NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(mean,age.pos.vector.creator)
S3method(select,summary.params)
export(AR.groups.fun.agemix)
export(ART.coverage.calculator)
export(ART.coverage.vector.creator)
export(ART.retention)
export(CAR.groups.fun.agemix)
export(EAAA.F.a.wrapper)
export(EAAA.F.c.wrapper)
export(EAAA.P.a.wrapper)
export(EAAA.P.c.wrapper)
export(EAAA.SciRep.revision.behaviourchange.calibration.wrapper)
export(EAAA.SciRep.revision.calibration.wrapper)
export(EAAA.SciRep.revision2.calibration.wrapper)
export(EAAA.calibration.wrapper)
export(EAAA.revised.F.a.wrapper)
export(EAAA.revised.F.c.wrapper)
export(EAAA.revised.wrapper)
export(EAAA.wrapper)
export(HIVinNetworks.calibration.wrapper)
export(HIVinNetworks.output.wrapper)
export(IDs.Seq.Age.Groups)
export(IDs.Seq.Random)
export(IDs.indiv.seq.gender.fun)
export(VL.suppression.calculator)
export(age.group.time.window)
export(agedif.median)
export(agedistr.creator)
export(agemix.df.maker)
export(agemix.episodes.df.maker)
export(agemix.rels.df.maker)
export(agemixing.1a.wrapper.for.SimpactPaper)
export(agemixing.1b.wrapper.for.SimpactPaper)
export(agemixing.2a.wrapper.for.SimpactPaper)
export(agemixing.wrapper.for.SimpactPaper)
export(agemixing.wrapper.withhiv)
export(alive.infected)
export(amp.modeller)
export(art.person.years)
export(bsd.extractor)
export(cd4.atARTinit)
export(cd4.atARTinit.calculator)
export(cd4.vl.atARTinit)
export(choose.sequence.ind)
export(client.facility)
export(concurr.pointprev.calculator)
export(degree.df.frac)
export(degree.df.maker)
export(degree.distr.fitter)
export(degree.hist.maker)
export(dummy.wrapper)
export(epi2tree2)
export(hiv.infected.group)
export(hiv.negative.lifeyears)
export(incidence.calculator)
export(incidence.vector.creator)
export(input.params.creator)
export(intervention.introduced)
export(life.years.lived)
export(pattern.modeller)
export(pattern.plotter)
export(phylo.AR.groups.fun.agemix)
export(phylo.CAR.groups.fun.agemix)
export(phylogenetic.tree.fasttree)
export(phylogenetic.tree.fasttree.par)
export(phylogenetic.tree.phangorn.par)
export(pop.growth.calculator)
export(prevalence.calculator)
export(prevalence.plotter)
export(prevalence.vector.creator)
export(readthedata)
export(recruit.study.clients)
export(sequence.simulation.seqgen)
export(sequence.simulation.seqgen.par)
export(simpact.config.inputs)
export(simpact.config.inputs.add.sample)
export(simpact.config.inputs.par.select)
export(simpact.errFunction)
export(simpact.parallel)
export(simpact.params.boundaries)
export(simpact.wrapper)
export(timespentsingle.calculator)
export(trans.network2tree)
export(transm.network.builder)
export(transmission.network.builder)
export(varied.simpact.params)
export(vl.atARTinit)
export(vl.suppressed)
export(wave1.creator)
import(RSimpactCyan)
import(ape)
import(dplyr)
import(fitdistrplus)
import(ggplot2)
import(phangorn)
import(treedater)
importFrom(MASS,glm.nb)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,getSeq)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,seqinfo)
importFrom(ape,write.dna)
importFrom(data.table,fread)
importFrom(data.table,setDT)
importFrom(data.table,setnames)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(exactci,poisson.exact)
importFrom(fitdistrplus,fitdist)
importFrom(gtools,smartbind)
importFrom(igraph,graph.edgelist)
importFrom(igraph,subcomponent)
importFrom(lhs,augmentLHS)
importFrom(lhs,randomLHS)
importFrom(lme4,lmer)
importFrom(magrittr,"%>%")
importFrom(nlme,VarCorr)
importFrom(nlme,lme)
importFrom(nlme,varPower)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapplyLB)
importFrom(parallel,stopCluster)
importFrom(randtoolbox,sobol)
importFrom(readcsvcolumns,read.csv.columns)
importFrom(stats,aggregate)
importFrom(stats,binom.test)
importFrom(stats,median)
importFrom(stats,pweibull)
importFrom(stats,qunif)
importFrom(tibble,as_tibble)
importFrom(tidyr,gather)