Function Reference

Allowed in IQRmodel
`IQRmodel()`	IQRmodel
`and()`	And function
`ge()`	Greater equal function
`gt()`	Greater than function
`interp0()`	Zero order interpolation function
`interp1()`	First order interpolation function
`interpcs()`	Cubic spline interpolation function
`le()`	Less equal function
`lt()`	Less than function
`mod()`	Modulo function
`or()`	Or function
`piecewise()`	Piecewise function
Auxiliary
`IQRloadCSVdata()`	Simple auxiliary to load a CSV dataset
`IQRsaveCSVdata()`	Simple auxiliary to save a CSV dataset with attributes
`and()`	And function
`aux_explode()`	Splits a string based on a separator substring
`aux_explodePC()`	Splits strings by separator only if separators not in parentheses
`aux_fileparts()`	aux_fileparts function
`aux_fileread()`	aux_fileread function
`aux_filewrite()`	aux_filewrite function
`aux_getRelPath()`	aux_getRelPath
`aux_mkdir()`	aux_mkdir function
`aux_na_locf()`	Last observation carry forward (non NA values)
`aux_postFillChar()`	Postpad string with char to defined length
`aux_preFillChar()`	Prepad string with char to defined length
`aux_quantilenumber()`	Return quantile number information for numeric vector entries
`aux_rmdir()`	aux_rmdir function
`aux_simplifypath()`	Remove unnecessary dot-dot from (relative) paths.
`aux_splitVectorEqualPieces()`	Split vector into equal pieces
`aux_strFindAll()`	Returns indices of occurrence of strings in strings
`aux_strrep()`	Replaces some string in a string
`aux_strtrim()`	Trims a strings leading and trailing white spaces
`aux_unlevel()`	Removes factors from a vector
`aux_version()`	Check version function for packages
`calcAICBIC()`	Calculation of AIC and BIC from OFV, etc.
`clusterX()` `statXY()`	Cluster Data in Blocks of Similar x Values and Summarize y Values per Block
`compare_IQRmodel_IQRsysModel_simulation()`	Comparing IQRmodel with IQRsysModel simulation
`fit_EmaxModel()`	Fit Emax model to data
`format_GUM()`	Format numbers (with uncertainty) according to the "Guide to the Expression of Uncertainty in Measurement (GUM)"
`ge()`	Greater equal function
`gen_aux_version()`	Generate aux_version string for script-based analyses with IQR Tools
`geocv()`	geometric CV auxiliary
`geomean()`	geometric mean auxiliary
`geosd()`	geometric sd auxiliary
`ginv()`	Generalized Inverse of a Matrix
`gt()`	Greater than function
`interp0()`	Zero order interpolation function
`interp1()`	First order interpolation function
`interpcs()`	Cubic spline interpolation function
`inv_logit()`	Inverse Logit auxiliary - so far only used in NLMIXR interface
`le()`	Less equal function
`logit()`	Logit auxiliary - so far only used in NLMIXR interface
`lt()`	Less than function
`mod()`	Modulo function
`mvrnorm()`	Simulate from a Multivariate Normal Distribution
`norm_M3()`	Estimate parameters of the normal distribution accounting for censoring
`or()`	Or function
`piecewise()`	Piecewise function
`progressBar()`	Simple progress bar
`remove_duplicates()`	Reduce character to the non-repeating entries
`run_silent_IQR()`	Run expression silently
`stopIQR()`	Replacement for stop function to be used in IQRtools
`tempdirIQR()`	Replacement for tempdir function to be used in IQRtools
`tempfileIQR()`	Replacement for tempfile function to be used in IQRtools
`warningIQR()`	Replacement for warning function to be used in IQRtools
Bootstrap
`bootstrap_IQRnlmeProject()`	Perform a non-parametric bootstrap on an IQRnlmeProject
Covariate analysis
`covariateEffect_IQRnlmeProject()`	Assess impact of covariates on parameters
Data exploration
`fitCOR()`	Correlation analysis with plot and stats table
Data handling
`IQRcalcTAD()`	Calculate TAD column
`IQRexpandADDLII()`	Expand ADDL and II dosing information
`date2dateday_IQRdataProgramming()`	Conversion of date/time in string format to day in string format
`date2datetime_IQRdataProgramming()`	Conversion of date/time in string format to time in string format
`date2time_IQRdataProgramming()`	Conversion of date/time in string format to numeric values
`getLabels_dataframe()`	Extract label information of columns in data.frames
`removeCommata_dataframe()`	Remove commata in elements in data.frame
`unlabel_dataframe()`	Remove labelled class and label
Formatting
`remove_duplicates()`	Reduce character to the non-repeating entries
GPF
`GPF()`	Create a GPF object
`export_GPF()`	Export a GPF to and XLS file
`generate_GPFFromIQRnlmeEst()`	Generate GPF from IQRnlmeEst or IQRsysEst
`generate_GPFFromIQRnlmeProject()`	Generate GPF from IQRnlmeProject of IQRsysProject
`generate_GPFFromProjectInfo()`	Rename/pick parameters and covariates in a GPF
`generate_GPFFromProjectInfoList()`	From multiple projectInfos, generate one combined GPF
`load_GPF()`	Load a GPF from different sources
`sample_GPF()`	Sample wrapper with syntax as sample_IQRnlmeProject for GPF excel files
`select_FromGPF()`	Select and, optionally, rename parameters and covariates in a GPF
Help & Documentation
`doc_IQRtools()`	Open IQRtools documentation in browser
