ModelOfDiagnostic {diemr}

R Documentation

Model of Diagnostic Marker Based on All Individual State Counts

Description

Estimates a diagnostic marker for the state counts of all genomic markers for all individuals. Using the hypothetical, diagnostic marker, calculates individual state counts with respect to their weighted similarity to the diagnostic marker states.

Usage

ModelOfDiagnostic(I4, OriginalHI, epsilon = 0.99, verbose = FALSE, ...)

Arguments

I4	a matrix or data.frame with 4 numeric columns representing character state counts for missing data, homozygots for allele 1, heterozygots, and homozygots for allele 2. Individuals in rows.
OriginalHI	numeric vector of length equal to number of rows in I4, representing hybrid indices of individuals.
epsilon	numeric, specifying how much the hypothetical diagnostic markers should contribute to the likelihood calculations. Must be in [0,1), keeping tolerance setting of the R session in mind.
verbose	logical or character with path to directory where run diagnostics will be saved.
...	parameters to be passed to other functions.

Details

The OriginalHI can be calculated with pHetErrOnStateCount.

Value

Matrix with dimensions of I4.

See Also

diem for utilising the model to determine appropriate marker polarisation in estimating barriers to geneflow.

Examples

# state count matrix
dat <- matrix(c(0, 0, 1, 3, 1, 2, 2, 0, 2, 1, 4, 1), ncol = 4)

# hybrid index calculation, assuming diploid markers
HI <- apply(dat * 2, MARGIN = 1, FUN = pHetErrOnStateCount)[1, ]

# run model of diagnostics, with the weight of the ideal diagnostic marker being 0.8
ModelOfDiagnostic(I4 = dat, OriginalHI = HI, epsilon = 0.8)
#      [,1] [,2] [,3] [,4]
# [1,]  0.0  5.4  0.4  0.2
# [2,]  0.0  0.2  0.0  5.6
# [3,]  0.4  4.4  0.8  0.4

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