validate_kinship: Validate a kinship matrix

In popkin: Estimate Kinship and FST under Arbitrary Population Structure

Validate a kinship matrix

Description

Tests that the input is a valid kinship matrix (a numeric, square, and optionally symmetric R matrix). Intended for matrices to plot and for other uses, including biased estimates, so there is flexibility as to what constitutes a valid kinship matrix. Throws errors if the input is not as above. Can instead return TRUE/FALSE if logical = TRUE.

Usage

validate_kinship(kinship, sym = TRUE, name = "kinship", logical = FALSE)

Arguments

kinship	The kinship matrix to validate.
sym	If TRUE (default), the matrix is required to be symmetric. Otherwise this particular test is skipped.
name	Default "kinship". Change to desired variable name for more informative error messages (i.e. "A" when used to validate the A matrix inside popkin_A_min_subpops).
logical	If FALSE (default), function stops with an error message if the input is not a kinship matrix. If TRUE, function instead returns TRUE if the input passed all tests (appears to be a valid kinship matrix) or FALSE otherwise.

Details

True kinship matrices have values strictly between 0 and 1, and diagonal values strictly between 0.5 and 1. However, estimated matrices may contain values slightly out of range. For greater flexibility, this function does not check for out-of-range values.

Value

If logical = FALSE (default), nothing. If logical = TRUE, returns TRUE if the input is a valid kinship matrix, FALSE otherwise.

Examples

# this is a valid (positive) example
kinship <- matrix(c(0.5, 0, 0, 0.6), nrow=2)
# this will run without errors or warnings
validate_kinship(kinship)

# negative examples

# dies if input is missing
try( validate_kinship() )

# and if input is not a matrix
try( validate_kinship( 1:5 ) )

# and for non-numeric matrices
char_mat <- matrix(c('a', 'b', 'c', 'd'), nrow=2)
try( validate_kinship( char_mat ) )

# and non-square matrices
non_kinship <- matrix(1:2, nrow=2)
try( validate_kinship( non_kinship ) )

# and non-symmetric matrices
non_kinship <- matrix(1:4, nrow=2)
try( validate_kinship( non_kinship ) )
# but example passes if we drop symmetry requirement this way
validate_kinship( non_kinship, sym = FALSE )

# instead of stopping, can get a logical value
# this returns FALSE
validate_kinship( non_kinship, logical = TRUE )

popkin documentation built on Jan. 7, 2023, 1:26 a.m.