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QT {QT}

QT knowledge management system
Package: 
QT
Version: 
1.3

Description

This package performs QTc-RR, QT-time, and concentration-QTc analyses.

Usage

    QT(data,info)

Arguments

         

data
Data specifications and controlled terms:         
subjid or id
Unique subject identifier (numeric or character) (required)
treat or trt
Treatment group (numeric or character) (required)
period
Treatment period for crossover studies (numeric or character) (optional)
day
Day relative to first dose (within period for crossover studies) (numeric) (required)
time
Time (hr) relative to dose (numeric) (required)
rr
RR (ms) interval (numeric) (required)
hr
Heart rate (bpm) (numeric) (required)
qt/qtc
QT/QTc interval (ms) for (numeric) (QT, QTcB, and QTcF are required)
qt.bs/qtc.bs
Baseline QT/QTc interval (ms) (numeric) (QT, QTcB, and QTcF are required)
qt.cfb/qtc.cfb
Change from baseline QT/QTc (ms) (numeric) (QT, QTcB, and QTcF are required)
conc
Parent drug concentration (numeric) (optional)
meta
Metabolite concentration (numeric) (optional)
moxi
Moxifloxacin concentrationHeart rate (numeric) (optional)
weight
Body weight (kg) (numeric) (optional)
height
Height (cm) (numeric) (optional)
age
Age (years) (numeric) (optional)
Race
Race (numeric or character) (optional)
sex
Gender (controlled term, M=male, F=female) (required)

    

info
A list including the following elements:     
alpha
Alpha level for mean in quantile plot (default is 0.1, not implemented yet).
bins
Cut-off points to group concentrations by.                     The minumum and maximum value of the covariate will automatically be added and values outside the range of the concentrations will be removed (default is to use quantiles).
cex
Size of symbols (default is 1).
col
Colors for symbols (default is 'black', 'blue', 'red', 'green', 'orange', 'yellow', 'brown').
conc
Concentration to be used for concentration-QTc analysis (Default: 'conc').
corr
Correlation structure for inter-individual random effects (Options: 'un' (default), 'diag').
correction
QT correction to use for analyses (Default: 'qtcf'). The derived QTcI from QTcorrections function is used if 'qtci' argument is TRUE.
days
Vector of unique days in study design.
delta
Dependent variable for concentration-QTc analysis (Options: 'double' (default), 'single').
design
Study design (Required: 'parallel' or 'crossover').
device
Graphical device to print to (options: 'wmf', 'bmp', 'jpg', 'pdf', 'png', or 'tiff' (pdf is default)).
digits
Number of significant digits to be used in tables (default is 4, not implemented yet).
gof
Quantile concentration to be used in quantile plots (Options: 'median' (default), 'mid').
intercept
Which concentration-QTc model should be used for predictions and graphs (Options: 'Yes' (default), 'No', or 'Fix').
label
Label for treatment arms (Optional, default is labels=trt).
lty
Line types for parameter-covariate equations (default is 1 (solid)).
lwd
Line width (default is 1).
output
Output folder for graphs and tables (default is NA which prints on screen).
pch
Symbols (default is 20,1,15,22,17,2,215,3).
pk
List of PK information (Options: 'drugname', 'drugunit', 'metaname', and 'metaunit').
primary
List of primary endpoint days for the different treatment arms in trt (except Placebo).
qtci
Calculate QTcI using baseline (parallel studies) or placebo (crossover studies) data by QTcI=QT/(RR)^beta where log(QT)=alpha+beta*log(RR/1000) (Options: TRUE or FALSE).
quantiles
Number of bins to group the covariates in (default is 10).
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
Concentration scale for concentration-QTc analysis (Options: 'normal' (default) or 'log').
trt
List of treatment arms (Required: 'Placebo', 'Moxi', 'Therapeutic', and 'Supra', use "NA" when missing).
visit
Vector of names for each day the same length as 'days' argument (Required: 'Primary Endpoint' and 'Baseline' (only for parallel studies)).

    

Values

Creates standard graphs and tables to summarize TQT analyses.

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 QT package is at your own risk.

Examples

#Path of SAS executable should be in global path before trying to run the example
 
data(qtpk)
data <- qtpk
 
info <- list(
    #Output folder (Graphs are shown on screen when NA)
    output=NA,
 
    #Study design, options: 'parallel' or 'crossover'
    design = "crossover",
 
    #Treatment information (Match treatment names in data set to "Placebo", "Therapeutic", "Supra", and "Moxi" (Remember spelling) 
    trt = data.frame(Placebo="Placebo",Therapeutic="Therapeutic",Supra="Supra",Moxi="Moxifloxacin"),
 
    #Optional graph legend information
    label = data.frame(Placebo="Placebo",Therapeutic="Drug X 10 mg",Supra="Drug X 100 mg",Moxi="Moxifloxacin 400 mg"),
 
    #Primary endpoint days
    primary = data.frame(Therapeutic=1,Supra=1,Moxi=1),
 
    #Unique days in design
    days = c(1),
 
    #Visit names, "Primary Endpoint" (required) (for parallel studies "Baseline" is also required)
    visit  = c("Primary Endpoint"),
 
    #PK information about therapeutic and supra-therapeutic dose levels (tdose, stdose)
    # drug name and concentration unit and metabolite name and concentration unit
    pk = data.frame(drugname="Drug X",drugunit="ng/mL",metaname=NA,metaunit=NA),
 
    #QT Correction method, "qtcf" (default), "qtcb", "qtci" (or anything starting with qtc)
    correction = "qtcf",
 
    ####Concentration for Concentration-QTc analysis
    conc = "conc",
 
    #Should log concentrations be used for the concentration-QT analysis, Options "normal" (default) or "log"
    scale = "normal", 
 
    #Which mixed-model should be used for plotting, Options "Yes" (default),"No", or "Fix"
    intercept = "Yes",
 
    #Number of concentration quantiles for goodness of fit plots (default = 10)
    quantiles =10,
 
    #Dependent variable for CQT analysis, options "double" (default), and "single"
    delta="double", 
 
    #Perform QT-RR analysis to calculate QTcI by log QT = alpha + beta * log RR + epsilon using off-treatment data
    qtci=TRUE,
 
    #Quantile concentration to be used in GOF plots, options "median" (default), "mid"
    gof = "median",
 
    #IIV structure, options "diag" (vc), "un" (default)
    corr = "un", 
 
    #Write summary analysis report to Word (requires R2wd package)
    report=TRUE
)
 
 
## Not run:
    #Drug X Analysis
    QTcorrections(data,info)
    DataCheck(data,info)
    MeanData(data,info)
    QTtime(info)
    QTconc(info)
 
    #Moxifloxacin Analysis
    data <- qtpk
    info$conc <- "moxi"
 
    info$trt[,c("Therapeutic","Supra")] <- NA 
    info$label[,c("Therapeutic","Supra")] <- NA 
    info$primary[,c("Therapeutic","Supra")] <- NA
    info$pk$drugname <- "Moxifloxacin"
    info$report <- FALSE
 
    MeanData(data,info)
    QTconc(info)## End(Not run)

Author(s)

Christoffer W. Tornoe <pharmacometrics@fda.hhs.gov>

Documentation reproduced from package QT, version 1.3. License: LGPL (>= 2.1)