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

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

or()

Or function

piecewise()

Piecewise function

progressBar()

Simple progress bar

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 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

GPF generating and I/O

GPF()

Constructor for GPF

addIIVCov_toGPF()

Add IIV from vcov-Matrix to GPF

combineGPF()

Generate masterGPF multiple GPF

export_GPF()

Export a GPF to and XLS file

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

read_GPFFromCSV()

Read NLME model parameter estimates from a csv file

read_GPFFromXLS()

Read NLME model parameter estimates from an excel file

GPF helpers

GPF()

Constructor for GPF

addIIVCov_toGPF()

Add IIV from vcov-Matrix to GPF

imputeTYPEcol_GPF()

Impute TYPE based on patterns in PARAMETER

Help & Documentation

doc_IQRtools()

Open IQRtools documentation in browser

examples_IQRtools()

Copy example files from the IQRreport documentation book to desired location

install_workshop()

Installs workshop material

libraryPK_IQRtools()

Copy PK model library from the IQR tools material folder to desired location

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

IQR plot

IQRggplot()

ggplot functionality implementing IQRtools style

IQRoutputFigure()

Create IQRoutputFigure object and/or print graph object to file

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

printGrid() 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() 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

install_IQRnlme()

Install the IQRnlme App

install_IQRsim()

Install the IQRsim App

loadSetupOptions_IQRtools()

Loading IQRtools setup options

run_IQRsim()

Run the IQRsim App

IQR slides

GPF()

Constructor for GPF

GPFprojectInfo()

Collect information about models to sample from.

IQRcalcTAD()

Calculate TAD column

IQRcoxRegression()

Proportional Hazard Cox regression with a multiple predictors

IQRdataGENERAL()

Imports a CSV dataset as an IQRdataGENERAL object

IQRdataNCA()

Constructor of an IQRdataNCA object

IQRdosing()

IQRdosing class

IQReport()

Interface to the IQReport command line interface tool

IQReventTable()

IQReventTable class

IQRexpandADDLII()

Expand ADDL and II dosing information

IQRggplot()

ggplot functionality implementing IQRtools style

IQRinitCompliance()

Initializes the compliance mode

IQRloadCSVdata()

Simple auxiliary to load a CSV dataset

IQRloadSASdata()

Loading SAS data

IQRlogisticRegression()

Logistic regression with multiple predictors

IQRmodel()

IQRmodel

IQRnca()

Generate NCA results

IQRsysData() IQRnlmeData()

Imports a csv dataset as IQRnlmeData object

IQRnlmeEst()

Creating an IQRnlmeEst object

IQRnlmeProject()

Creating an IQRnlmeProject object

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

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

IQRpopEDdb()

Create a PopED database for an IQRmodel

IQRsaveCSVdata()

Simple auxiliary to save a CSV dataset with attributes

IQRsysEst()

Creating an IQRnlmeEst object

IQRsysModel()

Generate an IQRsysModel

IQRsysProject()

Creating an IQRsysProject object

IQRtable()

Flexibly generate output tables based on a data frame and derived statistical quantities

IQRtoolsColors

Color table for IQRtools

IQRtteProject()

Generation of a MONOLIX TTE project

addCatColumnAsText_IQRdataGENERAL()

Function to add a column for a covariate containing the levels as text values

addCovariateToModelSpec_IQRest()

Extends the model specification by covariate relationships.

addIIVCov_toGPF()

Add IIV from vcov-Matrix to GPF

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

addOutputs_IQRmodel()

Add output equations to IQR model

addPar_modelSpec() addCov_modelSpec() removePar_modelSpec() removeCov_modelSpec()

Convenience functions for model spec manipulation

addRelations_IQRmodel()

Add new relations to an IQR model

and()

And function

as.data.frame(<IQRtable>)

Convert IQRtable (matrix) to data frame

as_IQRdataNCA()

Converts data.frame to IQRdataNCA object if possible

as_IQRnlmeProject()

Creating an IQRnlmeProject from a path

as_IQRnlmeProjectMulti()

Creating an IQRnlmeProjectMulti project

as_IQRsysEst()

Coerce to IQRsysEst object

as_IQRsysProject()

Creating an IQRsysProject from a path

as_IQRsysProjectMulti()

