prosecution.hypothesis: likeLTD::prosecution.hypothesis
In likeLTD: Tools to Evaluate DNA Profile Evidence

Description Usage Arguments Details Value See Also Examples

Helper function to create the input for the prosecution.

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, ...)

`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.

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.

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

defence.hypothesis

## 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))

## End(Not run)