insilico.fit: Implement InSilicoVA methods with more flexible customization

In InSilicoVA: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm

Implement InSilicoVA methods with more flexible customization

Description

This function implements InSilicoVA model. This is the lower level core function of InSilicoVA with more flexibility in customized input. For more detail of model specification, see the paper on https://arxiv.org/abs/1411.3042 and the default function insilico.

Usage

insilico.fit(
  data,
  data.type = c("WHO2012", "WHO2016")[1],
  sci = NULL,
  isNumeric = FALSE,
  updateCondProb = TRUE,
  keepProbbase.level = TRUE,
  CondProb = NULL,
  CondProbNum = NULL,
  datacheck = TRUE,
  datacheck.missing = TRUE,
  warning.write = FALSE,
  directory = NULL,
  external.sep = TRUE,
  Nsim = 4000,
  thin = 10,
  burnin = 2000,
  auto.length = TRUE,
  conv.csmf = 0.02,
  jump.scale = 0.1,
  levels.prior = NULL,
  levels.strength = 1,
  trunc.min = 1e-04,
  trunc.max = 0.9999,
  subpop = NULL,
  java_option = "-Xmx1g",
  seed = 1,
  phy.code = NULL,
  phy.cat = NULL,
  phy.unknown = NULL,
  phy.external = NULL,
  phy.debias = NULL,
  exclude.impossible.cause = c("subset2", "subset", "all", "InterVA", "none")[1],
  impossible.combination = NULL,
  no.is.missing = FALSE,
  customization.dev = FALSE,
  Probbase_by_symp.dev = FALSE,
  probbase.dev = NULL,
  table.dev = NULL,
  table.num.dev = NULL,
  gstable.dev = NULL,
  nlevel.dev = NULL,
  indiv.CI = NULL,
  groupcode = FALSE,
  ...
)

Arguments

data	see insilico
data.type	see insilico
sci	see insilico
isNumeric	see insilico
updateCondProb	see insilico
keepProbbase.level	see insilico
CondProb	see insilico
CondProbNum	see insilico
datacheck	see insilico
datacheck.missing	see insilico
warning.write	see insilico
directory	see insilico
external.sep	see insilico
Nsim	see insilico
thin	see insilico
burnin	see insilico
auto.length	see insilico
conv.csmf	see insilico
jump.scale	see insilico
levels.prior	see insilico
levels.strength	see insilico
trunc.min	see insilico
trunc.max	see insilico
subpop	see insilico
java_option	see insilico
seed	see insilico
phy.code	see insilico
phy.cat	see insilico
phy.unknown	see insilico
phy.external	see insilico
phy.debias	see insilico
exclude.impossible.cause	see insilico
impossible.combination	see insilico.train
no.is.missing	see insilico
customization.dev	Logical indicator for customized variables
Probbase_by_symp.dev	Not tested yet.
probbase.dev	The customized conditional probabilities of symptoms given causes, which could be in a different format than InterVA default, but it should consist of nlevel.dev levels rather than numerical values.
table.dev	The table of level names in probbase.dev. Default to be NULL
table.num.dev	The corresponding prior numerical values for each level in probbase.dev, in the same order as table.dev. Default to be NULL
gstable.dev	Table of gold standard causes for each death. Default to be NULL
nlevel.dev	number of levels in probbase.dev. Default to be NULL
indiv.CI	credible interval for individual probabilities
groupcode	logical indicator of including the group code in the output causes
...	unused arguments

Value

a insilico fit object, see see insilico for more detail.

Author(s)

Zehang Li, Tyler McCormick, Sam Clark

Maintainer: Zehang Li <[e-mail]>

References

Tyler H. McCormick, Zehang R. Li, Clara Calvert, Amelia C. Crampin, Kathleen Kahn and Samuel J. Clark(2014) Probabilistic cause-of-death assignment using verbal autopsies, https://arxiv.org/abs/1411.3042
Working paper no. 147, Center for Statistics and the Social Sciences, University of Washington

See Also

plot.insilico, summary.insilico

InSilicoVA documentation built on Sept. 29, 2022, 9:06 a.m.