`examples_IQRtools()`	Copy example files from the IQRreport documentation book to desired location
`install_MIDDmodule()`	Installs defined webinar module from the web
`install_workshop()`	Installs workshop material
`libraryPK_IQRtools()`	Copy PK model library from the IQR tools material folder to desired location
`support()`	Open support webpage
Installation
`IQRinitCompliance()`	Initializes the compliance mode
`getRepos()`	Getting the URL for the MRAN time machine repository for current R version
`is_enabled_rdsMode()`	Checks if the rds mode is enabled
`setup_IQRtools()`	Opening the setup_options_IQRtools.R file for editing
`test_IQReport()`	Test IQReport integration
`test_IQRsbml()`	Test IQRsbml integration
`test_IQRtools()`	Test IQRtools simulation
`test_MONOLIX()`	Test MONOLIX interface
`test_NONMEM()`	Test NONMEM interface
IQR plot
`IQRggplot()`	ggplot functionality implementing IQRtools style
`applyPaginate()`	Get list of paginated plots
`aux_plotlayout()`	Determine layout for distribution single plots to rows, columns, and pages
`createPages_IQRoutputFigure()`	Create pages from IQRoutputFigure
`plot(<IQRoutputFigure>)`	Plot function for IQRoutputFigure (calls print)
`print(<IQRoutputFigure>)`	Print IQRoutputFigure to pages (ggplot objects)
`print(<IQRoutputFigureList>)`	Prints summary for the IQRoutputFigures contained in the list
`print(<IQRslideplot>)`	Generic print function for IQRslideplot objects
`printGrid()`	Plotting a list of ggplot objects in a grid defined by nrow and ncol
`scale_color_IQRtools()`	Color table for IQRtools
`scale_fill_IQRtools()`	Color table for IQRtools
`scale_y_log10_IQRtools()` `scale_x_log10_IQRtools()`	Log scale for x or y axis with proper grid lines
`summary(<IQRoutputFigure>)`	Summary function for IQRoutputFigure
`themeIQRtools()`	IQR Tools' standard theme
IQR report
`IQReport()`	Interface to the IQReport command line interface tool
`export_IQRrmd()`	Export IQRrmd object to an rmd file
`has_IQReport_executable()`	Check if IQReport is installed and available
`+`(<IQRrmd>)	Concatenate IQRrmd objects
`print(<IQRrmd>)`	Overloading "print" for IQRrmd objects
`rmdAPPROVALS()`	Add an approvals page to the report (after title)
`rmdCOMMENT()`	Generate RMD command to include a Word comment
`rmdEMPTY()`	Create empty IQRrmd object
`rmdFIGURE()`	Generate RMD command to include a figure from a file
`rmdFIGref()`	Figure Cross reference
`rmdLANDSCAPE()`	Switch to Landscape mode
`rmdLINEBREAK()`	Add a simple line break
`rmdNEWPAGE()`	Generate newpage RMD command
`rmdNOINTRO()`	Do not include TOC/TOF/TOT in DOCX report
`rmdPARAGRAPH()`	Start a new paragraph
`rmdPDF()`	Generate RMD command to include a PDF from a file
`rmdPORTRAIT()`	Switch to Portrait mode
`rmdSECTION()`	Generate Section RMD command
`rmdSECref()`	Section Cross reference
`rmdTABLE()`	Generate RMD command to include a table from a file
`rmdTABLEDF()`	Generate RMD command to include a table from a dataframe
`rmdTABref()`	Table Cross reference
`rmdTEXTSTYLE()`	Change the size, color, and/or style of a text piece
`rmdTITLE()`	Generate title RMD command
`rmdTXT()`	Generate RMD command to include a text from a file
`rmdTXTref()`	Text Cross reference
`rmdURL()`	Generate RMD command to include a URL
`rmdVALref()`	Value Table cross reference
IQR shiny
`loadSetupOptions_IQRtools()`	Loading IQRtools setup options
IQR slides
`print(<IQRslideplot>)`	Generic print function for IQRslideplot objects
IQR Table
`IQRtable()`	Flexibly generate output tables based on a data frame and derived statistical quantities
`as.data.frame(<IQRtable>)`	Convert IQRtable (matrix) to data frame
`as_IQRtable()` `is_IQRtable()`	IQRtables
`cjoin_IQRtable()` `rjoin_IQRtable()`	Join tables based on first column or first row
`composeByRule_IQRtable()`	Compose tables according to a rule provided by a pattern
`compose_IQRtable()`	Compose several tables to a new table following a construction pattern
IQRaedataER
`contingency_IQRaedataER()`	Generation of contingency table for AEs and categorical covariates
`is_IQRaedataER()`	Check function if it is an IQRaedataER object
`plotCorCat_IQRdataER()`	Plot correlation of categorical covariates in an IQRdataER/IQRaedataER object
`plotCorCovCat_IQRdataER()`	Plot correlation of continuous and categorical covariates in an IQRdataER/IQRaedataER object
`plotCorCov_IQRdataER()`	Plot correlation of continuous covariates in an IQRdataER/IQRaedataER object
`plotcontcovAE_IQRaedataER()`	Plotting relationship of AEs with continuous covariates
`summary(<IQRaedataER>)`	Generic summary function for IQRaedataER objects
`summaryN_IQRaedataER()`	Generates a basic summary of AE in the provided data
`summary_IQRaedataER()`	Simple summary of AEs in IQRaedataER dataset
IQRdataER
`addLabel_IQRaedataER()`	Add labels to data to allow subsequent XPT export
`createAEdata_IQRdataGENERAL()`	Creates an initial AE analysis dataset based on a general dataset
`exportXPT_IQRaedataER()`	Export IQRaedataER object as XPT file
