sim.regional.args: Input arguments to simulate sequences and viral phylogenetic...
In olli0601/PANGEA.HIV.sim: PANGEA.HIV.sim

Description Usage Arguments Value See Also

Set all input arguments to the simulation. Please see for model details https://github.com/olli0601/PANGEA.HIV.sim

sim.regional.args(yr.start = 1985, yr.end = 2020, seed = 42,
  s.INC.recent = NA, s.INC.recent.len = NA, s.PREV.min = NA,
  s.PREV.max = NA, s.PREV.base = NA, s.INTERVENTION.start = 2015,
  s.INTERVENTION.mul = NA, s.ARCHIVAL.n = 50, s.MODEL = "Fixed2Prop",
  s.PREV.max.n = 1600, s.INTERVENTION.prop = 0.5, epi.model = "HPTN071",
  epi.acute = "high", epi.intervention = "fast", epi.dt = 1/48,
  epi.import = 0.05, root.edge.fixed = 0, v.N0tau = 1, v.r = 2.851904,
  v.T50 = -2, wher.mu = log(0.00447743) - 0.5^2/2, wher.sigma = 0.5,
  bwerm.mu = log(0.002239075) - 0.3^2/2, bwerm.sigma = 0.3, er.gamma = 4,
  er.gtr = "GTR_VARIABLE", sp.prop.of.sexactive = 0.05,
  report.prop.recent = 1, dbg.GTRparam = 0, dbg.rER = 0,
  index.starttime.mode = "fix1970", startseq.mode = "one",
  seqtime.mode = "AtDiag")

`yr.start`	Start year of the epi simulation (default: 1985)
`yr.end`	First year after the epi simulation (default: 2020; optional 2018)
`seed`	Random number seed (default: 42; optional integer)
`s.INC.recent`	Deprecated
`s.INC.recent.len`	Deprecated
`s.PREV.min`	Deprecated
`s.PREV.max`	Deprecated
`s.INTERVENTION.start`	Year in which the community intervention starts (default: 2015). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.
`s.INTERVENTION.mul`	Deprecated
`s.ARCHIVAL.n`	Total number of sequences sampled at random from infected individuals before 2000 (default: 50). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.
`s.MODEL`	Sampling model to use (default: 'Fixed2Prop'). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.
`s.PREV.max.n`	Number of infected cases sampled (default: 1600; optional 3200). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.
`s.INTERVENTION.prop`	Proportion of infected cases that are sampled from after intervention start (default: 0.5; optional 0.85). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.
`epi.model`	The epi model used to create the epi simulation (default: 'HPTN071')
`epi.acute`	The proportion of transmissions in 2015 from individuals in their first three months of infection (default: 'high'/40%, optional: 'low'/10%)
`epi.intervention`	The scale of the intervention package (default:'fast', optional: 'slow', 'none')
`epi.dt`	Time increment of the epi simulation (default: 1/48, this is fixed to the underlying epidemic simulation)
`epi.import`	Proportion of viral introductions amongst new cases per year (default: 0.05, optional: 0.2). See https://github.com/olli0601/PANGEA.HIV.sim#viral-introductions.
`root.edge.fixed`	Fix evolutionary rate of root edges of new lineages in the population to mean evolutionary rate (default: 1, optional: 0). See https://github.com/olli0601/PANGEA.HIV.sim#overall-evolutionary-rates-of-transmission-and-non-transmission-lineages.
`v.N0tau`	Within host effective population size at time of infection (default 1). See https://github.com/olli0601/PANGEA.HIV.sim#dated-viral-phylogenies.
`v.r`	Parameter logistic growth model (default 2.851904). See https://github.com/olli0601/PANGEA.HIV.sim#dated-viral-phylogenies.
`v.T50`	Parameter logistic growth model (default -2). See https://github.com/olli0601/PANGEA.HIV.sim#dated-viral-phylogenies.
`wher.mu`	Mean of within host evolutionary rate (default: log(0.00447743)-0.5^2/2). See https://github.com/olli0601/PANGEA.HIV.sim#overall-evolutionary-rates-of-transmission-and-non-transmission-lineages.
`wher.sigma`	Standard deviation of within host evolutionary (default: 0.5). See https://github.com/olli0601/PANGEA.HIV.sim#overall-evolutionary-rates-of-transmission-and-non-transmission-lineages.
`bwerm.mu`	Mean of between host evolutionary rate (default: log(0.002239075)-0.3^2/2). See https://github.com/olli0601/PANGEA.HIV.sim#overall-evolutionary-rates-of-transmission-and-non-transmission-lineages.
`bwerm.sigma`	Standard deviation of between host evolutionary rate (default: 0.3). See https://github.com/olli0601/PANGEA.HIV.sim#overall-evolutionary-rates-of-transmission-and-non-transmission-lineages.
`er.gamma`	Site heterogeneity parameter (default: 4, optional 0)
`er.gtr`	Evolution model identifier. Default: GTR_VARIABLE. Alternatively: GTR_POL_CP1.
`sp.prop.of.sexactive`	Proportion of population sampled in seroprevalence survey (default: 0.05)
`report.prop.recent`	Proportion of individuals in seroprevalence survey for whom recency of infection should be reported (default: 1)
`dbg.GTRparam`	Use mean GTR rates instead of samples from empirical prior (default: 0, optional 1)
`dbg.rER`	Use mean evolutionary rate instead of samples from empirical prior (default: 0, optional 1)
`index.starttime.mode`	Sampling distribution of sampling times of starting sequences (default: 'fix1970', optional 'fix19XX' where XX between 45-79, 'normal' meaning Normal(1955,7)). See https://github.com/olli0601/PANGEA.HIV.sim#seed-sequences.
`startseq.mode`	Number of different starting sequences (default: 'one', optional 'many'). See https://github.com/olli0601/PANGEA.HIV.sim#seed-sequences.
`seqtime.mode`	Time at which sequences are sampled (default: 'AtDiag'). See https://github.com/olli0601/PANGEA.HIV.sim#sequence-sampling-model.