Creating an IQsysProjectMulti project

as_IQRtable() is_IQRtable()

IQRtables

as_IQRtteProject()

Creating an IQRtteProject from a path

as_IQRtteProjectMulti()

Creating an IQRtteProjectMulti project

attributes0() obsNAMES() doseNAMES() covInfo() catInfo()

Access Attributes of IQRdataGENERAL Object

aux_explode()

Splits a string based on a separator substring

aux_explodePC()

Splits strings by separator only if separators not in parentheses

aux_extractObjects()

Extracting objects of specific class from a possible nested list

aux_fileparts()

aux_fileparts function

aux_fileread()

aux_fileread function

aux_filewrite()

aux_filewrite function

aux_getFileGitRevision()

Function to extract an ASCII file from a specific git revision

aux_getRelPath()

aux_getRelPath

aux_mkdir()

aux_mkdir function

aux_na_locf()

Last observation carry forward (non NA values)

aux_plotlayout()

Determine layout for distribution single plots to rows, columns, and pages

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

blloqInfo_IQRdataGENERAL()

Determine summary information for BLLOQ values in an IQRdataGENERAL object

blloq_IQRdataGENERAL()

Updates an IQRdataGENERAL object for a specific BLLOQ handling method

blockMatrixDiagonal()

Combine square matrices to block-diagonal matrix

bootstrap_IQRnlmeProject()

Perform a non-parametric bootstrap on an IQRnlmeProject

calcAICBIC()

Calculation of AIC and BIC from OFV, etc.

calcIndParamValues()

Calculate individual parameter values by applying sampled random effects to typical individual parameter values

calcTypicalIndParamValues()

Calculate typical individual parameter values by applying covariate formulae to reference population parameter values

check_IQRdataGENERAL()

Checks consistency or a general dataset

cjoin_IQRtable() rjoin_IQRtable()

Join tables based on first column or first row

clean_IQRdataGENERAL()

Wrapper for several IQRdataGENERAL cleaning functions

clusterX() statXY()

Cluster Data in Blocks of Similar x Values and Summarize y Values per Block

combineGPF()

Generate masterGPF multiple GPF

combine_IQRdataGENERAL()

Concatenate IQRrmd objects

compareModels_IQRnlmeProjectMulti()

Compare the estimation specifications or results between multiple NLME projects

comparePars_IQRsysModel()

Simulate and plot an IQRsysModel for provided parameterizations

compare_IQRmodel_IQRsysModel_simulation()

Comparing IQRmodel with IQRsysModel simulation

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

convert2dMod_IQRdata()

Read IQRsysData file

convertCat2Text()

Convert numerical values of a categorical covariate into text values

convertDataRxODE_IQRnlmixr()

Converts an IQRdataGENERAL or IQRnlmeData object to RxODE format

convertETAINDIVPRED_IQRnlmeProject()

Generates eta, indiv, and pred results

covImpute_IQRdataGENERAL()

Imputes missing covariates

covariateEffect_IQRnlmeProject()

Assess impact of covariates on parameters

createDataVPC_IQRnlmeProject()

Create data for VPC

createPages_IQRoutputFigure()

Create pages from IQRoutputFigure

createSubmissionPack()

Create submission package for analysis

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

dMod_approxHessian()

Approximate the diagonal of the hessian by finite differences

dMod_nll_ALOQ()

Non-linear log likelihood for the ALOQ part of the data

dMod_nll_BLOQ()

Non-linear log likelihood for the BLOQ part of the data

dMod_nlmeEst2dModFrame()

Convert a given nlmeEst object into a dMod.frame which can be used for fitting

dMod_res()

Compare data and model prediction by computing residuals

dMod_sysProject_computations()

Do the computation part of a project

data_IQRest()

Defines a data list for use in setting up estimation objects.

