##--------------------------------------------------------------------------------------------------------
## example pipeline to simulate sequences for a given DSPS epi simulation
##--------------------------------------------------------------------------------------------------------
\dontrun{
indir <- system.file(package="PANGEA.HIV.sim", "misc")
# re-name the following:
tmpdir <- '/Users/Oliver/git/HPTN071sim/tmp140912'
dir.create(tmpdir, showWarnings=FALSE)
# simulation input files from the epi-simulator
infile.trm <- '140911_DSPS_RUN002_TRM.csv'
infile.ind <- NULL
# input arguments for the pipeline
pipeline.args <- sim.regional.args( yr.start=1980, yr.end=2020, seed=42, s.PREV.min=0.01, s.PREV.max=0.70, epi.model='DSPS', epi.dt=1/48, epi.import=0.1 )
infile.args <- paste(tmpdir,'/',substr(infile.trm, 1, nchar(infile.trm)-7), 'PipeArgs.R',sep='')
save(pipeline.args, file=infile.args)
#
# call simulation pipeline
# this generates a UNIX batch file if no HPC system is detected, or
# this generates and runs a qsub file if an HPC system is detected
#
file <- sim.regional(indir, infile.ind, infile.trm, tmpdir, pipeline.args=pipeline.args)
cat(file)
}
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