`export_IQRaedataER()`	Exports an IQRaedataER object
`load_IQRaedataER()`	Loads an IQRaedataER object from CSV and ATR file
`plotCorCat_IQRdataER()`	Plot correlation of categorical covariates in an IQRdataER/IQRaedataER object
`plotCorCovCat_IQRdataER()`	Plot correlation of continuous and categorical covariates in an IQRdataER/IQRaedataER object
`plotCorCov_IQRdataER()`	Plot correlation of continuous covariates in an IQRdataER/IQRaedataER object
`plotIndivAE_IQRdataGENERAL()`	Plotting AE occurrences and dosing times for each individual
`print(<IQRaedataER>)`	Generic print function for IQRaedataER objects
`summaryCat_IQRdataER()`	Generates a demographic summary table for categorical covariates
`summaryCov_IQRdataER()`	Generates a demographic summary table for continuous covariates
`summaryN_IQRaedataER()`	Generates a basic summary of AE in the provided data
`summary_IQRaedataER()`	Simple summary of AEs in IQRaedataER dataset
IQRdataGeneral
`IQRcalcTAD()`	Calculate TAD column
`IQRdataGENERAL()`	Imports a CSV dataset as an IQRdataGENERAL object
`IQRexpandADDLII()`	Expand ADDL and II dosing information
`IQRloadCSVdata()`	Simple auxiliary to load a CSV dataset
`IQRsaveCSVdata()`	Simple auxiliary to save a CSV dataset with attributes
`addCovariateInfo_IQRdataGENERAL()`	Addition of covariate information
`addIndivRegressors_IQRdataGENERAL()`	Adds individual parameter estimates from a IQRnlmeProject to a dataset. Existing regression parameters are kept. Existing columns with same names as regression parameters are substituted.
`addLabel_IQRdataGENERAL()`	Add labels to data to allow subsequent XPT export
`attributes0()` `obsNAMES()` `doseNAMES()` `covInfo()` `catInfo()`	Access Attributes of IQRdataGENERAL Object
`blloqInfo_IQRdataGENERAL()`	Determine summary information for BLLOQ values in an IQRdataGENERAL object
`blloq_IQRdataGENERAL()`	Updates an IQRdataGENERAL object for a specific BLLOQ handling method
`check_IQRdataGENERAL()`	Checks consistency or a general dataset
`clean_IQRdataGENERAL()`	Wrapper for several IQRdataGENERAL cleaning functions
`combine_IQRdataGENERAL()`	Concatenate IQRrmd objects
`convertCat2Text()`	Convert numerical values of a categorical covariate into text values
`covImpute_IQRdataGENERAL()`	Imputes missing covariates
`date2dateday_IQRdataProgramming()`	Conversion of date/time in string format to day in string format
`date2datetime_IQRdataProgramming()`	Conversion of date/time in string format to time in string format
`date2time_IQRdataProgramming()`	Conversion of date/time in string format to numeric values
`exportDEFINE_IQRaedataER()`	Exports a define file for the provided dataset (IQRaedataER)
`exportDEFINE_IQRdataGENERAL()`	Exports a define file for the provided dataset
`exportDEFINEpdf_IQRdataGENERAL()`	Exports a define file for the provided dataset as pdf via LaTeX.
`exportSYS_IQRdataGENERAL()` `exportNLME_IQRdataGENERAL()`	Exports an IQRdataGENERAL object as an NLME dataset
`export_IQRdataGENERAL()`	Exports an IQRdataGENERAL object
`getLabels_dataframe()`	Extract label information of columns in data.frames
`getNAcolNLME_IQRdataGENERAL()`	Finds columns in the NLME part with NA values
`handleSameTimeObs_IQRdataGENERAL()`	Adds tiny noise to TIME when TIME same for NAME in USUBJID
`is_IQRdataGENERAL()`	Check function if it is an IQRdataGENERAL object
`loadATRinfo_csvData()`	Attempts to load the atr info for a csv file
`loadAttributeFile()`	Loads the attributes from an atr file to a list. It ensures some backward compatibility as IQRtools versions until 0.9.3 saved the attributes as single variables and not as a list.
`load_IQRdataGENERAL()`	Loads an IQRdataGENERAL object from CSV and ATR file
`mapCategoricalCovariate_IQRnlmeProject()`	Attempts to map a continuous covariate by name of the covariate column to information such as NAME, VALUETXT, and TIME.VARYING
`mapCategoricalCovariate_csvData()`	Attempts to map a continuous covariate by name of the covariate column to information such as NAME, VALUETXT, and TIME.VARYING
`mapContinuousCovariate_IQRnlmeProject()`	Attempts to map a continuous covariate by name of the covariate column to information such as NAME, UNIT, and TIME.VARYING
`mapContinuousCovariate_csvData()`	Attempts to map a continuous covariate by name of the covariate column to information such as NAME, UNIT, and TIME.VARYING
`mutateCov_IQRdataGENERAL()`	Add Covariate to IQRdataGENERAL object
`obfuscate_IQRdataGENERAL()`	Obfuscated version of an IQRdataGENERAL object
`plot(<IQRdataGENERAL>)`	Generic print function for IQRdataGENERAL objects
`plotCorCat_IQRdataGENERAL()`	Plot correlation of categorical covariates in an IQRdataGENERAL object
`plotCorCovCat_IQRdataGENERAL()`	Plot correlation of continuous and categorical covariates in an IQRdataGENERAL object
`plotCorCov_IQRdataGENERAL()`	Plot correlation of continuous covariates in an IQRdataGENERAL object
`plotCovDistribution_IQRdataGENERAL()`	Plot distribution of continuous covariates in an IQRdataGENERAL object