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

detectSampleDiscrepancy()

Detect a discrepancy between the empirical normal distribution of a sample of (transformed to normal scale) NLME parameters and a specified "target" normal distribution.

doc_IQRtools()

Open IQRtools documentation in browser

dosing_IQRest()

Defines a dosing list for use in setting up estimation objects.

duplicate_IQRnlmeProject()

Duplicates a model at a different path

duplicate_IQRsysProject()

Duplicates a model at a different path

eigenvalues_IQRnlmeProject()

Determines eigenvalues of an NLME project

evaluate_IQRpopEDdb()

Evaluate IQRpopEDdb Object

examples_IQRtools()

Copy example files from the IQRreport documentation book to desired location

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

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_GPF()

Export a GPF to and XLS file

export_IQRcoxRegression()

Write cox proportional hazard regression object to project folder

export_IQRdataGENERAL()

Exports an IQRdataGENERAL object

export_IQRlogisticFit()

Write logistic regression object to project folder

export_IQRmodel()

Export of an IQRmodel object

export_IQRnlmeData()

Export function for IQRnlmeData object

export_IQRrmd()

Export IQRrmd object to an rmd file

export_IQRsysData()

Export IQRsysData with attributes

extractParamNamesFromIIVCorrParamName()

Extract parameter names from IIV correlation name Convention of IIV correlation estimate name: 'corr(par1,par2)'. The resulting character vector is c('par1', 'par2')

extract_IQRdosing()

Function to extract IQRdosing from modeling data set. A list of IQRdosing objects is returned containing each individual or each unique dosing.

fill_names()

Fill names for a vector of strings with the vector's values

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

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

generate_GPFfromIQRmodel()

Generate a GPF with the default model parameters

geocv()

geometric CV auxiliary

geomean()

geometric mean auxiliary

geosd()

geometric sd auxiliary

getCatValues_catInfo()

Extract numerical values of a covariate from covariate information table

getCorMatrixUncertainty()

Get the uncertainty correlation matrix from a IQRnlmeParamSpec object

getCovMatrixIIV()

Construct an IIV covariance matrix

getCovMatrixUncertainty()

Get the uncertainty covariance matrix from a IQRnlmeParamSpec object

getData_IQRnlmeProject()

Returns the dataset from an IQRnlmeProject

getDosing_IQRsysModel()

Get dosing information from IQRsysModel

getETAs_IQRnlmeProject()

Gets the individual ETAs for an IQRnlmeProject

getEmpiricalETACovarianceMatrix_IQRsysProject()

Empirical ETA covariance matrix IQRsysProjects

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

getLabels_dataframe()

Extract label information of columns in data.frames

getModel_IQRnlmeProject()

Returns the structural model used in an NLME project

getNAcolNLME_IQRdataGENERAL()

Finds columns in the NLME part with NA values

getNamesAllParameters()

Get the names of all parameters in IQRnlmeParamSpec object.

getNamesCovariateParameters()

Get the names of the covariate parameters in IQRnlmeParamSpec object

getNamesErrorParameters()

Get the names of the error parameters

getNamesIIVCorrParameters()

Get the names of the IIV correlation parameters at the normal scale

getNamesIIVParameters()

Get the names of the IIV standard deviations at normal scale

getNamesModelParameters()

Get the names of the model parameters in IQRnlmeParamSpec object

getOSIQR()

Get OS

getObsPred_IQRnlmeProject()

Gets the observations and individual as well as population predictions from a IQRnlmeProject

getOptTrace_IQRsysProject()

Read Optimization Trace Files

getParamEstimates()

Get parameter estimate values from a IQRnlmeParamSpec object.

getParamTransformationTypes()

Get parameter transformation types from a IQRnlmeParamSpec object.

getPars_IQRmodel()

Get parameter vector from an IQRmodel

getPars_IQRoptTrace()

Extract Vector of Parameter Values from Optimization Trace Data

getPars_IQRsysModel()

Get parameter vector from an IQRsysModel

getPopParameters_IQRnlmeProject()

Gets the population parameter estimates from a IQRnlmeProject

getPrediction_IQRsysModel()

Access simulation results

getRepos()

Getting the URL for the MRAN time machine repository for current R version

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.

getTableNnonmemOutput()

Helper function to read NONMEM output files into R.

getTextValues_catInfo()

Extract numerical values of a covariate from covariate information table

ginv()

Generalized Inverse of a Matrix

grow()

Grow matrix to certain dimensions

gt()

Greater than function

handleSameTimeObs_IQRdataGENERAL()

Adds tiny noise to TIME when TIME same for NAME in USUBJID

hasCcodeFunctions_IQRmodel()

