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End of an Era

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@krshedd krshedd released this 01 May 00:24
· 208 commits to master since this release
v1.12.0
dd868f1

Notable Changes

This is the final release for version 1 of GCL-R-Scripts! After this release we are going to start developing version 2 based on a new format for .gcl objects to integrate with R 4.0.0 and the tidyverse. A static version of this release will be parked on a separate branch v1.12.0-static, for posterity.

Below are all notable changes to the body of GCL-R-Scripts on the master branch since A Cat in Your Lap v1.11.0 was released on April 1, 2020.

See the README for this repository if you have questions. Note the code for Functions.GCL has been updated to pull all functions in this repository, not just the ones with a .GCL ending.

New Scripts

No new scripts!

Function Updates & Bug Fixes

  • FindAlternateSpecies
    • Bugfix, added drop=FALSE to prevent .gcl arrays from collapsing to matrices if only 1 fish in the silly
  • read_project_genotypes
    • Bugfix, filter for project_name if necessary, previously this function would pull all genotypes for fish involved in a project, including genotypes from older projects
  • save_sillys
    • Bugfix, report missing sillys correctly
  • treeColor
    • Bugfix, colors would not plot, now they will if colors are a character vector and found in colors()
  • HoFisFstTable
    • Update, added argument for path to fstatfile if already exists, rather than create a new one
  • QC
    • Update, replaced lattice::levelplot with plotly::ggplotly for an interactive view of genotyping success rate
  • FailureRate
    • Update, added plotly for interactive view of genotyping success rate

Tips

To avoid conflicts among packages that have the same function name, you can be more explicit in your function calls by adding package_name:: before the function name (i.e. dplyr::rename vs. rename, to avoid conflicts with reshape::rename). This makes your code more stable and less susceptible to package conflicts depending what the user has loaded in their workspace.

If you run into the following error when running LOKI2R.GCL
Error in .jcall(rp, "I", "fetch", stride, block) :
java.lang.OutOfMemoryError: GC overhead limit exceeded

  • Save your work
  • Re-start RStudio
  • Before doing anything else, run options(java.parameters = "-Xmx100g") to increase your heap space
  • Try to read data again
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