distance.comb: Distance matrices combination

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

This function allows combining distance matrices. The weight of each matrix must be defined by user.

Usage

distance.comb(matrices = NA, alphas = NA, method = "Corrected",
saveFile = TRUE, na.rm = FALSE)

Arguments

matrices	a vector of strings containing the names of the matrices to be combined
alphas	a vector of numerics containing the weight of each matrix. By default, combination is done giving the same same weight to all matrices.
method	a string defining whether each distance matrix must be divided by its maximum value before the combination ("Corrected") or not ("Uncorrected"). Consequently, if the "Corrected" method is chosen, both matrices will range between 0 and 1 before being combined.
saveFile	a logical; if TRUE (default), the output matrix is saved a text file.
na.rm	a logical; if TRUE, missing values are removed before the computation proceeds.

Details

Matrices do not require to contain rows in the same order. The algorithm will search and combine rows of matrices with identical names. If row names of any input matrix are not defined, the algorithm will combine rows in order.

Value

A matrix containing the weighted combination of the original matrices

Author(s)

A. J. Muñoz-Pajares

See Also

nt.gap.comb

Examples

# mat1<-matrix(rep(1,16),ncol=4)
# mat2<-matrix(rep(2,16),ncol=4)
# mat3<-matrix(rep(3,16),ncol=4)
# mat4<-matrix(rep(6,16),ncol=4)
# mat5<-matrix(c(rep(1,4),rep(3,4),rep(1,4),rep(1,4)),ncol=4)
# mat6<-matrix(c(rep(1,4),rep(4,4),rep(4,4),rep(4,4)),ncol=4)
# mat7<-mat6
# colnames(mat5)<-c("a","b","c","d")
# colnames(mat6)<-c("b","a","c","d")
# row.names(mat5)<-c("a","b","c","d")
# row.names(mat6)<-c("b","a","c","d")
# 
# # Matrices with information about the same elements (a-d)
# # but in different order, are automatically
# # sorted before combination....
# 
# distance.comb(matrices=c("mat5","mat6"),saveFile=FALSE,method="Uncorrected")
# 
# # ... but this is not possible if any of the matrices lack row names:
# 
# distance.comb(matrices=c("mat5","mat7"),saveFile=FALSE,method="Uncorrected")
# 
# # More examples:
# distance.comb(matrices=c("mat1","mat2","mat3","mat4"),alphas=rep(0.25,4),
# saveFile=FALSE,method="Uncorrected")
# 
# distance.comb(matrices=c("mat1","mat2","mat3","mat4"),alphas=rep(0.25,4),
# saveFile=FALSE,method="Corrected")
# 
# distance.comb(matrices=c("mat1","mat2","mat3","mat4"),alphas=c(0.66,0.33,0,0),
# saveFile=FALSE,method="Uncorrected")
# 
# distance.comb(matrices=c("mat1","mat2","mat3","mat6"),alphas=c(0.66,0.33,0,0),
# saveFile=FALSE,method="Uncorrected")

sidier documentation built on June 25, 2021, 5:10 p.m.