Man pages for wdelva/RSimpactHelp
Pre- and Post-simulation helper functions for RSimpact Cyan

agedif.medianAge difference median.
agedistr.creatorCreate an age distribution for the population at the start of...
age.group.time.windowSubset the datalist ptable to include only people who existed...
agemix.df.makerCreate dataframe for age-mixing calculations.
agemix.episodes.df.makerCreate dataframe of relationship episodes for agemixing...
agemixing.1a.wrapper.for.SimpactPaperWrapper function for age mixing example of Simpact paper.
agemixing.1b.wrapper.for.SimpactPaperWrapper function for age mixing example of Simpact paper.
agemixing.2a.wrapper.for.SimpactPaperWrapper function for age mixing example of Simpact paper.
agemixing.wrapper.for.SimpactPaperWrapper function for age mixing example of Simpact paper.
agemixing.wrapper.withhivWrapper function to test MICE-assisted calibration functions
agemixpatdatAge-mixing pattern model data.
agemix.rels.df.makerCreate dataframe of relationships for agemixing analysis.
alive.infectedSubset people alive at a point in time and adds their HIV...
amp.modellerModel age-mixing pattern.
ART.coverage.calculatorCalculate overall HIV prevalence and ART coverage aggregated...
ART.coverage.vector.creatorCreate a vector of ART coverage measurements.
art.person.yearsA function that returns the total number of person-years on...
ART.retentionA function that returns the percentage of clients who are on...
bsd.extractorCompute between-subject standard deviation from agemixing...
cd4.atARTinitA function that returns the total number of people who...
cd4.atARTinit.calculatorCD4 at ART initiation
cd4.vl.atARTinitA function that returns the total number of people between...
choose.sequence.indSubset sequences in fasta file based on sequence ID or Name
client.facilityA function that determines the facility the client attended...
concurr.pointprev.calculatorCalculate concurrent point prevalence, overall and...
datalistSimpact run datalist data.
degree.df.fracFraction of women within specified age group with more than...
degree.df.makerDegree distribution of persons in recent sexual...
degree.distr.fitterFitting parametric distributions to the degree data
degree.hist.makerPlot the histogram of a degree distribution.
dummy.wrapperFast and simple wrapper function to test MICE-assisted...
epi2tree2Build a transmission tree object from a transmission network...
err.functionWe expect this to grow and the returned summary statistics to...
hiv.infected.groupCalculate the number of HIV infections that occured between...
hiv.negative.lifeyearsA function that returns the total number of HIV-negative life...
HPC_MaCHPC-version of MICE-assisted calibration
IDs.indiv.seq.gender.funSubset sequences based on gender ratio and age of individuals
IDs.Seq.Age.GroupsSubset sequences based on gender ratio and age of individuals
IDs.Seq.RandomSubset sequences based on gender ratio and age of individuals
incidence.calculatorCalculate HIV incidence, overall and stratified.
incidence.vector.creatorCreate a vector of HIV incidence measurements.
input.output.dfInput and output dataset for MICE.
input.params.creatorCreate a default parameter configuration list.
intervention.introducedWe need to decide if we need to include all the intervention...
life.years.livedA function that returns the total number of life-years lived...
MaCMICE-assisted calibration
MaC.explorerDistribute simpact runs from MaC output over multiple cores
mean.age.pos.vector.creatorCreate a vector of mean ages among the HIV positive people
mice.parallelRun mice in parallel
mice.wrapperWrapper function for mice
pattern.modellerModel age-mixing pattern.
pattern.plotterPlot age-mixing pattern.
persreldfRelationship episodes from Simpact Simulation.
phylogenetic.tree.fasttreeConstruct and calibrate a phylogenetic tree from sequence...
phylogenetic.tree.fasttree.parConstruct and calibrate a phylogenetic tree from sequence...
pop.growth.calculatorCalculate population growth rate.
prevalence.calculatorCalculate HIV prevalence, overall and stratified.
prevalence.plotterPlot the overall HIV prevalence for the duration of the...
prevalence.vector.creatorCreate a vector of HIV prevalence measurements.
readthedataRead the Simpact output files.
recruit.study.clientsA function that recruits the MaxART clients
revised.MaC.incremental.parallel.miceMICE-assisted calibration
select.summary.paramsSelect the summary statistics that you want from the...
sequence.simulation.seqgenSimulate sequence data of individuals in the transmissiion...
sequence.simulation.seqgen.parSimulate sequence data of individuals in the transmissiion...
simpact.config.inputsSimpact config input parameters to be estimated.
simpact.config.inputs.add.sampleResampling of Simpact config input parameters to be...
simpact.config.inputs.par.selectSimpact config input parameters to be estimated.
simpact.errFunctionHandling Simpact errors.
simpact.parallelDistribute simpact runs over multiple cores
simpact.params.boundariesThese are the preset boundaries for most of the parameters...
simpact.wrapperWrapper function for running simpact simulations
timespentsingle.calculatorCalculate time spent being single.
transmission.network.builderBuild a list of HIV transmission networks data
transm.network.builderBuild a list with HIV transmission network data.
trans.network2treeBuild a transmission tree from a transmission network
varied.simpact.paramsSelect the parameters that need to be calibrated to meet the...
vl.atARTinitA function that returns the total number of people between...
vl.suppressedA function that returns the percentage of clients who are...
wave1.creatorCreate a csv file with parameter combinations for the first...
wdelva/RSimpactHelp documentation built on July 14, 2018, 8:44 a.m.