run.tr.diallel: run.tr.diallel: run tRD analysis.

In mauriziopaul/treatmentResponseDiallel: Package For the Analysis of Treatment-Response Phenotypes in the Influenza Diallel Project

Description

Run the treatment response diallel analysis.

Usage

run.tr.diallel(filename, savedir, treatment, trt.colname, phenotype, random,
  fixed, type, BS = TRUE, thin, lengthChains = 3000, numChains, burnin,
  force = TRUE, ...)

Arguments

filename	name of data file
savedir	directory to save files in
treatment	indicate subset
trt.colname	indicate treatment columname
phenotype	indicate parameter of interest
random	name of random effect, or NULL
fixed	name of fixed effect, or NULL
type	specify matched pairs or other type of analysis
BS	whether or not to use BayesSpike
thin	thinning factor for chains
lengthChains	MCMC chain length
numChains	number of independent MCMC chains
burnin	amount of burn-in (discarded) samples from warm-up
force	logical indicating whether to proceed despite warnings/errors
...	additional arguments

Value

runs the analysis, generating data files.

Examples

## This example may take a couple of minutes
data(FluDiData)
data(PiximusData, envir = environment())
write.csv(FluDiData, file="FluDiData.csv")
filename <- "FluDiData.csv"
args <- c("All", "D0", "NULL", "NULL", "pre", FALSE, "Trt")
treatment 		<- args[1]
phenotype  		<- args[2]
random 			<- args[3]
fixed 			<- args[4]
type				<- args[5]
BS 				<- as.logical(args[6])
trt.colname      <- args[7]
savedir			<- "."
run.tr.diallel(filename=filename, savedir=savedir, treatment=treatment, 
trt.colname=trt.colname, phenotype=phenotype, random=random,
fixed=fixed, type=type, BS=BS, thin=1, lengthChains=3000, numChains=5, 
burnin=500, force = TRUE)

mauriziopaul/treatmentResponseDiallel documentation built on May 21, 2019, 1:37 p.m.