insilico.fit: Implement InSilicoVA methods with more flexible customization

Description Usage Arguments Value Author(s) References See Also

View source: R/insilico_core.r

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

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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 <lizehang@uw.edu>

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 Aug. 2, 2021, 5:08 p.m.