NMdata0.1.8 package

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

addOmegaCorr

add Omega correlations to a parameter table

addTAPD

Add time since previous dose to data, time of previous dose, most rece...

cc

Create character vectors without quotation marks

checkColRow

check that col.row is not edited in Nonmem control stream

cl

Define a vector with factor levels in the same order as occurring in t...

cleanSpaces

Drop leading, trailing and repeated spaces in character strings

colLabels

Extract column labels as defined in SAS

compareCols

Compare elements in lists with aim of combining

deprecatedArg

Report if an argument is deprecated.

dims

Get dimensions of multiple objects

dt2mat

Convert a data.table of parameter estimates to a matrix

editCharCols

Replace strings in character character columns of a data set

egdt

Expand grid of data.tables

filePathSimple

Clean and standardize file system paths

findCovs

Extract columns that vary within values of other columns

findVars

Extract columns that vary within values of other columns in a data.fra...

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

getArgs

Get provided arguments as a named list

getFilePaths

Internal interpretation of file specification options

is.NMdata

Check if an object is 'NMdata'

listMissings

List rows with missing values across multiple columns

lstExtractTime

Extract run time from output control stream

mat2dt

upper or lower triangle or all values of a matrix as long-format

mergeCheck

Merge, order, and check resulting rows and columns.

messageWrap

Pretty wrapping of lines in NMdata vignettes

NMapplyFilters

Translate filters in Nonmem and apply to data

NMcheckColnames

Compare $INPUT in control stream to column names in input data

NMcheckData

Check data for Nonmem compatibility or check control stream for data c...

NMcheckDataFile

check input data based on control stream

NMcode2R

Translate Nonmem PK,PK, PRED sections or other Nonmem code to R code

NMdataConf

Configure default behavior of NMdata functions

NMdataConfOptions

Get NMdataConf parameter properties

NMdataDecideOption

Determine active parameter value based on argument and NMdataConf sett...

NMdataGetOption

Look up default configuration of an argument

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 s...

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 in data file

NMreadCsv

Read input data formatted for Nonmem

NMreadExt

Read information from Nonmem ext files

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

NMreadTab

Read an output table file from Nonmem

NMreadTabSlow

Read Nonmem table files without assumptions about what tables they con...

NMrelate

Relate parameter names and variables based on control stream code sect...

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 accordi...

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

NMtransInp

translate the column names according to the $INPUT section of a contro...

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

reduceTables

reduce tables from NMscanTables to fewer objects

renameByContents

Rename columns matching properties of data contents

searchColRow

Check row identifier in a model for necessary properties.

splitFields

splitFields splits the fields format string into the splitters and the...

summary.NMdata

summary method for NMdata objects

tmpcol

generate a name for a new data column that is not already in use.

uniquePresent

Extract unique non-missing value from vector

unNMdata

Remove NMdata class and discard NMdata meta data

writeNMinfo

Do the actual writing of meta data

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'.

  • Maintainer: Philip Delff
  • License: MIT + file LICENSE
  • Last published: 2024-10-31