Checks if an IQRmodel contains C functions

hasInitialAssignments_IQRmodel()

Checks if an IQRmodel contains initial assignments

has_IQReport_executable()

Check if IQReport is installed and available

hasrun_IQRnlmeProject()

Checks if an IQRnlmeProject has been run

hasrun_IQRnlmeProjectMulti()

Checks if projects within an IQRnlmeProjectMulti have been run

hasrun_IQRsysProject()

Checks if an IQRsysProject has been run

importSBML_IQRmodel()

Imports an SBML model

importVariant_IQRmodel()

Important a model structure with defined parameterization variant

import_IQRcoxRegression()

Load cox proportional hazard regression object from project folder

import_IQRdataOriginal()

Import a data file into the current folder structure

import_IQRlogisticFit()

Load logistic regression object from project folder

import_IQRsysData()

Convert data to an IQRsysData object

imputeTYPEcol_GPF()

Impute TYPE based on patterns in PARAMETER

informationContent_IQRnlmeProject()

Assess the expected information content wrt parameters, given a dosing and observation schedule.

install_IQRnlme()

Install the IQRnlme App

install_IQRsim()

Install the IQRsim App

install_workshop()

Installs workshop material

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

is.GPF()

Check if an object inherits from S3 class GPF

is.IQRnlmeParamSpec()

Check if an object has class IQRnlmeParamSpec

is_IQRdataGENERAL()

Check function if it is an IQRdataGENERAL object

is_IQRdataNCA()

Check if object is an IQRdataNCA object

is_IQRdosing()

Check function if it is an IQRdosing object

is_IQReventTable()

Check function if it is an IQReventTable object

is_IQRmodel()

Check if object is an IQRmodel

is_IQRnca()

Check if object is an IQRnca object

is_IQRnlmeData()

Check function if it is an IQRnlmeData object

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_IQRsimres()

Check function if it is an IQRsimres object

is_IQRsimresMulti()

Check function if it is an IQRsimresMulti 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

is_IQRtteProject()

Checks if given project path is an is_IQRtteProject

is_IQRtteProjectMulti()

Checks if given project path is an is_IQRtteProjectMulti

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 ----

is_enabled_complianceMode()

Checks if the compliance mode is enabled

is_enabled_rdsMode()

Checks if the rds mode is enabled

is_installed_NLMIXR()

Checks installation of NLMIXR

km_IQRsurvival()

Kaplan-Meier estimation and plotting.

le()

Less equal function

libraryPK_IQRtools()

Copy PK model library from the IQR tools material folder to desired location

license_IQRtools()

Allowing to set the personal IQRtools license key

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.

loadSetupOptions_IQRtools()

Loading IQRtools setup options

load_GPF()

Load a GPF from different sources

load_IQRdataGENERAL()

Loads an IQRdataGENERAL object from CSV and ATR file

load_IQRdataNCA()

Loads an IQRnca dataset

load_IQRsysProject()

Read an existing IQRsysProject

logit()

Logit auxiliary - so far only used in NLMIXR interface

lt()

Less than function

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

mod()

Modulo function

modelSpec_IQRest()

Defines a modelSpec list for use in setting up estimation objects.

modelSpec_IQRsysEst()

Model specification for IQRsysEst

model_IQRsysModel() dataSpec_IQRsysModel() modelSpec_IQRsysModel()

Retrieve model, data spec and model spec from IQRsysModel

mutateCov_IQRdataGENERAL()

Add Covariate to IQRdataGENERAL object

mvrnorm()

Simulate from a Multivariate Normal Distribution

new_IQRmodel()

Generates a new IQRmodel file and opens it in the RStudio editor

obfuscate_IQRdataGENERAL()

Obfuscated version of an IQRdataGENERAL object

obfuscate_IQRmodel()

Obfuscation of IQR models

obfuscate_NAME_VALUE()

Obfuscate pairs of name and value in data set

obfuscate_categoric()

Obfuscate categorical values

obfuscate_numeric()

Obfuscate numeric values

offsetTIME_IQRsysData()

Function to shift data right on time axis by a certain offset

opt.layout()

Convenience function for setting additional page layout options (opt.layout) for IQRoutputFigure

opt.pagesize()

