runexample: runexample

In oyvble/euroformix: A Quantitative Model for Interpreting DNA Mixtures

runexample

Description

Calculate LR based on the inbuilt methods in euroformix for a specific setting

Usage

runexample(
  NOC,
  popfn,
  evidfn,
  reffn,
  POIind = 1,
  condInd = NULL,
  kit = NULL,
  modelDegrad = FALSE,
  modelBWstutt = FALSE,
  modelFWstutt = FALSE,
  findOptimalModel = TRUE,
  fst = 0.01,
  lambda = 0.01,
  prC = 0.05,
  threshT = 50,
  alpha = 0.01,
  seed = 1,
  nDone = 2,
  mcmcIter = 500,
  mcmcDelta = 2,
  verbose = TRUE
)

Arguments

NOC	Number of contributors
popfn	Filename of population frequency file (must contain EFM compatible text file)
evidfn	Filename of evidence(s) profile file (must contain EFM compatible text file)
reffn	Filename of reference(s) profile file (must contain EFM compatible text file)
POIind	Index of the references being Person of interest (POI), only Hp
condInd	Index of conditional references (both Hp and Hd)
kit	Kitname (shortname of kit obtained by getKit()). Used to model degradation and visualize EPG.
modelDegrad	Whether degradation should be modeled (requires kit to be specified)
modelBWstutt	Whether backward stutter should be modeled
modelFWstutt	Whether forward stutter should be modeled
findOptimalModel	Whether to find the optimal model (using AIC criterion)
fst	The co-ancestry coefficient (theta-correction). Can be a vector (must be number of marker long)
lambda	Parameter in modeled peak height shifted exponential model. Can be a vector (must be number of marker long)
prC	Allele drop-in probability. Can be a vector (must be number of marker long)
threshT	The analytical/detection threshold given. Can be a vector (must be number of marker long, and named with marker names to plot)
alpha	The significance level used for the envelope test (validMLEmodel). Default is 0.01
seed	Seed used in contLikMLE/contLikMCMC)
nDone	Number of required optimizations in contLikMLE
mcmcIter	Number of iterations used in contLikMCMC
mcmcDelta	Scaling of variance used for proposal in contLikMCMC (calibrated based on mcmc$accrat object)
verbose	Boolean whether printing data (EPG) and progress

Details

Using following inbuilt methods: sample_tableToList,prepareData,contLikMLE,logLiki,validMLEmodel,deconvolve,contLikMCMC,contLikINT, calcGjoint,plotEPG2

Value

A list with calculated result elements

Author(s)

Oyvind Bleka

Examples

## Not run: 
kit = "ESX17"
popfn = paste(path.package("euroformix"),"FreqDatabases",
 paste0(kit,"_Norway.csv"),sep=.Platform$file.sep)
evidfn = paste(path.package("euroformix"),"examples",paste0(kit,"_3p.csv"),
 sep=.Platform$file.sep)
reffn = paste(path.package("euroformix"),"examples",paste0(kit,"_refs.csv"),
 sep=.Platform$file.sep)
resList = runexample(NOC=3,popfn,evidfn,reffn,POIind=1,condInd=2,kit=kit,
 modelDegrad=TRUE,modelBWstutt=TRUE,verbose=TRUE)

## End(Not run)

oyvble/euroformix documentation built on Aug. 25, 2023, 11:14 a.m.