`plotDoseSchedule_IQRdataGENERAL()`	Plot overview over dosing records
`plotIndiv_IQRdataGENERAL()`	Plot individual longitudinal data over time as lines (one graph per observation)
`plotObsSummarizedByCovCat_IQRdataGENERAL()`	Plot observations along with summaries for each covariate
`plotRange_IQRdataGENERAL()`	Plot summary (median, 90-percent interval) data over time
`plotSampleSchedule_IQRdataGENERAL()`	Plot sampling and dosing time points
`plotSpaghetti_IQRdataGENERAL()`	Plot individual longitudinal data over time as lines (one panel per observation)
`+`(<IQRdataGENERAL>)	Concatenate IQRrmd objects
`print(<IQRdataGENERAL>)`	Generic print function for IQRdataGENERAL objects
`removeCommata_dataframe()`	Remove commata in elements in data.frame
`rmAMT0_IQRdataGENERAL()`	Removes dose records with AMT=0
`rmDosePostLastObs_IQRdataGENERAL()`	Remove dose records post last individual observation
`rmIGNOREd_IQRdataGENERAL()`	Removes records from an IQRdataGENERAL object which have an entry in the IGNORE column
`rmMissingTIMEobsRecords_IQRdataGENERAL()`	Remove observation records that have missing (NA) TIME value
`rmNOobsSUB_IQRdataGENERAL()`	Removes subjects without MDV=0 observations
`rmNonTask_IQRdataGENERAL()`	Removes records non dose and non observation records
`rmPLACEBO_IQRdataGENERAL()`	Removes placebo subjects from the dataset
`rmSubjects_IQRdataGENERAL()`	Removes user defined subjects from dataset
`setIGNORErecords_IQRdataGENERAL()`	Sets IGNORE information on user defined records
`setMissingDVobsRecordsIGNORE_IQRdataGENERAL()`	Sets IGNORE information on observation records that have missing (NA) DV value
`subset(<IQRdataGENERAL>)`	Subsetting IQRdataGeneral Objects
`summary(<IQRdataGENERAL>)`	Generic summary function for IQRdataGENERAL objects
`summaryCat_IQRdataGENERAL()`	Generates a demographic summary table for categorical covariates
`summaryCov_IQRdataGENERAL()`	Generates a demographic summary table for continuous covariates
`summaryObservations_IQRdataGENERAL()`	Generates a summary of observations in an IQRdataGENERAL object
`transformObs_IQRdataGENERAL()`	Add New Observations by Transformation of an Existing Observable
`unlabel_dataframe()`	Remove labelled class and label
IQRdataGENERAL
`addCatColumnAsText_IQRdataGENERAL()`	Function to add a column for a covariate containing the levels as text values
`convertCatColsToFactors_IQRdataGENERAL()`	Apply Levels and Labels to Categorical Columns in a Data Frame
`plotIndivAE_IQRdataGENERAL()`	Plotting AE occurrences and dosing times for each individual
IQRdataGENERAL auxiliaries
`getCatValues_catInfo()`	Extract numerical values of a covariate from covariate information table
`getTextValues_catInfo()`	Extract numerical values of a covariate from covariate information table
IQReventTable
`addTminToEventTable()`	Add min(simtime) to eventTable
`split_eventTable()`	Split eventTable into smaller Tables
IQRmodel
`IQRmodel()`	IQRmodel
`addOutputs_IQRmodel()`	Add output equations to IQR model
`addRelations_IQRmodel()`	Add new relations to an IQR model
`createSimIQRmodelSpec()`	Collect and standardize input arguments for sim_IQRmodel
`exportSBML_IQRmodel()`	Exports an IQRmodel to SBML
`exportVariant_IQRmodel()`	Exports a model structure with associated parameterization variant
`export_IQRmodel()`	Export of an IQRmodel object
`getPars_IQRmodel()`	Get parameter vector from an IQRmodel
`hasCcodeFunctions_IQRmodel()`	Checks if an IQRmodel contains C functions
`hasInitialAssignments_IQRmodel()`	Checks if an IQRmodel contains initial assignments
`importSBML_IQRmodel()`	Imports an SBML model
`importVariant_IQRmodel()`	Important a model structure with defined parameterization variant
`is_IQRmodel()`	Check if object is an IQRmodel
`new_IQRmodel()`	Generates a new IQRmodel file and opens it in the RStudio editor
`print(<IQRmodel>)`	Generic print function
`print(<IQRsensitivity>)`	Print function for IQRsensitivity
`regenerate_IQRmodel()`	Regeneration of the compiled code of an IQRmodel
`replaceTerms_IQRmodel()`	Replace terms in ODEs of IQR model
`sensitivity_IQRmodel()`	Local parameter sensitivity analysis
`setParameters_IQRmodel()`	Set parameters in an IQRmodel to defined values
`setPars_IQRmodel()`	Set parameters of an IQRmodel
`sim_IQRmodel()`	Simulate an IQRmodel
`sim_IQRmodel_strict()`	sim_IQRmodel with strict output format
`simbio_CSV2namedVector()`	Load CSV file contents as named vector
`simbio_updateParamIC_IQRmodel()`	Return model with updated parameters and initial conditions defined in a CSV file
`stoichiometry_IQRmodel()`	Determination of stoichiometric matrix
`strReplace_IQRmodel()`	Replaces strings in IQRmodels
IQRnlmeData
`IQRcalcTAD()`	Calculate TAD column
`IQRexpandADDLII()`	Expand ADDL and II dosing information
`IQRloadCSVdata()`	Simple auxiliary to load a CSV dataset
`IQRsysData()` `IQRnlmeData()`	Imports a csv dataset as IQRnlmeData object
`IQRsaveCSVdata()`	Simple auxiliary to save a CSV dataset with attributes
