p4_functions: Calculate recombination frequency, LOD and log-likelihood...
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

This group of functions is called by linkage.

p4_1.0_1.0(x, p1, p2, ncores = 1)

p4_1.0_1.1(x, p1, p2, ncores = 1)

p4_1.0_1.2(x, p1, p2, ncores = 1)

p4_1.0_1.3(x, p1, p2, ncores = 1)

p4_1.0_2.0(x, p1, p2, ncores = 1)

p4_1.0_2.1(x, p1, p2, ncores = 1)

p4_1.0_2.2(x, p1, p2, ncores = 1)

p4_1.1_1.1(x, p1, p2, ncores = 1)

p4_1.1_1.2(x, p1, p2, ncores = 1)

p4_1.1_1.3(x, p1, p2, ncores = 1)

p4_1.1_2.2(x, p1, p2, ncores = 1)

p4_1.2_1.2(x, p1, p2, ncores = 1)

p4_1.2_2.1(x, p1, p2, ncores = 1)

p4_1.2_2.2(x, p1, p2, ncores = 1)

p4_1.3_1.2(x, p1, p2, ncores = 1)

p4_1.3_1.3(x, p1, p2, ncores = 1)

p4_1.3_2.1(x, p1, p2, ncores = 1)

p4_1.3_2.2(x, p1, p2, ncores = 1)

p4_2.0_1.1(x, p1, p2, ncores = 1)

p4_2.0_1.2(x, p1, p2, ncores = 1)

p4_2.0_1.3(x, p1, p2, ncores = 1)

p4_2.0_2.0(x, p1, p2, ncores = 1)

p4_2.0_2.1(x, p1, p2, ncores = 1)

p4_2.0_2.2(x, p1, p2, ncores = 1)

p4_2.1_2.2(x, p1, p2, ncores = 1)

p4_2.2_2.2(x, p1, p2, ncores = 1)

`x`	A frequency table of the different classes of dosages in the progeny. The column names start with `"n_"`. Followed by the dosage of the first marker and then of the second.
`p1`	Preferential pairing parameter for parent 1, numeric value in range 0 <= p1 < 2/3
`p2`	Preferential pairing parameter for parent 2, numeric value in range 0 <= p2 < 2/3
`ncores`	Number of cores to use for parallel processing (deprecated).

A list with the following items:

`r_mat`	A matrix with recombination frequencies for the different phases
`LOD_mat`	A matrix with LOD scores for the different phases
`logL_mat`	A matrix with log likelihood ratios for the different phases
`phasing_strategy`	A character string specifying the phasing strategy. `"MLL"` for maximum likelihood en `"MINR"` for minimum recombination frequency.
`possible_phases`	The phases between markers that are possible. Same order and length as column names of output matrices.