EcoGenetics (version 1.2.1-6)

ecogen2hierfstat: Converting an ecogen genetic data frame into a hierfstat data frame

Description

This function converts the genetic data of an ecogen object into a hierfstat data frame.

Usage

ecogen2hierfstat(
  eco,
  pop = NULL,
  to_numeric = FALSE,
  nout = 3,
  recode = c("all", "column", "paired"),
  replace_in = NULL,
  replace_out = NULL,
  ...
)

Arguments

eco

Object of class "ecogen".

pop

The name of the S slot column with the groups for the hierfstat data frame.

to_numeric

Recode the genetic data into numeric format? If TRUE, the functions performs the correction via eco.format. Additional formatting parameters can be passed to this function.

nout

Number of digits in the output when to_numeric = TRUE.

recode

Recode mode when to_numeric = TRUE: "all" for recoding the data considering all the individuals values at once (e.g., protein data), "column" for recoding the values by column (e.g., microsatellite data), "paired" for passing the values of allelic states and corresponding replacement values, using the replace_in and replace_out arguments (e.g. replace_in = c("A", "T", "C", "G"), replace_out = c(1,2,3,4)).

replace_in

vector with states of the data matrix to be replaced, when recode = "paired". This argument must be used in conjunction with the argument "replace_out".

replace_out

vector with states of the data matrix used for replacement, when recode = "paired". This argument must be used in conjunction with the argument "replace_in".

...

Additional parameters passed to eco.format when to_numeric = TRUE

Examples

# NOT RUN {
# }
# NOT RUN {
data(eco.test)
hiereco <- ecogen2hierfstat(eco, "pop", to_numeric = TRUE)
require("hierfstat")
basic.stats(hiereco)

# }
# NOT RUN {
# }

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