A Function Reference

This Appendix is still work in progress. An automtically generated list of all exported IQRtools functions will be available. Grouped by topic and hyperlinked to the function documentation.

Until V1.0.0 it will be done …

A.1 IQRtools setup

doc_IQRtools
examples_IQRtools
getRepos
license_IQRtools
loadSetupOptions_IQRtools
packageR_IQRtools
setup_IQRtools
test_IQRtools

A.2 General data handling

addIndivRegressors_IQRdataGENERAL
attributes0
blloq_IQRdataGENERAL
blloqInfo_IQRdataGENERAL
catInfo
check_IQRdataGENERAL
clean_IQRdataGENERAL
combine_IQRdataGENERAL
covImpute_IQRdataGENERAL
covInfo
doseNAMES
export_IQRdataGENERAL
exportDEFINE_IQRdataGENERAL
exportNLME_IQRdataGENERAL
exportSYS_IQRdataGENERAL
getNAcolNLME_IQRdataGENERAL
handleSameTimeObs_IQRdataGENERAL
IQRcalcTAD
IQRdataGENERAL
IQRloadCSVdata
is_IQRdataGENERAL
IQRsaveCSVdata
load_IQRdataGENERAL
loadATRinfo_csvData
mapCategoricalCovariate_csvData
mapContinuousCovariate_csvData
mutateCov_IQRdataGENERAL
obsNAMES
rmIGNOREd_IQRdataGENERAL
rmMissingTIMEobsRecords_IQRdataGENERAL
rmNonTask_IQRdataGENERAL
rmNOobsSUB_IQRdataGENERAL
rmPLACEBO_IQRdataGENERAL
rmSubjects_IQRdataGENERAL
setIGNORErecords_IQRdataGENERAL
setMissingDVobsRecordsIGNORE_IQRdataGENERAL
transformObs_IQRdataGENERAL

A.3 Modeling dataset handling

convertDataRxODE_IQRnlmixr
export_IQRnlmeData
is_IQRnlmeData

A.4 Model handling

export_IQRmodel
hasCcodeFunctions_IQRmodel
importSBML_IQRmodel
IQRmodel
is_IQRmodel
new_IQRmodel
regenerate_IQRmodel
stoichiometry_IQRmodel

A.5 Simulation

IQRdosing
IQRexpandADDLII
IQReventTable
is_IQRdosing
is_IQReventTable
is_IQRsimres
is_IQRsimresMulti
setParameters_IQRmodel
sim_IQRmodel
sim_IQRsysCondition

A.6 Parameter estimation

data_IQRest
dosing_IQRest
modelSpec_IQRest

A.7 NCA

as_IQRdataNCA
IQRdataNCA
IQRnca
is_IQRdataNCA
is_IQRnca
load_IQRdataNCA
plotbyGroup_IQRnca
report_IQRnca
slopeTest_IQRnca
summarybyGroup_IQRnca

A.8 Data analysis

km_IQRsurvival
plotCorCat_IQRdataGENERAL
plotCorCov_IQRdataGENERAL
plotCorCovCat_IQRdataGENERAL
plotCovDistribution_IQRdataGENERAL
plotDoseSchedule_IQRdataGENERAL
plotIndiv_IQRdataGENERAL
plotRange_IQRdataGENERAL
plotSampleSchedule_IQRdataGENERAL
plotSpaghetti_IQRdataGENERAL
simple_IQRlogisticRegression
summaryCat_IQRdataGENERAL
summaryCov_IQRdataGENERAL
summaryObservations_IQRdataGENERAL

A.9 Model specification

IQRnlmeData
IQRnlmeEst
IQRsysData
IQRsysEst
is_IQRnlmeEst
is_IQRsysData
is_IQRsysEst

A.10 NLME project handling and assessment

as_IQRnlmeProject
as_IQRnlmeProjectMulti
as_IQRtteProject
as_IQRtteProjectMulti
bootstrap_IQRnlmeProject
covariateEffect_IQRnlmeProject
duplicate_IQRnlmeProject
eigenvalues_IQRnlmeProject
getData_IQRnlmeProject
getETAs_IQRnlmeProject
getIndivParameters_IQRnlmeProject
getIndivPredictions_IQRnlmeProject
getObsPred_IQRnlmeProject
getPopParameters_IQRnlmeProject
getResults_IQRnlmeProject
getResults_IQRnlmeProjectMulti
hasrun_IQRnlmeProject
informationContent_IQRnlmeProject
IQRnlmeProject
IQRsysFit
IQRtteProject
is_IQRnlmeProject
is_IQRnlmeProjectMulti
is_IQRsysFit
is_IQRsysFitMulti
is_IQRtteProject
is_IQRtteProjectMulti
is_MONOLIX_IQRnlmeProject
is_NLMIXR_IQRnlmeProject
is_NONMEM_IQRnlmeProject
mapCategoricalCovariate_IQRnlmeProject
mapContinuousCovariate_IQRnlmeProject
outlier_IQRnlmeProject
plotConvergence_IQRnlmeProject
plotETA_IQRnlmeProject
plotETACOV_IQRnlmeProject
plotGOF_IQRnlmeProject
plotINDIV_IQRnlmeProject
plotVPC_IQRtteProject
run_IQRnlmeProject
run_IQRnlmeProjectMulti
run_IQRtteProject
run_IQRtteProjectMulti
sample_IQRnlmeProject
summaryComments_IQRnlmeProjectMulti
summaryCorrelations_IQRnlmeProjectMulti
summaryCovariates_IQRnlmeProjectMulti
summaryParameters_IQRnlmeProjectMulti
vpc_IQRnlmeProject

A.11 QSP project handling and assessment

IQRsysProfileLL
plot_PathIQRprofLL

A.12 Model comparison

A.13 Experimental design

evaluate_IQRpopEDdb
IQRpopEDdb
sim_IQRpopEDdb

A.14 Reporting

export_IQRrmd
has_IQReport_executable
IQReport
rmAMT0_IQRdataGENERAL
rmdAPPROVALS
rmdCOMMENT
rmdEMPTY
rmdFIGref
rmdFIGURE
rmdLANDSCAPE
rmdLINEBREAK
rmdNEWPAGE
rmdNOINTRO
rmDosePostLastObs_IQRdataGENERAL
rmdPARAGRAPH
rmdPDF
rmdPORTRAIT
rmdSECref
rmdSECTION
rmdTABLE
rmdTABLEDF
rmdTABref
rmdTEXTSTYLE
rmdTITLE
rmdTXT
rmdTXTref
rmdURL
rmdVALref

A.15 Compliance output

IQRinitCompliance
IQRoutputCSV
IQRoutputFile
IQRoutputPDF
IQRoutputPDFend
IQRoutputPDFstart
IQRoutputPNG
IQRoutputTable
is_enabled_complianceMode

A.16 Auxiliary functions

aux_explode
aux_explodePC
aux_fileparts
aux_fileread
aux_filewrite
aux_getRelPath
aux_mkdir
aux_na_locf
aux_postFillChar
aux_preFillChar
aux_quantilenumber
aux_rmdir
aux_splitVectorEqualPieces
aux_strFindAll
aux_strrep
aux_strtrim
aux_unlevel
aux_version

A.17 Miscellaneous

calcAICBIC
clusterX
format_GUM
IQRggplot
IQRtoolsColors
scale_color_IQRtools
scale_fill_IQRtools
statXY
trust
text_IQRoutputTable

A.18 Mathematical operations

and
ge
geocv
geomean
geosd
interp0
interp1
interpcs
inv_logit
ginv
gt
le
logit
lt
mod
mvrnorm
or
piecewise