write_hzar: Write a HZAR file from a tidy data frame.

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Write a HZAR file from a tidy data frame.

Description

Write a HZAR file (Derryberry et al. 2013), from a tidy data frame. Used internally in radiator and might be of interest for users.

Usage

write_hzar(
  data,
  distances = NULL,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1
)

Arguments

data	A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.
distances	(optional) A file with 2 columns, POP_ID and the distance information per populations. With default: distances = NULL, the column is left empty.
filename	(optional) The file name prefix for the HZAR file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_hzar_.
parallel.core	(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

Details

Integrated filters: Only polymorphic markers found in common between populations/strata are used to generate the HZAR file.

Value

A HZAR file is written in the working directory.

Author(s)

Thierry Gosselin [e-mail]

References

Derryberry EP, Derryberry GE, Maley JM, Brumfield RT. hzar: hybrid zone analysis using an R software package. Molecular Ecology Resources. 2013;14: 652-663. doi:10.1111/1755-0998.12209

Examples

## Not run: 
# The simplest form of the function:
hzar.data <- radiator::write_hzar(data = tidydata)


# Using genepop dataset, nancycats, from adegenet
# require(adegenet)
nancycats <- system.file("files/nancycats.gen", package = "adegenet")


# using genomic_converter:
nanycats.hzar <- radiator::genomic_converter(data = nancycats, output = "hzar")


# using the separate modules:
# tidy the genepop file then pipe the result in write_hzar
nanycats.hzar <- radiator::tidy_genepop(data = nancycats) %>%
    radiator::write_hzar(data = .)

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.