`date2dateday_IQRdataProgramming()`	Conversion of date/time in string format to day in string format
`date2datetime_IQRdataProgramming()`	Conversion of date/time in string format to time in string format
`date2time_IQRdataProgramming()`	Conversion of date/time in string format to numeric values
`export_IQRnlmeData()`	Export function for IQRnlmeData object
`getLabels_dataframe()`	Extract label information of columns in data.frames
`is_IQRnlmeData()`	Check function if it is an IQRnlmeData object
`plot(<IQRnlmeData>)`	Generic plot for an IQRnlmeData object
`print(<IQRnlmeData>)`	Generic print function for IQRnlmeEst objects
`removeCommata_dataframe()`	Remove commata in elements in data.frame
`unlabel_dataframe()`	Remove labelled class and label
IQRnlmeProject
`IQRnlmeEst()`	Creating an IQRnlmeEst object
`IQRnlmeProject()`	Creating an IQRnlmeProject object
`addCovariateToModelSpec_IQRest()`	Extends the model specification by covariate relationships.
`addPar_modelSpec()` `addCov_modelSpec()` `addErr_modelSpec()` `removePar_modelSpec()` `removeCov_modelSpec()` `removeErr_modelSpec()`	Convenience functions for model spec manipulation
`as_IQRnlmeProject()`	Creating an IQRnlmeProject from a path
`as_IQRnlmeProjectMulti()`	Creating an IQRnlmeProjectMulti project
`bootstrap_IQRnlmeProject()`	Perform a non-parametric bootstrap on an IQRnlmeProject
`compareModels_IQRnlmeProjectMulti()`	Compare the estimation specifications or results between multiple NLME projects
`convertETAINDIVPRED_IQRnlmeProject()`	Generates eta, indiv, and pred results
`covariateEffect_IQRnlmeProject()`	Assess impact of covariates on parameters
`data_IQRest()`	Defines a data list for use in setting up estimation objects.
`dosing_IQRest()`	Defines a dosing list for use in setting up estimation objects.
`duplicate_IQRnlmeProject()`	Duplicates a model at a different path
`eigenvalues_IQRnlmeProject()`	Determines eigenvalues of an NLME project
`exportVirtualSubjects_IQRnlmeProject()`	Exports virtual subjects obtained through individual parameter estimation or sampling from population distribution
`getData_IQRnlmeProject()`	Returns the dataset from an IQRnlmeProject
`getETAs_IQRnlmeProject()`	Gets the individual ETAs for an IQRnlmeProject
`getEst_IQRnlmeProject()`	Returns the estimation object for an NLME project
`getHeader_IQRnlmeProject()`	Return the meta data header of an IQRnlmeProject
`getIndivParameters_IQRnlmeProject()`	Gets the individual parameter estimates from a IQRnlmeProject
`getIndivPredictions_IQRnlmeProject()`	Gets the individual predictions from a IQRnlmeProject
`getModel_IQRnlmeProject()`	Returns the structural model used in an NLME project
`getObsPred_IQRnlmeProject()`	Gets the observations and individual as well as population predictions from a IQRnlmeProject
`getPopParameters_IQRnlmeProject()`	Gets the population parameter estimates from a IQRnlmeProject
`getResults_IQRnlmeProject()`	Return parameter estimates for NLME projects
`getResults_IQRnlmeProjectMulti()`	Gets the results from projects in the IQRnlmeProjectMulti object that were run. A list is return with one field for each project containing metadata and estimation results of all run projects. List entries should retain provided names.
`hasrun_IQRnlmeProject()`	Checks if an IQRnlmeProject has been run
`hasrun_IQRnlmeProjectMulti()`	Checks if projects within an IQRnlmeProjectMulti have been run
`informationContent_IQRnlmeProject()`	Assess the expected information content wrt parameters, given a dosing and observation schedule.
`is_IQRnlmeEst()`	Check function if it is an IQRnlmeEst object
`is_IQRnlmeProject()`	Checks if given project path is an IQRnlmeProject
`is_IQRnlmeProjectMulti()`	Checks if given project path is an IQRnlmeProjectMulti
`is_MONOLIX_IQRnlmeProject()`	Checks if given project path is a MONOLIX IQRnlmeProject
`is_NLMIXR_IQRnlmeProject()`	Checks if given project path is a NLMIXR IQRnlmeProject
`is_NONMEM_IQRnlmeProject()`	Checks if given project path is a NONMEM IQRnlmeProject —-
`modelSpec_IQRest()`	Defines a modelSpec list for use in setting up estimation objects.
`outlier_IQRnlmeProject()`	Generates a table with outlier information
`plot(<IQRnlmeProject>)`	Generic plot for an IQRnlmeProject object
`plot(<IQRnlmeProjectMulti>)`	Generic plot function for IQRnlmeProjectMulti objects
`plotBLQVPC_IQRdataVPC()`	Create VPC plot for fraction BLQ values
`plotConvergence_IQRnlmeProject()`	Generates plots of convergence trajectories for NLME projects
`plotETACOV_IQRnlmeProject()`	Generates plots of eta/covariate (lin and log cont cov) correlations for NLME projects
`plotETA_IQRnlmeProject()`	Generates plots of etas and their correlations for NLME projects
`plotGOF_IQRnlmeProject()`	Create GOF plots for IQRnlmeProjects
`plotINDIVSIM_IQRnlmeProject()`	Plot the individual fits for NLME projects using simulated individual fits.
`plotINDIV_IQRnlmeProject()`	Generates individual DV/PRED/IPRED plost for NLME projects
