SimPower: power in designing a new cluster randomized trial with the...

In shanRpackage/pprincrt: Bayesian Power Prior Design and Analysis of Cluster Randomized Trials

Description

SimPower returns power in designing a new cluster randomized trial with the power prior method

Usage

SimPower(family, to.do.option, cSet, cNarmVar = "narm",
  cNcluster.armVar = "ncluster.arm", cNpat.clusterVar = "npat.cluster",
  cBtwVar = "sigma.b", cWthVar = "sigma.e", cTrtVecVar, hSet = NULL,
  hNarmVar = "narm", hNpat.armVar = "npat.arm", hWthVar = "sigma.e",
  hTrtVecVar = NULL, hData = NULL, hTrtVar = "x", hOutcomeVar = "y",
  hSumVar = "n", cRdmSeed.init = 0, hRdmSeed.init = 0, weight = "asym",
  cover.level = 0.95, nchain = 1, niter = 2000, nburnin = 1000,
  nthin = 1, file.dir.init = tempdir(), cfile.name = "cmodelfile",
  hfile.name = "hmodelfile", pprfile.name = "pprmodelfile",
  graphics.name = "graphics", file.rm = T, OpenBUGS.dir = NULL,
  OpenBUGS.seed = 1, Rep = 1, num.core = parallel::detectCores(logical =
  F) - 1)

Arguments

family	outcome distribution.
to.do.option	a value in 'sim_power', 'sim_SSD' and 'real_SSD'.
cSet	current trial setting. It should be a list.
cNarmVar	the variable name of arm in current trial.
cNcluster.armVar	the variable name of total clusters in each arm in current trial. Its default value is 'ncluster.arm'.
cNpat.clusterVar	the variable name of total patients in each cluster in current trial. Its default value is 'npat.cluster'.
cBtwVar	the variable name of between cluster variation in current trial.
cWthVar	the variable name of within cluster variation in current trial.
cTrtVecVar	the variable name of treatment in current trial. It should be in the order of first treatment, second treatment until the last one.
hSet	historical trial setting. It should be in a list. It is NULL by default.
hNarmVar	the variable name of arm in historical trial.
hNpat.armVar	the variable name of total patients in each arm in historical trial. Its default value is 'npat.arm'.
hWthVar	the variable name of within cluster variation in historical trial.
hTrtVecVar	the variable name of treatment in historical trial. It should be in the order of first treatment, second treatment until the last one.
hData	Real historical trial data. It is NULL by default.
hTrtVar	the variable name of treatment in historical trial data.
hOutcomeVar	the variable name of outcome in historical trial data.
hSumVar	the variable name of total observation in historical trial data.
cRdmSeed.init	the initial value of random seed to generate current trial data.
hRdmSeed.init	the initial value of random seed to generate historical trial data.
weight	discounting parameter. It is 'asym' by default.
cover.level	nomial coverage level of HPD interval.
nchain	number of mcmc chains to run.
niter	length of mcmc chains.
nburnin	length of burnin of mcmc chains.
nthin	thinning rate of mcmc chain.
file.dir.init	the start of the directory to save the model BUGS file and input and output files of OpenBUGS.
cfile.name	the file name of current BUGS model.
hfile.name	the file name of historical BUGS model.
pprfile.name	the file name of power prior BUGS model.
graphics.name	the file name of mcmc convergence graphics.
file.rm	whether to remove all files after Bayesian computations are done.
OpenBUGS.dir	directory to install OpenBUGS package.
OpenBUGS.seed	the random number generator state of OpenBUGS.
Rep	number of replications to determine power.
num.core	number of cores for parallel computation.

Value

power in designing a new cluster randomized trial with the power prior method

Examples

## Not run: 
#### SSD with simulated historical data;
my.curset <- list(narm=2,ncluster.arm=rep(10,2),npat.cluster=rep(20,20),
'trt1'=-0.1,'trt2 v.s. trt1'=log(4),sigma.b=1)
my.histset <- list(narm=2,npat.arm=rep(200,2),'trt1'=0.1,'trt2 v.s. trt1'=log(4))
mypower <- SimPower(family='binomial', to.do.option='sim_SSD', cSet=my.curset,
cTrtVecVar=c('trt1','trt2 v.s. trt1'), hSet=my.histset,
hTrtVecVar=c('trt1','trt2 v.s. trt1'),
weight="asym",nchain=2,niter=500,nburnin=100,nthin=5,Rep=1,num.core=3,file.rm=T,
OpenBUGS.dir="C:\\Program Files (x86)\\OpenBUGS\\OpenBUGS323\\OpenBUGS.exe",
OpenBUGS.seed=12)
 #### SSD with real historical data;
my.curset <- list(narm=2,ncluster.arm=rep(10,2),npat.cluster=rep(20,20),
'trt1'=-0.1,'trt2 v.s. trt1'=log(4),sigma.b=1)
my.histdata <- data.frame(x=c(1,2),y=c(10,15),n=c(20,20))
mypower <- SimPower(family='binomial', to.do.option='real_SSD',cSet=my.curset,
cTrtVecVar=c('trt1','trt2 v.s. trt1'),hData=my.histdata,weight='sym',
nchain=2,niter=500,nburnin=100,nthin=5,file.rm=T, Rep=4,num.core=2,
OpenBUGS.dir="C:\\Program Files (x86)\\OpenBUGS\\OpenBUGS323\\OpenBUGS.exe")

## End(Not run)

shanRpackage/pprincrt documentation built on May 23, 2019, 1:11 p.m.