Convenience function for setting additional page printing options (opt.pagesize) for IQRoutputFigure

or()

Or function

outlier_IQRnlmeProject()

Generates a table with outlier information

packageR_IQRtools()

R Packaging function for reproducibility

piecewise()

Piecewise function

plot(<IQRdataGENERAL>)

Generic print function for IQRdataGENERAL objects

plot(<IQRdataNCA>)

Plot information about an IQRdataNCA object

plot(<IQRnca>)

Plot information about an IQRnca object

plot(<IQRnlmeData>)

Generic plot for an IQRnlmeData object

plot(<IQRnlmeProject>)

Generic plot for an IQRnlmeProject object

plot(<IQRnlmeProjectMulti>)

Generic plot function for IQRnlmeProjectMulti objects

plot(<IQRoutputFigure>)

Plot function for IQRoutputFigure (calls print)

plot(<IQRsimres>)

Generic plot function for IQRsimres objects

plot(<IQRsimresMulti>)

Generic plot function for IQRsimresMulti objects

plot(<IQRsysProject>)

Generic plot for an IQRsysProject object

plot(<IQRtteProject>)

Generic plot for an IQRtteProject object

plotConvergence_IQRnlmeProject()

Generates plots of convergence trajectories for NLME projects

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

plotDVPRED_IQRsysModel()

Data vs prediction diagnostics plot

plotDoseSchedule_IQRdataGENERAL()

Plot overview over dosing records

plotETACOV_IQRnlmeProject()

Generates plots of eta/covariate correlations for NLME projects

plotETA_IQRnlmeProject()

Generates plots of etas and their correlations for NLME projects

plotFit_IQRsysModel()

Plot model fit and data

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

plotIndiv_IQRdataGENERAL()

Plot individual longitudinal data over time as lines (one graph per observation)

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

plotProfiles_IQRdataNCA()

Plot information about an IQRdataNCA object

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)

plotVPC_IQRdataVPC()

Create VPC plot

plotVPC_IQRtteProject()

Plots the VPC for an IQRtteProject

plotWRES_IQRsysModel()

Weighted residuals diagnostics plot

plotWaterfall_IQRsysModel()

Waterfall plot of objective values

plot_IQRcoxRegression()

Plot some diagnostics for fitted Cox proportional hazard regression model

plot_IQRlogistRegressFit()

Plot predictions for fitted logistic regression model

plot_IQRoptTrace()

Plot Optimization Traces

plot_IQRsysModel()

Plot model and data represented by IQRsysModel

plotbyGroup_IQRnca()

Plot IQRnca result summaries over dose with optional color stratification

`+`(<IQRdataGENERAL>)

Concatenate IQRrmd objects

`+`(<IQRrmd>)

Concatenate IQRrmd objects

pred_IQRnlmeProject()

Predict values based on provided NLME project

print(<IQRdataGENERAL>)

Generic print function for IQRdataGENERAL objects

print(<IQRdataNCA>)

Print information about an IQRdataNCA object

print(<IQRdosing>)

Generic print function for IQRdosing objects

print(<IQReventTable>)

Generic print function for IQReventTable objects

print(<IQRmodel>)

Generic print function

print(<IQRnca>)

Print information about an IQRnca object

print(<IQRnlmeData>)

Generic print function for IQRnlmeEst objects

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(<IQRoutputFigure>)

Print IQRoutputFigure to pages (ggplot objects)

print(<IQRoutputFigureList>)

Prints summary for the IQRoutputFigures contained in the list

print(<IQRoutputTable>)

Overloading "print" for IQRoutputTable objects

print(<IQRrmd>)

Overloading "print" for IQRrmd objects

print(<IQRsensitivity>)

Print function for IQRsensitivity

print(<IQRsimres>)

Generic print function for IQRsimres objects

print(<IQRsimresMulti>)

Generic print function for IQRsimresMulti objects

print(<IQRsysEst>)

Generic print function for IQRsysEst objects

print(<IQRsysProject>)

Generic print function for IQRsysProject objects

print(<IQRtteProject>)

Generic print function for IQRtteProjects objects

print(<IQRtteProjectMulti>)

Generic print function for IQRtteProjectMulti objects

printGrid() printGrid()

