Package: NMdata 0.2.0

Philip Delff

NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

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'.

Authors:Philip Delff [aut, cre], Brian Reilly [ctb], Eric Anderson [ctb], Matthew Fidler [ctb]

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NMdata.pdf |NMdata.html✨
NMdata/json (API)
NEWS

# Install 'NMdata' in R:
install.packages('NMdata', repos = c('https://nmautoverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmautoverse/nmdata/issues

Pkgdown site:https://nmautoverse.github.io

On CRAN:

Conda:

nonmempharmacometrics

7.72 score 17 stars 2 packages 88 scripts 697 downloads 59 exports 4 dependencies

Last updated 10 days agofrom:843b72ce41. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
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R-4.5-macOKMar 24 2025
R-4.5-linuxOKMar 24 2025
R-4.4-winOKMar 24 2025
R-4.4-macOKMar 24 2025
R-4.4-linuxOKMar 24 2025
R-4.3-winOKMar 24 2025
R-4.3-macOKMar 24 2025

Exports:addCoraddOmegaCorraddTAPDccclcolLabelscompareColsdimsdt2mateditCharColsegdtfindCovsfindVarsflagsAssignflagsCountfnAppendfnExtensionis.NMdatalistMissingsmat2dtmergeCheckNMcheckColnamesNMcheckDataNMdataConfNMexpandDosesNMextractDataFileNMextractTextNMgenTextNMinfoNMisNumericNMorderColumnsNMreadCovNMreadCsvNMreadExtNMreadFiltersNMreadInitsNMreadParsTextNMreadPhiNMreadSectionNMreadShkNMreadSizesNMreadTabNMrelateNMreplaceDataFileNMscanDataNMscanInputNMscanMultipleNMscanTablesNMstampNMwriteDataNMwriteFiltersNMwriteInitsNMwriteSectionNMwriteSizesrenameByContentstmpcoltriagSizeuniquePresentunNMdata

Dependencies:data.tablefstfstcoreRcpp

Readme and manuals

Help Manual

Help pageTopics
add correlations of off-diagonal OMEGA and SIGMA elements to a parameter tableaddCor
Deprecated: use addCor. Add correlations to parameter tableaddOmegaCorr
Add time since previous dose to data, time of previous dose, most recent dose amount, cumulative number of doses, and cumulative dose amount.addTAPD
Create character vectors without quotation markscc
Define a vector with factor levels in the same order as occurring in the vector.cl
Extract column labels as defined in SAScolLabels
Compare elements in lists with aim of combiningcompareCols
Get dimensions of multiple objectsdims
Convert a data.table of parameter estimates to a matrixdt2mat
Replace strings in character character columns of a data seteditCharCols
Expand grid of data.tablesegdt
Extract columns that vary within values of other columnsfindCovs
Extract columns that vary within values of other columns in a data.framefindVars
Assign exclusion flags to a dataset based on specified tableflagsAssign
Create an overview of number of retained and discarded datapoints.flagsCount
paste something before file name extension.fnAppend
Change file name extensionfnExtension
Check if an object is 'NMdata'is.NMdata
List rows with missing values across multiple columnslistMissings
upper or lower triangle or all values of a matrix as long-formatmat2dt
Merge, order, and check resulting rows and columns.mergeCheck
Compare $INPUT in control stream to column names in input dataNMcheckColnames
Check data for Nonmem compatibility or check control stream for data compatibilityNMcheckData
Configure default behavior of NMdata functionsNMdataConf
Basic arithmetic on NMdata objectscbind.NMdata dimnames.NMdata merge.NMdata NMdataOperations rbind.NMdata t.NMdata
Transform repeated dosing events (ADDL/II) to individual dosing eventsNMexpandDoses
Extract the data file used in a control streamNMextractDataFile
Versatile text extractor from Nonmem (input or output) control streamsNMextractText
Generate text for INPUT and possibly DATA sections of NONMEM control streams.NMgenText
Get metadata from an NMdata objectNMinfo
Test if a variable can be interpreted by NonmemNMisNumeric
Standardize column order in Nonmem input dataNMorderColumns
Read in data fileNMreadCov
Read input data formatted for NonmemNMreadCsv
Read information from Nonmem ext filesNMreadExt
Read data filters from a NONMEM modelNMreadFilters
Tabulate information from parameter sections in control streamsNMreadInits
Read comments to parameter definitions in Nonmem control streamsNMreadParsText
Read information from Nonmem phi filesNMreadPhi
Extract sections of Nonmem control streamsNMreadSection
Read Shrinkage data reported by NonmemNMreadShk
Read SIZES info from a control streamNMreadSizes
Read an output table file from NonmemNMreadTab
Relate parameter names and variables based on control stream code sections.NMrelate
Replace data file used in Nonmem control streamNMreplaceDataFile
Automatically find Nonmem input and output tables and organize dataNMscanData
Find and read input data and optionally translate column names according to the $INPUT sectionNMscanInput
Run NMscanData on multiple models and stack resultsNMscanMultiple
Find and read all output data tables in Nonmem runNMscanTables
stamp a dataset or any other objectNMstamp
Write dataset for use in Nonmem (and R)NMwriteData
Write IGNORE/ACCEPT filters to NONMEM modelNMwriteFilters
Writes a parameter values to a control streamNMwriteInits
Replace ($)sections of a Nonmem control streamNMwriteSection
Create or update $SIZES in a control streamNMwriteSizes
print method for NMdata summariesprint.summary_NMdata
Rename columns matching properties of data contentsrenameByContents
summary method for NMdata objectssummary.NMdata
Calculate number of elements for matrix specificationtriagSize
Extract unique non-missing value from vectoruniquePresent
Remove NMdata class and discard NMdata meta dataunNMdata