
This function simulates the LR distribution for the true missing person in a reference family. The output contains both the total and marker-wise LR of each simulation, as well as various summary statistics. If a specific LR threshold is given, the inclusion power is computed as the probability that LR exceeds the threshold.
missingPersonIP(
reference,
missing,
markers,
nsim = 1,
threshold = NULL,
disableMutations = NA,
seed = NULL,
verbose = TRUE
)
A mpIP
object, which is essentially a list with the following
entries:
LRperSim
: A numeric vector of length nsim
containing the total LR for
each simulation.
meanLRperMarker
: The mean LR per marker, over all simulations.
meanLR
: The mean total LR over all simulations.
meanLogLR
: The mean total log10(LR)
over all simulations.
IP
: A named numeric of the same length as threshold
. For each element
of threshold
, the fraction of simulations resulting in a LR exceeding the
given number.
time
: The total computation time.
params
: A list containing the input parameters missing
, markers
,
nsim
, threshold
and disableMutations
A ped
object with attached markers.
The ID label of the missing pedigree member.
A vector indicating the names or indices of markers attached
to the source pedigree. If NULL (default), then all markers attached to the
source pedigree are used. If alleles
or afreq
is non-NULL, then this
parameter is ignored.
A positive integer: the number of simulations
A numeric vector with one or more positive numbers used as the likelihood ratio thresholds for inclusion
This parameter determines how mutation models are treated. Possible values are as follows:
NA
(the default): Mutations are disabled only for those markers whose
known genotypes are consistent with the pedigree. This is determined by
temporarily removing all mutation models and checking which markers have
nonzero likelihood.
TRUE
: Mutations are disabled for all markers. This will result in an
error if any markers are inconsistent.
FALSE
: No action is done to disable mutations.
A vector containing the names or indices of those markers for which mutations should be disabled.
An integer seed for the random number generator (optional).
A logical.
# Four siblings; the fourth is missing
x = nuclearPed(4)
# Remaining sibs typed with 5 triallelic markers
x = markerSim(x, N = 5, ids = 3:5, alleles = 1:3, seed = 123, verbose = FALSE)
# Compute inclusion power statistics
ip = missingPersonIP(x, missing = 6, nsim = 5, threshold = c(10, 100))
ip
# LRs from each simulation
ip$LRperSim
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