prosecution.hypothesis.peaks: likeLTD::prosecution.hypothesis.peaks
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 using peak height data.

prosecution.hypothesis.peaks(peaksFile, refFile, ethnic='NDU1', nUnknowns=0,
                        adj=1e0, fst=0.03, 
                        linkageFile=NULL, databaseFile=NULL, 
                        detectionThresh=20, doDropin=FALSE, 
                        doDoubleStutter=TRUE,doOverStutter=TRUE,
                        combineRare=TRUE, rareThreshold=1,
                        kit=NULL, relationship=0, ...)

`peaksFile`	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`. Must include longest uninterrupted sequence (LUS) values for alleles.
`linkageFile`	Path to recombination rate information. If NULL then defaults to the linkage file provided with `likeLTD`. Only used if `relationship` is not 0 or 1 i.e. when Q and X are closely related but not parent/offspring.
`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.
`detectionThresh`	Detection threshold for peaks. Can be a single value, or a named list containing one value per locus.
`doDropin`	Whether or not to model drop-in. Note dropin is not currently possible with the peak heights model.
`doDoubleStutter`	Logical. Whether or not to model double stutter.
`doOverStutter`	Logical. Whether or not to model over stutter.
`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.

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

defence.hypothesis.peaks

## Not run: 
# datapath to example files
datapath = file.path(system.file("extdata", package="likeLTD"),"laboratory")

# File paths and case name for allele report
admin = pack.admin.input.peaks(
            peaksFile = file.path(datapath, 'laboratory-CSP.csv'),
            refFile = file.path(datapath, 'laboratory-reference.csv'),
            caseName = "Laboratory",
            detectionThresh = 20
             )

# Enter arguments
args = list(
        nUnknowns = 1
        )

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

## End(Not run)