Plotting a list of ggplot objects in a grid defined by nrow and ncol

print_modelSpec()

Print function for model specification list

profile_IQRsysModel()

Compute profile likelihood

progressBar()

Simple progress bar

rbind_IQRdosing()

Combines 2 or more IQRdosing objects together

read_GPFFromCSV()

Read NLME model parameter estimates from a csv file

read_GPFFromXLS()

Read NLME model parameter estimates from an excel file

regenerate_IQRmodel()

Regeneration of the compiled code of an IQRmodel

reload_DLLIQRmodel()

Load the dll of an IQRmodel and attach the pointer

removeCommata_dataframe()

Remove commata in elements in data.frame

replaceTerms_IQRmodel()

Replace terms in ODEs of IQR model

report_IQRnca()

Reporting of NCA results to MS Word

results_MONOLIX()

Generates tabular and graphical information for a MONOLIX model

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

rmdAPPROVALS()

Add an approvals page to the report (after title)

rmdCOMMENT()

Generate RMD command to include a Word comment

rmdEMPTY() 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

run_IQRnlme()

Run the IQRnlme App

run_IQRnlmeProject()

Runs an IQRnlmeProject

run_IQRnlmeProjectMulti()

Runs an IQRnlmeProjectMulti object (each IQRnlmeProject within)

run_IQRsim()

Run the IQRsim App

run_IQRsysProject()

Runs an IQRsysProject

run_IQRsysProjectMulti()

Runs an IQRsysProjectMulti object (each IQRsysProject within)

run_IQRtteProject()

Runs an IQRtteProject

run_IQRtteProjectMulti()

Runs an IQRtteProjectMulti object (each IQRtteProject within)

run_silent_IQR()

Run expression silently

sampleIDs()

Sample or subset records from a matrix or a data.frame

sampleIndParamValues()

Sample individual parameter values, based on a NLME parameter specification

sampleParamFromUncertainty()

Sample NLME parameters from their uncertainty distribution

sampleRandomEffects()

Sample NLME random effects given population parameter values describing the inter-individual variability distribution

sample_IQRnlmeProject()

Samples parameters from an IQRnlmeProject

sample_IQRsysModel()

Sample model parameters using covariates.

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

sensitivity_IQRmodel()

Local parameter sensitivity analysis

setIGNORErecords_IQRdataGENERAL()

Sets IGNORE information on user defined records

setMissingDVobsRecordsIGNORE_IQRdataGENERAL()

Sets IGNORE information on observation records that have missing (NA) DV value

setParameters_IQRmodel()

Set parameters in an IQRmodel to defined values

setPars_IQRmodel()

Set parameters of an IQRmodel

setPars_IQRsysModel()

Set parameters of an IQRsysModel

setup_IQRtools()

Opening the setup_options_IQRtools.R file for editing

sim_IQRmodel()

Simulate an IQRmodel

sim_IQRpopEDdb()

Simulate from IQRpopEDdb Object

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

simple_IQRlogisticRegression()

Simple logistic regression with a single predictor

slopeTest_IQRnca()

Calculation of R2 and R2ADJ for slope of profile

specifyParamSampling()

Create an IQRnlmeParamSpec object

spmIIV_IQRsysProject()

Stepwise Parameter Modeling for QSP - random effects

spm_IQRsysProject()

Stepwise Parameter Modeling for QSP - fixed effects

statCI()

Return key statistical quantities generated from value, lower and upper confidence bounds

statSE()

Return key statistical quantities generated from value and standard error

stoichiometry_IQRmodel()

Determination of stoichiometric matrix

stopIQR()

Replacement for stop function to be used in IQRtools

strReplace_IQRmodel()

Replaces strings in IQRmodels

subset(<IQRdataGENERAL>)

Subsetting IQRdataGeneral Objects

summary(<IQRdataGENERAL>)

Generic summary function for IQRdataGENERAL objects

summary(<IQRnca>)

Summary information about an IQRnca object

summary(<IQRnlmeProject>)

Generic summary function for IQRnlmeProject objects

summary(<IQRnlmeProjectMulti>)

Generic summary function for IQRnlmeProjectMulti objects

summary(<IQRoutputFigure>)

Summary function for IQRoutputFigure

summaryCat_IQRdataER()

