alleleinit: Diploid loci matrix initialization

Description

alleleinit converts genetic data with diploid loci as generated by alleleconvert into an object of class alleleobject. print.alleleobject is a print method for such objects.

Usage

alleleinit(file = NULL, allelematrix=NULL,
                        rows.are.individuals = TRUE, 
    neighborhood = "none", distance = "alleledist", namode="variables",
                       nachar="-", distcount=FALSE) 

# S3 method for alleleobject
print(x, ...)

Value

alleleinit produces an object of class alleleobject (note that this is similar to class prab; for example both can be used with

prabclust), which is a list with components

distmat: distance matrix between individuals.
amatrix: data frame of input data with string variables in the input format, see details. Note that in the output for an individual the whole locus is declared missing if at least one of its alleles is missing in the input.
charmatrix: matrix of characters in which there are two rows for every individual corresponding to the two alleles in every locus (column). Entries are allele codes but missing values are coded as NA.
nb: neighborhood list, see above.
ext.nblist: a neighborhood list in which for every row in charmatrix the second row number corresponding to the neighboring individuals is listed.
n.variables: number of loci.
n.individuals: number of individuals.
n.levels: maximum number of different alleles in a locus.
n.species: identical to n.individuals used for compatibility with prabclust.
alevels: character vector with all used allele codes not including missing values.
leveldist: matrix in which rows are loci, columns are alleles and entries are frequencies of alleles per locus.
prab: useless matrix of number of factor levels corresponding to amatrix added for compatibility with objects of class prab.
regperspec: vector of row-wise sums of prab added for compatibility with objects of class prab.
specperreg: vector of column-wise sums of prab added for compatibility with objects of class prab.
distance: string denoting the chosen distance measure, see above.
namode: see above.
naprob: probability of missing values, numeric or vector, see documentation of argument namode.
nasum: number of missing entries (individual/loci) in amatrix.
nachar: see above.
spatial: logical. TRUE if a neighborhood was submitted.

Arguments

file: string. File name. File must be in "prabclus" format, see details. Either file or allelematrix needs to be specified.
allelematrix: matrix in "prabclus"-format as generated by alleleconvert, see details. Either file or allelematrix needs to be specified.
rows.are.individuals: logical. If TRUE, rows are interpreted as individuals and columns are interpreted as loci.
neighborhood: A string or a list with a component for every individual. The components are vectors of integers indicating neighboring individuals. An individual without neighbors should be assigned a vector numeric(0). If neighborhood is a filename, it is attempted to read such a list from a file, where every row should correspond to one region (such as example dataset nb.dat). If neighborhood="none", all neighborhoods are set to numeric(0). The neighborhood can be tested by nbtest for consistency.
distance: "alleledist" or "none". The distance measure between individuals to compute by alleleinit.
namode: one of "single", "individuals", "variables" , or "none". Determines whether a single probability for the entry to be missing is computed for a single locus of an individual ("single"), a vector of individual-wise probabilities for loci to be missing ("individuals"), a vector of loci-wise probabilities for individuals to be missing ("variables") or no missingness probability at all.
nachar: character denoting missing values.
distcount: logical. If TRUE, during distance computation individuals are counted on the screen.
x: object of class alleleobject.
...: necessary for print method.

Author

Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

Details

The required input format is the output format "prabclus" of alleleconvert. Alleles are coded by a single character, so diploid loci need to be pairs of characters without space between the two alleles (e.g., "AC"). The input needs to be an individuals*loci matrix or data frame (or a file that produces such a data frame by read.table(file,stringsAsFactors=FALSE))

Examples

Run this code

# Only 50 observations are used in order to have a fast example.
  data(tetragonula)
  tnb <-
  coord2dist(coordmatrix=tetragonula.coord[1:50,],cut=50,file.format="decimal2",neighbors=TRUE)
  ta <- alleleconvert(strmatrix=tetragonula[1:50,])
  tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist)
  print(tai)

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