`plotMEANSIM_IQRnlmeProject()`	Simulate with individual parameters or population parameters (considering covariates) and plot the result
`plotVPC_IQRdataVPC()`	Create VPC plot
`pred_IQRnlmeProject()`	Predict values based on provided NLME project
`print(<IQRnlmeEst>)`	Generic print function for IQRnlmeEst objects
`print(<IQRnlmeProject>)`	Generic print function for IQRnlmeProject objects
`print(<IQRnlmeProjectMulti>)`	Generic print function for IQRnlmeProjectMulti objects
`print_modelSpec()`	Print function for model specification list
`run_IQRnlmeProject()`	Runs an IQRnlmeProject
`run_IQRnlmeProjectMulti()`	Runs an IQRnlmeProjectMulti object (each IQRnlmeProject within)
`sample_IQRnlmeProject()`	Samples parameters from an IQRnlmeProject
`scm_IQRnlmeProject()`	Perform a stepwise covariate modeling (SCM)
`summary(<IQRnlmeProject>)`	Generic summary function for IQRnlmeProject objects
`summary(<IQRnlmeProjectMulti>)`	Generic summary function for IQRnlmeProjectMulti objects
`summaryComments_IQRnlmeProjectMulti()`	Generates a table with MODEL names and MODEL comments for an IQRnlmeProjectMulti object
`summaryCorrelations_IQRnlmeProjectMulti()`	Allows to generate a summary of correlation coefficients for an IQRnlmeProjectMulti object
`summaryCovariates_IQRnlmeProjectMulti()`	Allows to generate a summary of covariates for an IQRnlmeProjectMulti object
`summaryParameters_IQRnlmeProjectMulti()`	Allows to generate a summary of parameters for an IQRnlmeProjectMulti object
`vpc_IQRnlmeProject()`	Create data for VPC
IQRtteProject
`IQRtteProject()`	Generation of a MONOLIX TTE project
`as_IQRtteProject()`	Creating an IQRtteProject from a path
`as_IQRtteProjectMulti()`	Creating an IQRtteProjectMulti project
`is_IQRtteProject()`	Checks if given project path is an is_IQRtteProject
`is_IQRtteProjectMulti()`	Checks if given project path is an is_IQRtteProjectMulti
`plot(<IQRtteProject>)`	Generic plot for an IQRtteProject object
`plotVPC_IQRtteProject()`	Plots the VPC for an IQRtteProject and joint models based on IQRnlmeProject
`print(<IQRtteProject>)`	Generic print function for IQRtteProjects objects
`print(<IQRtteProjectMulti>)`	Generic print function for IQRtteProjectMulti objects
`run_IQRtteProject()`	Runs an IQRtteProject
`run_IQRtteProjectMulti()`	Runs an IQRtteProjectMulti object (each IQRtteProject within)
Logistic regression
`IQRlogisticRegression()`	Logistic regression with multiple predictors
`export_IQRlogisticFit()`	Write logistic regression object to project folder
`import_IQRlogisticFit()`	Load logistic regression object from project folder
`modelEvaluation_IQRlogisticRegression()`	Model evaluation IQRlogisticRegression projects
`plot_IQRlogistRegressFit()`	Plot predictions for fitted logistic regression model
`simple_IQRlogisticRegression()`	Simple logistic regression with a single predictor
`summary_IQRlogisticRegression()`	Table comparing estimates and
MONOLIX
`results_MONOLIX()`	Generates tabular and graphical information for a MONOLIX model
NLMIXR
`convertDataRxODE_IQRnlmixr()`	Converts an IQRdataGENERAL or IQRnlmeData object to RxODE format
`is_installed_NLMIXR()`	Checks installation of NLMIXR
Optimal Experiment Design
`IQRpopEDdb()`	Create a PopED database for an IQRmodel
`evaluate_IQRpopEDdb()`	Evaluate IQRpopEDdb Object
`sim_IQRpopEDdb()`	Simulate from IQRpopEDdb Object
Other functions
`expand.grid2()`	Expand.grid which takes in data.frames as well
`verifyArg()`	Verify that input arguments meet certain conditions
Output
`IQRinitCompliance()`	Initializes the compliance mode
`IQRoutputCSV()`	Exporting a data.frame as CSV file
`IQRoutputDEFINE()`	Exports a define file for the provided dataset
`IQRoutputFigure()`	Create IQRoutputFigure object and/or print graph object to file
`IQRoutputFile()`	Exporting a text file with added compliance information log file
`IQRoutputPDF()`	Printing ggplot object or list of objects to a PDF file with added compliance information log file
`IQRoutputPDFParallel()`	Output multipage pdf in parallelized manner
`IQRoutputPDFend()`	Ends export to PDF (deprecated)
`IQRoutputPDFstart()`	Start export to PDF (deprecated)
`IQRoutputPNG()`	Printing a single ggplot object to png file with added compliance information log file
`IQRoutputRDS()`	Exporting an R object to RDS format with added compliance information log file
`IQRoutputTable()`	Convert dataframe to IQRoutputTable object and allow export
`IQRoutputValueTable()`	Exporting a value with label and potential description for reporting
`IQRoutputXPT()`	Export general data.frame object as XPT file
`createSubmissionPack()`	Create submission package for analysis
`getModelSpecification()`	Default specifications for models copied to submission package
`getProgramSpecification()`	Default specifications for programs (scripts) to be copied to submission package
`import_IQRdataOriginal()`	Import a data file into the current folder structure
`is_enabled_complianceMode()`	Checks if the compliance mode is enabled
