Files in wdelva/RSimpactHelp

Pre- and Post-simulation helper functions for RSimpact Cyan

.Rapp.history

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/AR.groups.fun.agemix.R R/ART.coverage.calculator.R R/ART.coverage.vector.creator.R R/ART.person.years.R R/ART.retention.R R/CAR.groups.fun.agemix.R R/CD4.atARTinit.R R/EAAA.F.a.wrapper.R R/EAAA.F.c.wrapper.R R/EAAA.P.a.wrapper.R R/EAAA.P.c.wrapper.R R/EAAA.SciRep.revision.behaviourchange.calibration.wrapper.R R/EAAA.SciRep.revision.calibration.wrapper.R R/EAAA.SciRep.revision2.calibration.wrapper.R R/EAAA.calibration.wrapper.R R/EAAA.revised.F.a.wrapper.R R/EAAA.revised.F.c.wrapper.R R/EAAA.revised.wrapper.R R/EAAA.wrapper.R R/HIVinNetworks.calibration.wrapper.R R/HIVinNetworks.output.wrapper.R R/IDs.Seq.Age.Groups.R R/IDs.Seq.Random.R R/IDs.indiv.seq.gender.fun.R R/Misc/David/calibration.MaC.R R/Misc/David/toy_example_MaC.R R/Misc/EasyABC.hhohho/easyabc.simpact.simulation.R R/Misc/EasyABC.hhohho/easyabc.simpact.wrapper.R R/Misc/MaxARTFinal.Sim/MaxART.simpact.wrapper.easyABC.run.R R/Misc/MaxARTFinal.Sim/maxart.sim.summary.targets.creator.R R/Misc/MaxARTFinal.Sim/maxart.simpact.parameters.R R/Misc/MaxARTFinal.Sim/maxart.summary.statistics.creator.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/OLD.pre.hho.simpact.wrapper.easyABC.run.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/hho.rsimpacthelper.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/mice.calibration.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/OLD.pre.hho.simpact.wrapper.easyABC.run.R

R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/SummaryOutPut-df-KedzVRYEhM-pdbMPI.csv

R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/SummaryOutPut-df-LVjtvpcEPK-pdbMPI.csv

R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/SummaryOutPut-df-LVjtvpcEPK.csv

R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/T.pre.hho.simpact.wrapper.easyABC.run.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/parallel/pre.hho.simpact.wrapper.easyABC.run.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/pre.hho.sim.summary.targets.creator.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/pre.hho.simpact.parameters.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/pre.hho.summary.statistics.creator.R R/Misc/Pre.hhohhoMaxARTFinal.Sim/simpact.mice.calibration.run.R R/Misc/SimpactCalibration/mice.calibration.Template.R R/Misc/SimpactCalibration/simpact.mice.calibration.run.Template.R R/Misc/SimpactWrapper/sim.summary.targets.creator.R R/Misc/SimpactWrapper/simpact.parameters.R R/Misc/SimpactWrapper/simpact.wrapper.easyABC.run.R R/Misc/SimpactWrapper/summary.statistics.creator.R R/Misc/hhohhoMaxARTFinal.Sim/hhohho.sim.summary.targets.creator.R R/Misc/hhohhoMaxARTFinal.Sim/hhohho.simpact.parameters.R R/Misc/hhohhoMaxARTFinal.Sim/hhohho.simpact.wrapper.easyABC.run.R R/Misc/hhohhoMaxARTFinal.Sim/hhohho.summary.statistics.creator.R R/Misc/incidence-4000.Rmd R/Misc/incidence-degree-exploration.Rmd

R/Misc/incidence-degree-exploration.html

R/Misc/pbdMPI.hhohho/pbdmpi.simpact.simulation.R R/Misc/pbdMPI.hhohho/pbdmpi.simpact.wrapper.R R/Misc/test.R R/VL.atARTinit.R R/VL.suppressed.R R/VL.suppression.calculator.R R/age.group.time.window.R R/agedif.median.R R/agedistr.creator.R R/agemix.df.maker.R R/agemix.episodes.df.maker.R R/agemix.rels.df.maker.R R/agemixing.1a.wrapper.for.SimpactPaper.R R/agemixing.1b.wrapper.for.SimpactPaper.R R/agemixing.2a.wrapper.for.SimpactPaper.R R/agemixing.wrapper.for.SimpactPaper.R R/agemixing.wrapper.withhiv.R R/agemixpatdat.R R/alive.infected.R R/amp.modeller.R R/bsd.extractor.R R/cd4.atARTinit.calculator.R R/cd4.vl.atARTinit.R R/choose.sequence.ind.R R/client.facility.R R/concurrent.point.prevalence.R R/datalist.R R/degree.df.frac.R R/degree.df.maker.R R/degree.distr.fitter.R R/degree.hist.maker.R R/dummy.wrapper.R R/epi2tree2.R R/err.function.R R/hiv.infected.group.R R/hiv.negative.lifeyears.R R/incidence.calculator.R R/incidence.vector.creator.R R/input.params.creator.R R/intervention.introduced.R R/life.years.lived.R R/mean.age.pos.vector.creator.R R/pattern.modeller.R R/pattern.plotter.R R/persreldf.R R/phylo.AR.groups.fun.agemix.R R/phylo.CAR.groups.fun.agemix.R R/phylogenetic.tree.fasttree.R R/phylogenetic.tree.fasttree.par.R R/phylogenetic.tree.phangorn.par.R R/pop.growth.calculator.R R/prevalence.calculator.R R/prevalence.plotter.R R/prevalence.vector.creator.R R/readthedata.R R/recruit.study.clients.R R/select.summary.params.R R/sequence.simulation.seqgen.R R/sequence.simulation.seqgen.par.R R/simpact.config.inputs.R R/simpact.config.inputs.add.sample.R R/simpact.config.inputs.par.select.R R/simpact.errFunction.R R/simpact.parallel.R R/simpact.params.boundaries.R R/simpact.wrapper.R R/timespentsingle.calculator.R R/trans.network2tree.R R/transm.network.builder.R R/transmission.network.builder.R R/varied.simpact.params.R R/wave1.creator.R README.md

