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Write a HZAR file from a tidy data frame.

Source: R/write_hzar.R
write_hzar.Rd

Write a HZAR file (Derryberry et al. 2013), from a tidy data frame. Used internally in genometranslator 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 genometranslator tidy_genome.

distances

(optional) A file with 2 columns, POP_ID and the distance information per populations. With default: distances = NULL, the column is left empty. Default: distances = NULL.

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_. Default: filename = NULL.

parallel.core

Default: parallel.core = parallel::detectCores() - 1.

Value

A HZAR file is written in the working directory.

Data filtering

This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.

Dependencies

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

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

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
# The simplest form of the function:
hzar.data <- genometranslator::write_hzar(data = tidydata)


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


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


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