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
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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. |
data.table with columns 'stat' (name of input argument) and 'v' (value of input argument).
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