Generates a demographic summary table for categorical covariates

summaryCat_IQRdataGENERAL()

Generates a demographic summary table for categorical covariates

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

summaryCov_IQRdataER()

Generates a demographic summary table for continuous covariates

summaryCov_IQRdataGENERAL()

Generates a demographic summary table for continuous covariates

summaryCovariates_IQRnlmeProjectMulti()

Allows to generate a summary of covariates for an IQRnlmeProjectMulti object

summaryObservations_IQRdataGENERAL()

Generates a summary of observations in an IQRdataGENERAL object

summaryPKbyNT_IQRdataNCA()

Summary stats for each scheduled timepoint and GROUP in IQRdataNCA dataset. Scheduled timepoint column ("NT") needs to be present.

summaryParameters_IQRnlmeProjectMulti()

Allows to generate a summary of parameters for an IQRnlmeProjectMulti object

summary_IQRcoxRegression()

Table comparing estimates of Cox proportional harzard regression models

summary_IQRlogisticRegression()

Table comparing estimates and

summarybyGroup_IQRnca()

Summary information about an IQRnca object

switchOpt_IQRsysModel()

Switch the selected optimum

tablePars_IQRsysModel()

Generate table output of estimated modle parameters

tempdirIQR()

Replacement for tempdir function to be used in IQRtools

tempfileIQR()

Replacement for tempfile function to be used in IQRtools

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

text_IQRoutputTable()

Convert IQRoutputTable to text representation

themeIQRtools()

IQR Tools' standard theme

transformObs_IQRdataGENERAL()

Add New Observations by Transformation of an Existing Observable

transformParamToNormal()

Transform model parameter values to a normal scale based on a specified transformation type

unlabel_dataframe()

Remove labelled class and label

untransformParamFromNormal()

Transfrom model parameter values from a normal to their original scale, based on a specified transformation type

vpc_IQRnlmeProject()

VPC for NLME projects

warningIQR()

Replacement for warning function to be used in IQRtools

zip_IQRdataGENERAL()

Zip IQRdataGENERAL and meta-information

IQRdataER

summaryCat_IQRdataER()

Generates a demographic summary table for categorical covariates

summaryCov_IQRdataER()

Generates a demographic summary table for continuous covariates

IQRdataGENERAL

addCatColumnAsText_IQRdataGENERAL()

Function to add a column for a covariate containing the levels as text values

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

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

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_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)

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

IQRdataNLME

IQRloadCSVdata()

Simple auxiliary to load a CSV dataset

IQRsaveCSVdata()

Simple auxiliary to save a CSV dataset with attributes

IQRmodel

IQRmodel()

IQRmodel

addOutputs_IQRmodel()

Add output equations to IQR model

addRelations_IQRmodel()

Add new relations to an IQR model

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

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

IQRsysData() IQRnlmeData()

Imports a csv dataset as IQRnlmeData object

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() removePar_modelSpec() removeCov_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

createDataVPC_IQRnlmeProject()

Create data for VPC

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

plotConvergence_IQRnlmeProject()

Generates plots of convergence trajectories for NLME projects

plotETACOV_IQRnlmeProject()

Generates plots of eta/covariate 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

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

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()

VPC for NLME projects

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

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)

Installation

IQRinitCompliance()

Initializes the compliance mode

getOSIQR()

Get OS

getRepos()

Getting the URL for the MRAN time machine repository for current R version

is_enabled_rdsMode()

Checks if the rds mode is enabled

license_IQRtools()

Allowing to set the personal IQRtools license key

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

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

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

NCA

IQRdataNCA()

Constructor of an IQRdataNCA object

IQRnca()

Generate NCA results

as_IQRdataNCA()

Converts data.frame to IQRdataNCA object if possible

is_IQRdataNCA()

Check if object is an IQRdataNCA object

is_IQRnca()

Check if object is an IQRnca object

load_IQRdataNCA()

Loads an IQRnca dataset

plot(<IQRdataNCA>)

Plot information about an IQRdataNCA object

plot(<IQRnca>)

Plot information about an IQRnca object

plotProfiles_IQRdataNCA()

Plot information about an IQRdataNCA object

plotbyGroup_IQRnca()

