pop.dist: Distances among populations
In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description Usage Arguments Details Value Author(s) Examples

This function computes the population pairwise distance matrix based on the frequency of haplotypes per population and the haplotypes pairwise distance matrix. It is mandatory to define haplotype and population names in the input file. See example for details.

pop.dist(DistFile = NA, distances = NA, HaploFile = NA, Haplos = NA,
 outType = "O", logfile = TRUE, saveFile = TRUE, NameIniPopulations
 = NA, NameEndPopulations = NA, NameIniHaplotypes = NA,
 NameEndHaplotypes = NA)

`DistFile`	the name of the file containing the distance matrix among haplotypes to be analysed. Alternatively, you can define a distance matrix stored in memory using 'distances'.
`distances`	the distance matrix among haplotypes (stored in memory) to be analysed. Alternatively, you can define the name of a file containing the distance matrix using 'DistFile'.
`HaploFile`	the name of the file containing the matrix with the number of haplotypes found per population (see 'HapPerPop' to obtain this matrix). Alternatively, you can define a matrix stored in memory using 'Haplos'.
`Haplos`	the name of the matrix (stored in memory) containing the number of haplotypes found per population (see 'HapPerPop' to obtain this matrix). Alternatively, you can define the name of a file containing the matrix using 'HaplosFile'.
`outType`	a string; the format of output matrix. "L" for lower diagonal hemi-matrix; "7" for upper diagonal hemi-matrix; "O" for both hemi-matrices (default).
`logfile`	a logical; if TRUE (default), it saves a file containing the names of the matrices used for computation (inputDist and HaploFile).
`saveFile`	a logical; if TRUE (default), function output is saved as a text file.
`NameIniPopulations`	a numeric indicating the position of the initial character of population names within the individual name in the matrix containing the number of haplotypes found per population (see example for details).
`NameEndPopulations`	a numeric indicating the position of the last character of population names within the individual name in the matrix containing the number of haplotypes found per population (see example for details). If NA (default), NameIniPopulations and NameEndPopulations are set to use the 'Haplos' (or HaploFile) matrix row names as population names.
`NameIniHaplotypes`	a numeric indicating the position of the initial character of haplotype names within the individual name in the distance matrix (see example for details).
`NameEndHaplotypes`	a numeric indicating the position of the last character of haplotype names within the individual name in the distance matrix (see example for details). If NA (default), NameIniHaplotypes and NameEndHaplotypes are set to use the 'distances' (or DistFile) matrix row names as haplotype names.

Each element in the population distance matrix is calculated as the arithmetic mean of the distances among all the sequences sampled in the two compared populations, as follows:

dist(i,j) = \frac{∑_{k=1}^{m}{∑_{l=1}^{n}{dist(H_{ki},H_{lj})}}}{m*n}

where dist(i,j) represents the distance between populations i and j, m and n are the number of sequences in populations i and j, respectively, and dist(H_ki,H_lj) is the distance between the k-th sequence found in population i and the l-th sequence found in population j.

A matrix containing the genetic distances among populations, based on the haplotype distances and their frequencies per populations.

A. J. Muñoz-Pajares

# cat(" H1 H2 H3 H4 H5",
# "Population1 1 2 1 0 0",
# "Population2 0 0 0 4 1",
# "Population3 0 1 0 0 3",
#      file = "4_Example3_HapPerPop_Weighted.txt", sep = "\n")
# 
# 
# cat("H1 H2 H3 H4 H5",
# "H1 0 1 2 3 1",
# "H2 1 0 3 4 2",
# "H3 2 3 0 1 1",
# "H4 3 4 1 0 2",
# "H5 1 2 1 2 0",
#      file = "4_Example3_IndelDistanceMatrixMullerMod.txt", sep = "\n")
#      example3_2 <- read.table("4_Example3_IndelDistanceMatrixMullerMod.txt"
# ,header=TRUE)
# 
# # Checking row names to estimate NameIniHaplotypes,NameEndHaplotypes:
#  row.names(read.table(file="4_Example3_IndelDistanceMatrixMullerMod.txt"))
# ## [1] "H1" "H2" "H3" "H4" "H5" NameIniHaplotypes=1. NameEndHaplotypes=2
# # Checking row names to estimate NameIniPopulations, and NameEndPopulations
#  row.names(read.table(file="4_Example3_HapPerPop_Weighted.txt"))
# ## [1] "Population1" "Population2" "Population3"
# ## NameIniPopulations=1 NameEndPopulations =11
# 
# # Reading files. Distance matrix must contain haplotype names. Abundance
# # matrix must contain both, haplotype and population names:
# 
# pop.dist (DistFile="4_Example3_IndelDistanceMatrixMullerMod.txt", 
# HaploFile="4_Example3_HapPerPop_Weighted.txt", outType="O",
# NameIniHaplotypes=1,NameEndHaplotypes=2,NameIniPopulations=1,
# NameEndPopulations=11)