Man pages for wdelva/RSimpactHelp
Pre- and Post-simulation helper functions for RSimpact Cyan
| agedif.median | Age difference median. |
| agedistr.creator | Create an age distribution for the population at the start of... |
| age.group.time.window | Subset the datalist ptable to include only people who existed... |
| agemix.df.maker | Create dataframe for age-mixing calculations. |
| agemix.episodes.df.maker | Create dataframe of relationship episodes for agemixing... |
| agemixing.1a.wrapper.for.SimpactPaper | Wrapper function for age mixing example of Simpact paper. |
| agemixing.1b.wrapper.for.SimpactPaper | Wrapper function for age mixing example of Simpact paper. |
| agemixing.2a.wrapper.for.SimpactPaper | Wrapper function for age mixing example of Simpact paper. |
| agemixing.wrapper.for.SimpactPaper | Wrapper function for age mixing example of Simpact paper. |
| agemixing.wrapper.withhiv | Wrapper function to test MICE-assisted calibration functions |
| agemixpatdat | Age-mixing pattern model data. |
| agemix.rels.df.maker | Create dataframe of relationships for agemixing analysis. |
| alive.infected | Subset people alive at a point in time and adds their HIV... |
| amp.modeller | Model age-mixing pattern. |
| AR.groups.fun.agemix | A function that returns age mixing patterns quantities in... |
| ART.coverage.calculator | Calculate overall HIV prevalence and ART coverage aggregated... |
| ART.coverage.vector.creator | Create a vector of ART coverage measurements. |
| art.person.years | A function that returns the total number of person-years on... |
| ART.retention | A function that returns the percentage of clients who are on... |
| bsd.extractor | Compute between-subject standard deviation from agemixing... |
| CAR.groups.fun.agemix | A function that returns age mixing patterns quantities in... |
| cd4.atARTinit | A function that returns the total number of people who... |
| cd4.atARTinit.calculator | CD4 at ART initiation |
| cd4.vl.atARTinit | A function that returns the total number of people between... |
| choose.sequence.ind | Subset sequences in fasta file based on sequence ID or Name |
| client.facility | A function that determines the facility the client attended... |
| concurr.pointprev.calculator | Calculate concurrent point prevalence, overall and... |
| datalist | Simpact run datalist data. |
| degree.df.frac | Fraction of women within specified age group with more than... |
| degree.df.maker | Degree distribution of persons in recent sexual... |
| degree.distr.fitter | Fitting parametric distributions to the degree data |
| degree.hist.maker | Plot the histogram of a degree distribution. |
| dummy.wrapper | Fast and simple wrapper function to test MICE-assisted... |
| EAAA.calibration.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.F.a.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.F.c.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.P.a.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.P.c.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.revised.F.a.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.revised.F.c.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.revised.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.SciRep.revision2.calibration.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.SciRep.revision.behaviourchange.calibration.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.SciRep.revision.calibration.wrapper | Wrapper function for running simpact simulations for the... |
| EAAA.wrapper | Wrapper function for running simpact simulations for the... |
| epi2tree2 | Build a transmission tree object from a transmission network... |
| err.function | We expect this to grow and the returned summary statistics to... |
| hiv.infected.group | Calculate the number of HIV infections that occured between... |
| HIVinNetworks.calibration.wrapper | Wrapper function for running simpact simulations for the... |
| HIVinNetworks.output.wrapper | Wrapper function for running simpact simulations for the... |
| hiv.negative.lifeyears | A function that returns the total number of HIV-negative life... |
| IDs.indiv.seq.gender.fun | Subset sequences based on gender ratio |
| IDs.Seq.Age.Groups | Random subset of sequences based on gender ratio and age... |
| IDs.Seq.Random | Completely random subset of sequences of individuals |
| incidence.calculator | Calculate HIV incidence, overall and stratified. |
| incidence.vector.creator | Create a vector of HIV incidence measurements. |
| input.params.creator | Create a default parameter configuration list. |
| intervention.introduced | We need to decide if we need to include all the intervention... |
| life.years.lived | A function that returns the total number of life-years lived... |
| mean.age.pos.vector.creator | Create a vector of mean ages among the HIV positive people |
| pattern.modeller | Model age-mixing pattern. |
| pattern.plotter | Plot age-mixing pattern. |
| persreldf | Relationship episodes from Simpact Simulation. |
| phylo.AR.groups.fun.agemix | A function that returns age mixing patterns quantities in... |
| phylo.CAR.groups.fun.agemix | A function that returns age mixing patterns quantities in... |
| phylogenetic.tree.fasttree | Construct and calibrate a phylogenetic tree from sequence... |
| phylogenetic.tree.fasttree.par | Construct phylogenetic tree with FastTree and calibrate same... |
| phylogenetic.tree.phangorn.par | Construct phylogenetic tree with Phangorn and calibrate same... |
| pop.growth.calculator | Calculate population growth rate. |
| prevalence.calculator | Calculate HIV prevalence, overall and stratified. |
| prevalence.plotter | Plot the overall HIV prevalence for the duration of the... |
| prevalence.vector.creator | Create a vector of HIV prevalence measurements. |
| readthedata | Read the Simpact output files. |
| recruit.study.clients | A function that recruits the MaxART clients |
| select.summary.params | Select the summary statistics that you want from the... |
| sequence.simulation.seqgen | Simulate sequence data of individuals in the transmissiion... |
| sequence.simulation.seqgen.par | Simulate sequence data of individuals in the transmissiion... |
| simpact.config.inputs | Simpact config input parameters to be estimated. |
| simpact.config.inputs.add.sample | Resampling of Simpact config input parameters to be... |
| simpact.config.inputs.par.select | Simpact config input parameters to be estimated. |
| simpact.errFunction | Handling Simpact errors. |
| simpact.parallel | Distribute simpact runs over multiple cores |
| simpact.params.boundaries | These are the preset boundaries for most of the parameters... |
| simpact.wrapper | Wrapper function for running simpact simulations |
| timespentsingle.calculator | Calculate time spent being single. |
| transmission.network.builder | Build a list of HIV transmission networks data |
| transm.network.builder | Build a list with HIV transmission network data. |
| trans.network2tree | Build a transmission tree from a transmission network |
| varied.simpact.params | Select the parameters that need to be calibrated to meet the... |
| vl.atARTinit | A function that returns the total number of people between... |
| vl.suppressed | A function that returns the percentage of clients who are... |
| VL.suppression.calculator | Calculate viral suppression fraction. |
| wave1.creator | Create a csv file with parameter combinations for the first... |