Plot IQRnca result summaries over dose with optional color stratification

print(<IQRdataNCA>)

Print information about an IQRdataNCA object

print(<IQRnca>)

Print information about an IQRnca object

report_IQRnca()

Reporting of NCA results to MS Word

slopeTest_IQRnca()

Calculation of R2 and R2ADJ for slope of profile

summary(<IQRnca>)

Summary information about an IQRnca object

summaryPKbyNT_IQRdataNCA()

Summary stats for each scheduled timepoint and GROUP in IQRdataNCA dataset. Scheduled timepoint column ("NT") needs to be present.

summarybyGroup_IQRnca()

Summary information about an IQRnca object

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

Output

IQRoutputCSV()

Exporting a data.frame as CSV file

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

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

IQRoutputValueTable()

Exporting a value with label and potential description for reporting

Output & Compliance

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

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

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

text_IQRoutputTable()

Convert IQRoutputTable to text representation

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

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

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.

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

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_IQRdataGENERAL()

Add labels to data to allow subsequent XPT export

createSubmissionPack()

Create submission package for analysis

exportDEFINE_IQRdataGENERAL()

Exports a define file for the provided dataset

exportDEFINEpdf_IQRdataGENERAL()

Exports a define file for the provided dataset as pdf via LaTeX.

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

createDataVPC_IQRnlmeProject()

Create data for VPC

plotVPC_IQRdataVPC()

Create VPC plot

plotVPC_IQRtteProject()

Plots the VPC for an IQRtteProject

vpc_IQRnlmeProject()

VPC for NLME projects

dMod interface

convert2dMod_IQRdata()

Read IQRsysData file

dMod_nlmeEst2dModFrame()

Convert a given nlmeEst object into a dMod.frame which can be used for fitting

dMod_res()

Compare data and model prediction by computing residuals

dMod_sysProject_computations()

Do the computation part of a project

functions in the NLME parameter sampling API

calcIndParamValues()

Calculate individual parameter values by applying sampled random effects to typical individual parameter values

calcTypicalIndParamValues()

Calculate typical individual parameter values by applying covariate formulae to reference population parameter values

combineGPF()

Generate masterGPF multiple GPF

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

getCorMatrixUncertainty()

Get the uncertainty correlation matrix from a IQRnlmeParamSpec object

getCovMatrixIIV()

Construct an IIV covariance matrix

getCovMatrixUncertainty()

Get the uncertainty covariance matrix from a IQRnlmeParamSpec object

getNamesAllParameters()

Get the names of all parameters in IQRnlmeParamSpec object.

getNamesCovariateParameters()

Get the names of the covariate parameters in IQRnlmeParamSpec object

getNamesErrorParameters()

Get the names of the error parameters

getNamesIIVCorrParameters()

Get the names of the IIV correlation parameters at the normal scale

getNamesIIVParameters()

Get the names of the IIV standard deviations at normal scale

getNamesModelParameters()

Get the names of the model parameters in IQRnlmeParamSpec object

getParamEstimates()

Get parameter estimate values from a IQRnlmeParamSpec object.

getParamTransformationTypes()

Get parameter transformation types from a IQRnlmeParamSpec object.

imputeTYPEcol_GPF()

Impute TYPE based on patterns in PARAMETER

is.GPF()

Check if an object inherits from S3 class GPF

is.IQRnlmeParamSpec()

Check if an object has class IQRnlmeParamSpec

read_GPFFromCSV()

Read NLME model parameter estimates from a csv file

read_GPFFromXLS()

Read NLME model parameter estimates from an excel file

sampleIDs()

Sample or subset records from a matrix or a data.frame

sampleIndParamValues()

Sample individual parameter values, based on a NLME parameter specification

sampleParamFromUncertainty()

Sample NLME parameters from their uncertainty distribution

sampleRandomEffects()

Sample NLME random effects given population parameter values describing the inter-individual variability distribution

specifyParamSampling()

Create an IQRnlmeParamSpec object

transformParamToNormal()

Transform model parameter values to a normal scale based on a specified transformation type

untransformParamFromNormal()

Transfrom model parameter values from a normal to their original scale, based on a specified transformation type

stat functions

statCI()

Return key statistical quantities generated from value, lower and upper confidence bounds