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popPK {popPK}

Summary of Population Pharmacokinetic Analysis
Package: 
popPK
Version: 
1.03

Description

This package creates graphs and tables for NONMEM runs

Usage

    popPK(info)

Arguments

info
A list including the following elements:     
path
The path where the NONMEM control stream, output, data, and tables are located (Required).
run.no
The NONMEM run number (e.g. 1 for run1.mod/ctl) (Required).
alpha
Alpha level for parameter mean in quantile plot (default is 0.05).
bins
Cut-off points to group specified covariates by. The minumum and maximum value of the covariate will automatically be added and values outside the range of the covariate will be removed (default is to use quantiles).
cat.level
Substitute categorical covariates values with text string (e.g. SEX=list(Male='0', Female='1')).
cex
Size of symbols (default is 1, 1, 1, 1, 1, 1, 1, 1).
col
Colors for symbols (default is 'black', 'red', 'grey', 'blue', 'orange', 'green', 'yellow', 'brown').
cov.rel
List of identified parameter-covariate equations to plot (maximum of 1 continuous and 1 categorical covariate per equation).
covs
List of labels for covariates (default is covariate name in patab/catab).
device
Graphical device to print to (options: "wmf", "bmp", "jpg", "pdf", "png", or "tiff") (default is "pdf").
digits
Number of significant digits to be used in tables.
drug.name
Drug name.
etas
List of labels for inter-individual variability parameters (default is omega name in control stream specified by ";").
group.by
Variable to group symbols in graphs by.
ind.plots
Plot individual concentration-time profiles (default is FALSE).
line.col
Line colors for parameter-covariate relationships (default is 'black', 'red', 'grey', 'blue', 'orange', 'green', 'yellow', 'brown').
lloq
Insert lower limit of quantification in goodness-of-fit graphs.
log.covs
Log transform covariates in Covariates function (default is FALSE).
log.obs
Log transform observations in Diagnostics function (default is FALSE).
log.parms
Log transform parameters in Covariates function (default is FALSE).
log.pred
Log transform predictions in Diagnostics function (default is FALSE).
lty
Line types for parameter-covariate equations (default is 1 (solid)).
lwd
Line width (default is 1).
mean
Parameter mean for quantile plots (default is "geometric", otherwise "arithmetic").
output
Output folder for graphs and tables (default is NA which will print to the screen).
pch
Symbols (default is 20 (closed circle), 1 (open circle), 15 (solid square), 22 (open square), 17 (solid triangle), 2 (open triangle), 215 (x), 3 (+)).
prefix
Prefix of your NONMEM control stream (default is run).
quantiles
Number of bins to group the covariates in (default is 4).
report
Create summary report in Word. This feature only works on Windows and requires R2wd package is installed along with statconnDCOM) (default is FALSE).
scale
Scale which the parameters were estimated in NONMEM (options='normal' or 'log').
smooth
Insert smooth (default is FALSE).
strat.by
Variable to stratify panels by in graphs.
suffix
NONMEM output table suffix (default is no suffix or .csv).
thetas
List of labels for fixed-effects parameters (default is theta name in control stream specified by ";").
units
Units for time and concentration.

Values

The popPK function creates standard graphs and tables to summarize population pharmacokinetic analysis using NONMEM.

Note

DISCLAIMER: This R package does not reflect the official policy of the FDA. No official endorsement by the FDA is intended or should be inferred. Use of the popPK package is at your own risk.

See Also

xposeData, Demographics, Diagnostics, Estimates, and Covariates

Examples

#Restrictions
    #No time-varying covariates
    #One $THETA, $OMEGA, and $SIGMA for each parameter in the NONMEM control stream
    #Only 1 continuous covariate pr equation in info$cov.rel
    #Only bivariate categorical covariates in info$cov.rel coded as THETA(X)**CAT
 
info <-list(
            path=paste(R.home(), "/library/popPK/extdata",sep=""),
        run.no=1,
        output=NA,
        thetas=list(CL="Clearance (L/hr)",V="Volume of distribution (L)",
                KA="Absorption rate constant (1/hr)"),
        etas= list(ETA1="CL",ETA2="V",ETA3="KA"),
        covs = list(BW="Weight (kg)",AGE="Age (years)",ISM="Sex",RACE="Race"),
        cat.level=list(ISM = list(Male=1,Female=0),
                RACE = list(White=1,Black=2,Asian=3,Other=4)),
        group.by ="ISM",
        units = list(time="hr",conc="ng/mL"),
        drug.name = "Drug X",
        quantiles=4,
        log.pred=TRUE,log.obs=TRUE,
        bins=list(AGE=c(25,41)),
        cov.rel=list(CL~THETA(1)*1.01^ISM*(BW/70)^THETA(4),
                "Estimated exponent"=V~THETA(2)*(BW/70)^THETA(5),
                "Allometric"=V~THETA(2)*(BW/70)^1),
        report=TRUE
    )
 
 
## Not run:
    xposeData(info)
    Demographics(info)
    Diagnostics(info)
    Estimates(info) 
    Covariates(info)## End(Not run)

Author(s)

Christoffer W. Tornoe & Fang Li pharmacometrics@fda.hhs.gov

Documentation reproduced from package popPK, version 1.03. License: GPL (>= 2)