`is_enabled_rdsMode()`	Checks if the rds mode is enabled
`packageR_IQRtools()`	R Packaging function for reproducibility
`print(<IQRoutputTable>)`	Overloading "print" for IQRoutputTable objects
`read_IQRoutputTable()`	Read IQRoutputTable txt file from disk as data frame
`text_IQRoutputTable()`	Convert IQRoutputTable to text representation
Parameter sampling
`generate_GPFFromIQRnlmeEst()`	Generate GPF from IQRnlmeEst or IQRsysEst
`generate_GPFFromIQRnlmeProject()`	Generate GPF from IQRnlmeProject of IQRsysProject
`generate_GPFFromProjectInfo()`	Rename/pick parameters and covariates in a GPF
`generate_GPFFromProjectInfoList()`	From multiple projectInfos, generate one combined GPF
`is_GPF()`	Check if an object inherits from S3 class GPF
`is_IQRnlmeParamSpec()`	Check if an object has class IQRnlmeParamSpec
`sample_GPF()`	Sample wrapper with syntax as sample_IQRnlmeProject for GPF excel files
`select_FromGPF()`	Select and, optionally, rename parameters and covariates in a GPF
QSP
`IQRsysEst()`	Creating an IQRnlmeEst object
`IQRsysModel()`	Generate an IQRsysModel
`IQRsysProject()`	Creating an IQRsysProject object
`addOutputs_IQRmodel()`	Add output equations to IQR model
`addRelations_IQRmodel()`	Add new relations to an IQR model
`as_IQRsysEst()`	Coerce to IQRsysEst object
`as_IQRsysProject()`	Creating an IQRsysProject from a path
`as_IQRsysProjectMulti()`	Creating an IQsysProjectMulti project
`comparePars_IQRsysModel()`	Simulate and plot an IQRsysModel for provided parameterizations
`duplicate_IQRsysProject()`	Duplicates a model at a different path
`exportVariant_IQRmodel()`	Exports a model structure with associated parameterization variant
`exportVirtualSubjects_IQRnlmeProject()`	Exports virtual subjects obtained through individual parameter estimation or sampling from population distribution
`export_IQRsysData()`	Export IQRsysData with attributes
`getDosing_IQRsysModel()`	Get dosing information from IQRsysModel
`getEmpiricalETACovarianceMatrix_IQRsysProject()`	Empirical ETA covariance matrix IQRsysProjects
`getOptTrace_IQRsysProject()`	Read Optimization Trace Files
`getPars_IQRoptTrace()`	Extract Vector of Parameter Values from Optimization Trace Data
`getPars_IQRsysModel()`	Get parameter vector from an IQRsysModel
`getPrediction_IQRsysModel()`	Access simulation results
`hasrun_IQRsysProject()`	Checks if an IQRsysProject has been run
`importVariant_IQRmodel()`	Important a model structure with defined parameterization variant
`import_IQRsysData()`	Convert data to an IQRsysData object
`is_IQRsysEst()`	Check function if it is an IQRsysEst object
`is_IQRsysModel()`	Check if object is an IQRsysModel
`is_IQRsysProject()`	Checks if given project path is an IQRsysProject
`is_IQRsysProjectMulti()`	Checks if given project path is an IQsysProjectMulti
`load_IQRsysProject()`	Read an existing IQRsysProject
`modelSpec_IQRsysEst()`	Model specification for IQRsysEst
`model_IQRsysModel()` `dataSpec_IQRsysModel()` `modelSpec_IQRsysModel()`	Retrieve model, data spec and model spec from IQRsysModel
`offsetTIME_IQRsysData()`	Function to shift data right on time axis by a certain offset
`plotDVPRED_IQRsysModel()`	Data vs prediction diagnostics plot
`plotFit_IQRsysModel()`	Plot model fit and data
`plotPars_IQRsysModel()`	Overview plot of the estimated parameter values
`plotPred_IQRsysModel()`	Plot model for estimated parameters from multi start estimation
`plotProfile_IQRsysModel()`	Generate profile likelihood plot from IQRsysModel object
`plotWRES_IQRsysModel()`	Weighted residuals diagnostics plot
`plotWaterfall_IQRsysModel()`	Waterfall plot of objective values
`plot_IQRoptTrace()`	Plot Optimization Traces
`plot_IQRsysModel()`	Plot model and data represented by IQRsysModel
`print(<IQRsensitivity>)`	Print function for IQRsensitivity
`print(<IQRsysProject>)`	Generic print function for IQRsysProject objects
`profile_IQRsysModel()`	Compute profile likelihood
`replaceTerms_IQRmodel()`	Replace terms in ODEs of IQR model
`run_IQRsysProject()`	Runs an IQRsysProject
`run_IQRsysProjectMulti()`	Runs an IQRsysProjectMulti object (each IQRsysProject within)
`sample_IQRsysModel()`	Sample model parameters using covariates.
`sensitivity_IQRmodel()`	Local parameter sensitivity analysis
`setPars_IQRsysModel()`	Set parameters of an IQRsysModel
`sim_IQRsysModel()`	Simulate IQRsysModel
`sim_IQRvirtualSubjects()`	Simulate Virtual Subjects, Cohorts, Populations
`simbio_CSV2namedVector()`	Load CSV file contents as named vector
`simbio_updateParamIC_IQRmodel()`	Return model with updated parameters and initial conditions defined in a CSV file
`spmIIV_IQRsysProject()`	Stepwise Parameter Modeling for QSP - random effects
`spm_IQRsysProject()`	Stepwise Parameter Modeling for QSP - fixed effects
`switchOpt_IQRsysModel()`	Switch the selected optimum
`tablePars_IQRsysModel()`	Generate table output of estimated modle parameters
SAS
`IQRloadSASdata()`	Loading SAS data
`getLabels_dataframe()`	Extract label information of columns in data.frames
