Write a gsi_sim file from a data frame (wide or long/tidy).

Write a gsi_sim file from a data frame (wide or long/tidy). Used internally in assigner and genometranslator and might be of interest for users.

Usage

write_gsi_sim(
  data,
  pop.levels = NULL,
  pop.labels = NULL,
  strata = NULL,
  filename = "gsi_sim.unname.txt"
)

Arguments

data: A tidy genomic data set in the working directory tidy formats. How to get a tidy data frame ? Look for genometranslator tidy_genome.
pop.levels: (option, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default alphabetical or numerical order. e.g. pop.levels = c("QUE", "ONT", "ALB") instead of the default pop.levels = c("ALB", "ONT", "QUE"). Default: pop.levels = NULL. If you find this too complicated, there is also the strata argument that can do the same thing, see below.
pop.labels: (optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": (1) First, define the levels for your pop with pop.levels argument: pop.levels = c("QUE", "ONT", "ALB"). (2) then, use pop.labels argument: pop.levels = c("NEW", "NEW", "ALB").#' To rename "QUE" to "TAS": pop.labels = c("TAS", "ONT", "ALB"). Default: pop.labels = NULL. If you find this too complicated, there is also the strata argument that can do the same thing, see below.
strata: (optional) A tab delimited file with 2 columns with header: INDIVIDUALS and STRATA. Default: strata = NULL. Use this argument to rename or change the populations id with the new STRATA column. The STRATA column can be any hierarchical grouping.
filename: The name of the file written to the working directory. Default: filename = "gsi_sim.unname.txt".

Value

A gsi_sim input file is saved to 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

Anderson, Eric C., Robin S. Waples, and Steven T. Kalinowski. (2008) An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 65, 7:1475-1486.

Anderson, E. C. (2010) Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased. Molecular ecology resources 10, 4:701-710.

Author

Thierry Gosselin thierrygosselin@icloud.com