes when listing say column names. So do cc(a,b,c) to get the exact same as c(“a”,“b”,“c”). You cannot do this with strings that contain special characters. In that case do cc(a,“b+c”) to get the same as c(“a”,“b+c”).
NMwriteSection has been updated with a few very useful features. Namely these are related to updating multiple nonmem files at once. The user can now supply multiple paths, regular expressions for finding files (like pattern in list.files) and even input data files for nonmem models to match. This is very useful when updating many models after modifying input data. You can specify say all models in a directory names like pd.mod where is anything (in regular expressions this would be “pd.+\.mod”) and only the using the data file that was just written. Since NMwriteData generates the $INPUT for you, you just need to add one line to get the update of all your models automatically.
flagsAssign has got a few updates related to separate handling of different types of events. Often, this will be used to assign flags to observations, doses etc. separately. You can easily specify a subset of data to run flagsAssign on, and it will by default check for whether values of EVID are unique. This is similar to what flagsCount does.
NMgenText is a new function that provides the generation of $INPUT and $DATA. This used to be part of NMwriteData. NMwriteData still calls NMgenText but the separation of the two functionalities allows for more intuitive separate uses of one dataset for different models.
NMcompareCols now takes the argument “cols.wanted” which is a character vector of column names of special interest. Helpful when building a data set with specific column names in mind.
egdt now reports dimensions of the two data sets to combine and the resulting data. Can be disabled with quiet argument.
NMcheckColumns Change of column name from DATA to INPUT in order to match $INPUT in the control streams.
NMreadSection is now case insensitive in the section specification (i.e. “input” is the same as “INPUT”).
In NMwriteData the datafile is now correctly included in the $DATA suggestion for NONMEM. No impact on data file output.
Bugfix in NMscanData related to searching for candidates for unique row identifiers.
In compareCols multiple classes of single columns would give a warning and sometimes confusing overview of columns. Fixed.
findCovs fixed in ordering output when by argument is of length > 1
The only change from 0.0.8 is a patch provided by Matt Dowle ensuring that tests pass after the release of data.table v1.14.2.
Meta data system rewritten. NMinfo and NMstamp are used to read and write meta data. Meta data is stored as an attribute to the data object (attributes(data)$NMdata).
Translation table includes a column ranking the match between input data file contents and $INPUT. OK: names match, diff: names do not match, off: diff and name is found elsewhere.
NMscanInput, NMaplyFilters, NMtransInp all return meta data compatibly with NMinfo.
merge.by.row=“ifAvailable”
Check for new values of row identifier
Check for disjoint ID’s when ID-level output tables found
Improved message from NMscanData
Support for custom (and NULL) values of col.model and col.nmout
Support for NONMEM filters without operators (COL XX)
NMreadCsv, NMscanInput, and NMscanData take argument args.fread. The contents of this list are passed as arguments to fread when reading csv files. This should only be needed in rare cases but offers full flexibility to match structure of csv files. Default contents of args.fread can be controlled using NMdataConf.
NMwriteData updated with more concise message.
NMreadSection now returns all sections if argument section is missing or equals NULL or “.”.
NMinfo is a new function that provides meta data, processed by as.fun.
If merge.by.row=TRUE, NMscanData now checks if col.row seems to be changed in the NONMEM code. If that is the case, an error is returned.
save argument added to flagsCount function to align with other functions.
NMwriteData now writes meta data to a txt file when writing csv file. NMreadCsv looks for this info and attaches it if found.
NMwriteData takes the argument args.fwrite - a list of arguments passed to fwrite. This is aligned with args.fread used by NMreadCsv. Defaults can be configured using NMdataConf.
Improved and shortened text to console from NMscanData (print.summary_NMdata).
mergeCheck will now throw an explained error if argument df1 has zero rows.
compareCols generalized to the single data set case.
mergeCheck has improved warnings when checks fail. This should in most cases provide information for the user to get a good idea what needs to be resolved for the merge to work as expected.
Support for pseudonyms when translating input data column names based on nonmem control stream. Now by default, the column will be returned (doubled) with both pseudonyms as column names.
new function - fnExtension is a simple function to replace the extension of a file name (say from file.mod to file.lst)
new function - dims is a simple function that returns a table of the dimensions of multiple data sets. It is used by multiple other functions in the package and may be useful on its own. However, compareCols reports this information too (by calling dims).
NMscanData now has an argument, translate.input, which can be used to skip the translation of column names according to $DATA in the listing file. This can be necessary if input data has changed and hence $DATA is outdated since last model run.
flagsCount now reports cumulative counts of discards too.
This is a major upgrade from 0.0.6.6 featuring many improvements and bug fixes. Everyone is strongly encouraged to upgrade.
The choice between data combination methods in NMscanData is now done in one argument, called merge.by.row. Before the method was decided based on values of two arguments, cbind.by.filters and col.row. A default value for col.row can now be set using NMdataConf and will not affect the data combination method.