RSimpactHelper.Rproj

data/agemixpatdat.rda

data/datalist.rda

data/input.output.EAAA.RData

data/input.output.RData

data/persreldf.rda

man/AR.groups.fun.agemix.Rd man/ART.coverage.calculator.Rd man/ART.coverage.vector.creator.Rd man/ART.retention.Rd man/CAR.groups.fun.agemix.Rd man/EAAA.F.a.wrapper.Rd man/EAAA.F.c.wrapper.Rd man/EAAA.P.a.wrapper.Rd man/EAAA.P.c.wrapper.Rd man/EAAA.SciRep.revision.behaviourchange.calibration.wrapper.Rd man/EAAA.SciRep.revision.calibration.wrapper.Rd man/EAAA.SciRep.revision2.calibration.wrapper.Rd man/EAAA.calibration.wrapper.Rd man/EAAA.revised.F.a.wrapper.Rd man/EAAA.revised.F.c.wrapper.Rd man/EAAA.revised.wrapper.Rd man/EAAA.wrapper.Rd man/HIVinNetworks.calibration.wrapper.Rd man/HIVinNetworks.output.wrapper.Rd man/IDs.Seq.Age.Groups.Rd man/IDs.Seq.Random.Rd man/IDs.indiv.seq.gender.fun.Rd man/VL.suppression.calculator.Rd man/age.group.time.window.Rd man/agedif.median.Rd man/agedistr.creator.Rd man/agemix.df.maker.Rd man/agemix.episodes.df.maker.Rd man/agemix.rels.df.maker.Rd man/agemixing.1a.wrapper.for.SimpactPaper.Rd man/agemixing.1b.wrapper.for.SimpactPaper.Rd man/agemixing.2a.wrapper.for.SimpactPaper.Rd man/agemixing.wrapper.for.SimpactPaper.Rd man/agemixing.wrapper.withhiv.Rd man/agemixpatdat.Rd man/alive.infected.Rd man/amp.modeller.Rd man/art.person.years.Rd man/bsd.extractor.Rd man/cd4.atARTinit.Rd man/cd4.atARTinit.calculator.Rd man/cd4.vl.atARTinit.Rd man/choose.sequence.ind.Rd man/client.facility.Rd man/concurr.pointprev.calculator.Rd man/datalist.Rd man/degree.df.frac.Rd man/degree.df.maker.Rd man/degree.distr.fitter.Rd man/degree.hist.maker.Rd man/dummy.wrapper.Rd man/epi2tree2.Rd man/err.function.Rd man/hiv.infected.group.Rd man/hiv.negative.lifeyears.Rd man/incidence.calculator.Rd man/incidence.vector.creator.Rd man/input.params.creator.Rd man/intervention.introduced.Rd man/life.years.lived.Rd man/mean.age.pos.vector.creator.Rd man/pattern.modeller.Rd man/pattern.plotter.Rd man/persreldf.Rd man/phylo.AR.groups.fun.agemix.Rd man/phylo.CAR.groups.fun.agemix.Rd man/phylogenetic.tree.fasttree.Rd man/phylogenetic.tree.fasttree.par.Rd man/phylogenetic.tree.phangorn.par.Rd man/pop.growth.calculator.Rd man/prevalence.calculator.Rd man/prevalence.plotter.Rd man/prevalence.vector.creator.Rd man/readthedata.Rd man/recruit.study.clients.Rd man/select.summary.params.Rd man/sequence.simulation.seqgen.Rd man/sequence.simulation.seqgen.par.Rd man/simpact.config.inputs.Rd man/simpact.config.inputs.add.sample.Rd man/simpact.config.inputs.par.select.Rd man/simpact.errFunction.Rd man/simpact.parallel.Rd man/simpact.params.boundaries.Rd man/simpact.wrapper.Rd man/timespentsingle.calculator.Rd man/trans.network2tree.Rd man/transm.network.builder.Rd man/transmission.network.builder.Rd man/varied.simpact.params.Rd man/vl.atARTinit.Rd man/vl.suppressed.Rd man/wave1.creator.Rd

wdelva/RSimpactHelp documentation built on Dec. 26, 2019, 3:42 a.m.