`unlabel_dataframe()`	Remove labelled class and label
Sensitivity analysis
`create_dFC_singlePar()`	Convenience function to create a "d"ata.frame of "F"old"C"hanges for sensitivity scan
`explodeEventTable_sensitivityScan()`	Expand the eventTable by the fold-change scenarios of interest and apply fold-changes
`sim_IQRmodel_sensitivityScan()`	Simulate an IQRmodel and scan the sensitivity of a specified parameter
Sensitivity Analysis
`informationContent_IQRnlmeProject()`	Assess the expected information content wrt parameters, given a dosing and observation schedule.
`print(<IQRsensitivity>)`	Print function for IQRsensitivity
`sensitivity_IQRmodel()`	Local parameter sensitivity analysis
Simulation
`IQRdosing()`	IQRdosing class
`IQReventTable()`	IQReventTable class
`createSimIQRmodelSpec()`	Collect and standardize input arguments for sim_IQRmodel
`create_IQReventData()`	Function to combine IQRdosing with individual regression parameters to construct data frame suitable as inputs to IQReventTable
`create_IQReventTable()`	Creates an IQReventTable based on IQR dosing and individual parameters
`extract_IQRdosing()`	Function to extract IQRdosing from modeling data set. A list of IQRdosing objects is returned containing each individual or each unique dosing.
`getDefaultEventTable()`	Get an IQReventTable from an IQRmodel, dosing and parameters
`is_IQRdosing()`	Check function if it is an IQRdosing object
`is_IQReventTable()`	Check function if it is an IQReventTable object
`is_IQRsimres()`	Check function if it is an IQRsimres object
`is_IQRsimresMulti()`	Check function if it is an IQRsimresMulti object
`plot(<IQRsimres>)`	Generic plot function for IQRsimres objects
`plot(<IQRsimresMulti>)`	Generic plot function for IQRsimresMulti objects
`print(<IQRdosing>)`	Generic print function for IQRdosing objects
`print(<IQReventTable>)`	Generic print function for IQReventTable objects
`print(<IQRsimres>)`	Generic print function for IQRsimres objects
`print(<IQRsimresMulti>)`	Generic print function for IQRsimresMulti objects
`rbind_IQRdosing()`	Combines 2 or more IQRdosing objects together
`sim_IQRmodel()`	Simulate an IQRmodel
`sim_IQRmodel_sensitivityScan()`	Simulate an IQRmodel and scan the sensitivity of a specified parameter
`sim_IQRmodel_strict()`	sim_IQRmodel with strict output format
stat functions
`statCI()`	Return key statistical quantities generated from value, lower and upper confidence bounds
Statistics
`statSE()`	Return key statistical quantities generated from value and standard error
Submission package
`IQRoutputDEFINE()`	Exports a define file for the provided dataset
`IQRoutputXPT()`	Export general data.frame object as XPT file
`addLabel_IQRaedataER()`	Add labels to data to allow subsequent XPT export
`addLabel_IQRdataGENERAL()`	Add labels to data to allow subsequent XPT export
`createSubmissionPack()`	Create submission package for analysis
`exportDEFINE_IQRaedataER()`	Exports a define file for the provided dataset (IQRaedataER)
`exportDEFINE_IQRdataGENERAL()`	Exports a define file for the provided dataset
`exportDEFINEpdf_IQRdataGENERAL()`	Exports a define file for the provided dataset as pdf via LaTeX.
`exportXPT_IQRaedataER()`	Export IQRaedataER object as XPT file
`getModelSpecification()`	Default specifications for models copied to submission package
`getProgramSpecification()`	Default specifications for programs (scripts) to be copied to submission package
Survival analysis
`IQRcoxRegression()`	Proportional Hazard Cox regression with a multiple predictors
`export_IQRcoxRegression()`	Write cox proportional hazard regression object to project folder
`import_IQRcoxRegression()`	Load cox proportional hazard regression object from project folder
`km_IQRsurvival()`	Kaplan-Meier estimation and plotting.
`plot_IQRcoxRegression()`	Plot some diagnostics for fitted Cox proportional hazard regression model
`summary_IQRcoxRegression()`	Table comparing estimates of Cox proportional harzard regression models
VPC
`extractBins_VPCplot()`	Extract the mapping between IXGDF and BIN of a VPC plot
`filterMutateDataVPC()`	Mutate and filter dataVPC
`plotBLQVPC_IQRdataVPC()`	Create VPC plot for fraction BLQ values
`plotVPC_IQRdataVPC()`	Create VPC plot
`plotVPC_IQRtteProject()`	Plots the VPC for an IQRtteProject and joint models based on IQRnlmeProject
`vpc_IQRnlmeProject()`	Create data for VPC

Function Reference

Allowed in IQRmodel

Auxiliary

Bootstrap

Covariate analysis

Data exploration

Data handling

Formatting

GPF

Help & Documentation

Installation

IQR plot

IQR report

IQR shiny

IQR slides

IQR Table

IQRaedataER

IQRdataER

IQRdataGeneral

IQRdataGENERAL

IQRdataGENERAL auxiliaries

IQReventTable

IQRmodel

IQRnlmeData

IQRnlmeProject

IQRtteProject

Logistic regression

MONOLIX

NLMIXR

Optimal Experiment Design

Other functions

Output

Parameter sampling

QSP

SAS

Sensitivity analysis

Sensitivity Analysis

Simulation

stat functions

Statistics

Submission package

Survival analysis

VPC