Other arguments which default values can now be modified using
NMdataConf are: merge.by.row, col.flagn,
col.flagc, use.input,
recover.rows, col.model,
modelname, file.mod, and
check.time, quiet, use.rds.
The tools to assign and count exclusion flags,
flagsAssign() and flagsCount(), have been
improved. They now support working on a subset of data (say samples
only), and the order (increasing/decreasing) of the exclusion flags is
optional. The printing of the count of exclusion flags has been
improved.
NMgetSection and NMwriteSection are new functions that can be used to extract sections from and write sections to NONMEM control streams. NMwriteData now returns a list of sections that can be passed directly to NMwriteSection, in order to update control streams to read the updated data file correctly.
compareCols is a very useful new data creation tool. See the difference between presence and classes of columns in data sets. This is useful before rbind’ing or merging - or maybe when those throw an error, and you want to figure out why.
renameByContents is a function that can rename columns which contents match a given criterion. In combination with the provided NMisNumeric, this can be used to rename (say to lowercase) columns that NONMEM cannot interpret (as numeric).
mergeCheck now informs about common column names that are not used to merge by. These will create new column names, and it’s often not intended. An argument has been added (ncols.expected) to check the number of columns added to df1 against expectation.
egdt is a new function for expanding grids of data.tables. This is quite technical, and it fills a whole when constructing data with data.tables. It mimics the behavior of merge.data.frame on objects with no common columns.
Central configuration mechanism implemented. The configuration function to use is NMdataConf. You can configure several options, corresponding to default values of arguments to different functions in the package. This is very useful if you want to change the directory and file naming structure, or if you want to change default column names.
The exclusion flag functions flagsAssign and flagsCount have been generalized to use customizable column names for the numerical and character flags. The default can be configured using NMdataConf.
If all common column names two data objects to merge are not used for merging (by), new column names are created by merge. The behavior of mergeCheck can now be controlled in case this happens. This is especially useful when using mergeCheck in programming.
A shortcut to system.file(…,package=“NMdata”) has been removed. The function was called NMdata_filepath and is no longer available. Use system.file instead.
Meta information added about the input data.
A summary function is provided for NMdata objects. There is a print function for the summary too. This is printed automatically by NMdata unless quiet=TRUE.
A lot of meta information has been added in an attribute to NMdata objects. This will help the user to understand and automatically document what has been read.
The argument to NMscanData previously called name has been renamed to modelname and generalized to take a function that derives the name from the file path. Also an general option “NMdata.modelname” has been added, so the default behavior can be configured.
The default class to generate is now data.frame rather than data.table. If you want to work with data.tables, do options(NMdata.as.fun=“none”)
General support for conversion of output to user-specified class. Setting the option “NMdata.as.fun” to a conversion function such as as.data.frame or tibble::as_tibble it is possible for the user to work with their preferred data class. An argument, as.fun, can be used for the individual functions too.
The translation from the output control stream file path (.lst in PSN) and the input control stream (.mod in PSN) can now be configured through the option “NM.file.mod”. Typically, all the models to be considered in an analysis have been run on the same system, so it makes most sense to define this behavior once and for all for most users.
NMwriteData improved with checks of column names and automated generation of $INPUT and $DATA NONMEM sections.
NMorderColumns simplified, and documentation improved.
Documentation has been upgraded with a pkgdown site.
New vignette on data set creation tools in NMdata.
New FAQ vignette.
NMtransInput now supports the case where additional unused column names are given in $INPUT than actually found in $DATA. A warning will be given.
This release introduces a consistent default NMscanData behavior that will work in most cases and provide the user with information on how to use a more robust approach to merging input and output data.
Naming of a few arguments to NMscanData has been changed from camelCase to lower.case for consistency.
NMscanTables keeps track of LASTONLY and FIRSTLASTONLY. LASTONLY are now treated like FIRSTONLY while FIRSTLASTONLY tables are disregarded (with a warning).
The most obvious change since 0.0.3 is that only one data.table is
being returned from NMscanData. This is what used to be the
row element in the returned objects previously. The main
reason for this change is that it makes it easier for users to
post-process only one dataset before splitting into different levels of
variability. The small cost is that the user will have to run findCovs,
or findVars to get the desired level of variability. These functions are
however very simple to use and very fast to run.
This release features numerous improvements to especially the NMscanData function. The work is mainly focused around use without a row identifier. Even without a row identifier, NMscanData should now work for the vast majority of models, including merging with input and recovering rows.
An attribute called vars has been added to the NMdata
objects coming out of NMscanData. It features a table of the columns in
the returned object and information about where they originate from.
More work is still to be done on this, but hopefully it is useful
already.
NMwriteData: Added support for passing arguments to saveRDS.
Last but far from least is a new vignette on using NMscanData. Check it out with vignette(“NMscanData”).
This release contains bugfixes and experimental support for merging nonmem input and output data without a row identifier.
A clearer cut has been made between the pmxtricks package (version 0.0.10) and NMdata. The packages should not overlap in exported functionality, and they do not depend on each other.