prosecution.hypothesis: likeLTD::prosecution.hypothesis

Description

Helper function to create the input for the prosecution.

Usage

prosecution.hypothesis(cspFile, refFile, ethnic='NDU1', nUnknowns=0,
                        adj=1e0, fst=0.02, databaseFile=NULL, 
                        linkageFile=NULL,
                        doDropin=FALSE, 
                        combineRare=TRUE, rareThreshold=0.05,
                        kit=NULL, relationship=0, ...)

Arguments

cspFile

Path to the crime scene profile.

refFile

Path to the known profiles.

ethnic

Ethnicity, e.g. subgroup within the allele frequency database.

nUnknowns

Number of unknown contributors for which to perform calculation.

adj

Allele frequency adjustment parameter.

fst

Allele fraction adjustment \(F_{ST}\).

databaseFile

Path to the allele database. If NULL, then defaults to the NGMSelect database provided with likeLTD.

linkageFile

Path to recombination rate information. If NULL then defaults to the linkage file provided with likeLTD. Only used if relatedness=c(0.5,0.25) i.e. when Q and X are siblings.

relationship

Specified relationship between Q and X. Can take values of 0=unrelated, 1=parent/offspring, 2=siblings, 3=uncle/nephew, 4=half-uncle/half-nephew, 5=cousins, 6=grandparent/grandchild, 7=half-siblings.

doDropin

Whether or not to model drop-in.

combineRare

Whether or not to combine rare unobserved alleles into a single allele.

rareThreshold

If combineRare=TRUE, this is the probability threshold below which an allele is classed as rare, and therefore combined with other rare unobserved alleles.

kit

Parameter specifying which allele database supplied with likeLTD to use if linkageFile is not specified. Possibilities are "DNA17", "Identifiler", "SGMplus", "NISTidentifiler" and "NISTglobalfiler".

...

Other parameters to determine how to perform calculations.

Value

A list of named input parameters, or hypothesis, suitable for the prosecution.

Details

It loads the CSP, known profiles, and allele database from file. It makes sure the relatedness factor is zero. It sets the reference individual to the first queried individual, unless it is not subject to dropout. In that case, the reference individual is the first individual with dropout.

Examples

Run this code

# NOT RUN {
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"hammer")

# File paths and case name for allele report
admin = pack.admin.input(
            cspFile = file.path(datapath, 'hammer-CSP.csv'),
            refFile = file.path(datapath, 'hammer-reference.csv'),
            caseName = "hammer",
	    kit= "SGMplus"
             )

# Enter arguments
args = list(
        nUnknowns = 1,
        doDropin = FALSE,
        ethnic = "EA1",
        adj = 1,
        fst = 0.02,
        relatedness = c(0,0)
        )

# Create hypotheses
hypP = do.call(prosecution.hypothesis, append(admin,args))
hypD = do.call(defence.hypothesis, append(admin,args))
# }