initialize,genind-method: genind constructor

Description

The function new has a method for building genind objects. See the class description of genind for more information on this data structure. The functions genind and as.genind are aliases for new("genind", ...).

Usage

"initialize"(.Object, tab, pop = NULL, prevcall = NULL, ploidy = 2L, type = c("codom", "PA"), strata = NULL, hierarchy = NULL, ...)
genind(...)
as.genind(...)

Arguments

.Object

prototyped object (generated automatically when calling 'new')

tab

A matrix of integers corresponding to the @tab slot of a genind object, with individuals in rows and alleles in columns, and containing either allele counts (if type="codom") or allele presence/absence (if type="PA")

pop

an optional factor with one value per row in tab indicating the population of each individual

prevcall

an optional call to be stored in the object

ploidy

an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length.

type

a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA")

strata

a data frame containing population hierarchies or stratifications in columns. This must be the same length as the number of individuals in the data set.

hierarchy

a hierarchical formula defining the columns of the strata slot that are hierarchical. Defaults to NULL.

...

further arguments passed to other methods (currently not used)

Value

a genind object

Details

Most users do not need using the constructor, but merely to convert raw allele data using df2genind and related functions.