insilico.fit: 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,
  ...
)

Value

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

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

Author

Zehang Li, Tyler McCormick, Sam Clark

Maintainer: Zehang Li <lizehang@uw.edu>

References