Package index • NMdata

Configuration Configure NMdata behaviour
`NMdataConf()`	Configure default behavior of NMdata functions
Data Preparation Functions for preparation of PK/PD data sets
`NMorderColumns()`	Standardize column order in Nonmem input data
`compareCols()`	Compare elements in lists with aim of combining
`listMissings()`	List rows with missing values across multiple columns
`uniquePresent()`	Extract unique non-missing value from vector
`mergeCheck()`	Merge, order, and check resulting rows and columns.
`renameByContents()`	Rename columns matching properties of data contents
`flagsAssign()`	Assign exclusion flags to a dataset based on specified table
`flagsCount()`	Create an overview of number of retained and discarded datapoints.
`addTAPD()`	Add time since previous dose to data, time of previous dose, most recent dose amount, cumulative number of doses, and cumulative dose amount.
`NMexpandDoses()`	Transform repeated dosing events (ADDL/II) to individual dosing events
`editCharCols()`	Replace strings in character character columns of a data set
`colLabels()`	Extract column labels as defined in SAS
Write data Write data and edit update NONMEM control streams
`NMwriteData()`	Write dataset for use in Nonmem (and R)
`NMgenText()`	Generate text for INPUT and possibly DATA sections of NONMEM control streams.
`NMstamp()`	stamp a dataset or any other object
`NMwriteSection()`	Replace ($)sections of a Nonmem control stream
`NMreplaceDataFile()`	Replace data file used in Nonmem control stream
Retrieve NONMEM data Functions for retrieving NONMEM input and output data
`NMscanData()`	Automatically find Nonmem input and output tables and organize data
`NMscanMultiple()`	Run NMscanData on multiple models and stack results
`NMscanTables()`	Find and read all output data tables in Nonmem run
`NMscanInput()`	Find and read input data and optionally translate column names according to the $INPUT section
`NMreadCov()`	Read covariance matrix from `.cov` file
`NMreadCsv()`	Read input data formatted for Nonmem
`NMreadExt()`	Read information from Nonmem ext files
`NMreadFilters()`	Read data filters from a NONMEM model
`NMreadInits()`	Tabulate information from parameter sections in control streams
`NMreadSizes()`	Read SIZES info from a control stream
`NMreadPhi()`	Read information from Nonmem phi files
`NMreadShk()`	Read Shrinkage data reported by Nonmem
`NMreadTab()`	Read an output table file from Nonmem
`NMreadParsText()`	Read comments to parameter definitions in Nonmem control streams
`NMrelate()`	Relate parameter names and variables based on control stream code sections.
`NMinfo()`	Get metadata from an NMdata object
`addCor()`	add correlations of off-diagonal OMEGA and SIGMA elements to a parameter table
`addOmegaCorr()`	Deprecated: use addCor. Add correlations to parameter table
Checking and Debugging Functions for checking data and input control streams
`NMcheckColnames()`	Compare $INPUT in control stream to column names in input data
`NMcheckData()`	Check data for Nonmem compatibility or check control stream for data compatibility
Programming Additional functions for programming
`cc()`	Create character vectors without quotation marks
`cl()`	Define a vector with factor levels in the same order as occurring in the vector.
`dt2mat()`	Convert a data.table of parameter estimates to a matrix
`mat2dt()`	upper or lower triangle or all values of a matrix as long-format
`egdt()`	Expand grid of data.tables
`dims()`	Get dimensions of multiple objects
`findCovs()`	Extract columns that vary within values of other columns
`findVars()`	Extract columns that vary within values of other columns in a data.frame
`fnAppend()`	paste something before file name extension.
`fnExtension()`	Change file name extension
`dtapply()`	Apply function and return a data.frame
`lapplydt()`	Apply function of subsets of `data.frame`, return named list
`is.NMdata()`	Check if an object is 'NMdata'
`unNMdata()`	Remove NMdata class and discard NMdata meta data
`NMisNumeric()`	Test if a variable can be interpreted by Nonmem
`NMreadSection()`	Extract sections of Nonmem control streams
`NMextractDataFile()`	Extract the data file used in a control stream
`NMextractText()`	Versatile text extractor from Nonmem (input or output) control streams
`merge(<NMdata>)` `t(<NMdata>)` `dimnames(<NMdata>)` `rbind(<NMdata>)` `cbind(<NMdata>)`	Basic arithmetic on NMdata objects
`tmpcol()`	generate a name for a new data column that is not already in use.
`triagSize()`	Calculate number of elements for matrix specification
Misc Miscellaneous
`summary(<NMdata>)`	summary method for NMdata objects
`print(<summary_NMdata>)`	print method for NMdata summaries

Reference

Configuration

Data Preparation

Write data

Retrieve NONMEM data

Checking and Debugging

Programming

Misc