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

## Documentation for package ‘NMdata’ version 0.2.5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

addCor | add correlations of off-diagonal OMEGA and SIGMA elements to a parameter table
addOmegaCorr | Deprecated: use addCor. Add correlations to parameter table
addTAPD | Add time since previous dose to data, time of previous dose, most recent dose amount, cumulative number of doses, and cumulative dose amount.
as.NMctl | Convert object to class NMctl
cbind.NMdata | Basic arithmetic on NMdata objects
cc | Create character vectors without quotation marks
cl | Define a vector with factor levels in the same order as occurring in the vector.
colLabels | Extract column labels as defined in SAS
compareCols | Compare elements in lists with aim of combining
dcastSe | A standard-evaluation interface to 'data.table::dcast()
dimnames.NMdata | Basic arithmetic on NMdata objects
dims | Get dimensions of multiple objects
dt2mat | Convert a data.table of parameter estimates to a matrix
dtapply | Apply function and return a data.frame
editCharCols | Replace strings in character character columns of a data set
egdt | Expand grid of data.tables
findCovs | Extract columns that are constant within values of other columns (covariates)
findVars | Extract columns that vary within values of other columns in a data.frame
flagsAssign | Assign exclusion flags to a dataset based on specified table
flagsCount | Create an overview of number of retained and discarded datapoints.
fnAppend | paste something before file name extension.
fnExtension | Change file name extension
is.NMdata | Check if an object is 'NMdata'
lapplydt | Apply function of subsets of 'data.frame', return named list
listMissings | List rows with missing values across multiple columns
mat2dt | upper or lower triangle or all values of a matrix as long-format
merge.NMdata | Basic arithmetic on NMdata objects
mergeCheck | Merge, order, and check resulting rows and columns.
mergeCoal | Overwrite values in one data.frame as available in another.
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
NMdataConf | Configure default behavior of NMdata functions
NMdataOperations | Basic arithmetic on NMdata objects
NMexpandDoses | Transform repeated dosing events (ADDL/II) to individual dosing events
NMextractDataFile | Extract the data file used in a control stream
NMextractText | Versatile text extractor from Nonmem (input or output) control streams
NMgenText | Generate text for INPUT and possibly DATA sections of NONMEM control streams.
NMinfo | Get metadata from an NMdata object
NMisNumeric | Test if a variable can be interpreted by Nonmem
NMorderColumns | Standardize column order in Nonmem input data
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
NMreadParsText | Read comments to parameter definitions in Nonmem control streams
NMreadPhi | Read information from Nonmem phi files
NMreadSection | Extract sections of Nonmem control streams
NMreadShk | Read Shrinkage data reported by Nonmem
NMreadSizes | Read SIZES info from a control stream
NMreadTab | Read an output table file from Nonmem
NMrelate | Relate parameter names and variables based on control stream code sections.
NMreplaceDataFile | Replace data file used in Nonmem control stream
NMscanData | Automatically find Nonmem input and output tables and organize data
NMscanInput | Find and read input data and optionally translate column names according to the $INPUT section
NMscanMultiple | Run NMscanData on multiple models and stack results
NMscanTables | Find and read all output data tables in Nonmem run
NMstamp | stamp a dataset or any other object
NMwriteData | Write dataset for use in Nonmem (and R)
NMwriteSection | Replace ($)sections of a Nonmem control stream
print.summary_NMdata | print method for NMdata summaries
rbind.NMdata | Basic arithmetic on NMdata objects
readCtl | Read as class NMctl
renameByContents | Rename columns matching properties of data contents
reorder2 | reorder with respect to multiple vectors
setOrderList | Reorder List Elements by Name
summary.NMdata | summary method for NMdata objects
t.NMdata | Basic arithmetic on NMdata objects
triagSize | Calculate number of elements for matrix specification
uniquePresent | Extract unique non-missing value from vector
unNMdata | Remove NMdata class and discard NMdata meta data