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NEWS.md

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qtl2pleio 1.4.3.9000

Major changes

  • None

Minor changes

  • Started using Github Actions for continuous integration testing.

qtl2pleio 1.4.3

Major changes

  • None

Minor changes

  • Updated RcppExports.cpp and deleted C++ test files that aren't used.

qtl2pleio 1.4.2.9000

Major changes

  • added function convert_to_scan1_output to convert multivariate, one-QTL lods to output format of qtl2::scan1, for use in qtl2::bayes_int.

Minor changes

  • None

qtl2pleio 1.4.1

Major changes

  • None

Minor changes

  • Added vignette to .Rbuildignore to ease CRAN submission.

qtl2pleio 1.4.0

Major changes

  • Refactored scan_pvl and boot_pvl to reduce duplicated code
  • Added functions for genomewide, multivariate, one-QTL scan

Minor changes

  • Returned to parallelization implemented by R package parallel.
  • Set default cores value to parallelly::availableCores() for compatibility with job schedulers.

qtl2pleio 1.3.0

Major changes

  • Replaced parallel package use with furrr. This led to removal of the argument n_cores from both boot_pvl and scan_pvl. A user may now use future::plan to run in parallel.
  • Moved vignettes to website: https://fboehm.us/software/qtl2pleio

Minor changes

  • Fixed argument name in boot_pvl, changing nboot_per_job to nboot.
  • Created function scan_pvl_clean to be called in both scan_pvl and boot_pvl. This change shouldn't affect most users' experiences.

qtl2pleio 1.2.4

Major changes

  • None

Minor changes

  • Updated calc_lrt_tib function to accommodate d-dimensional, d-variate scans

qtl2pleio 1.2.3

Major changes

  • None

Minor changes

  • I shortened title per CRAN recommendation

  • I added \value tags to document functions' outputs

qtl2pleio 1.2.2

Major changes

  • I added data to package to enable vignettes, examples, and tests.

Minor changes

  • Per CRAN submission feedback, I spelled out QTL in DESCRIPTION file and upon first use in vignettes.

  • Added citations with references to vignettes.

qtl2pleio 1.2.1

Major changes

  • none

Minor changes

  • removed examples' and vignettes' dependencies on qtl2 R package.

qtl2pleio 1.2.0

Major changes

  • changed output of scan_pvl to be log10 likelihood, not log (natural base) likelihood. Thank you to @HongHe0123 for suggesting this.

Minor changes

  • changed column name for tibble outputs to reflect log base 10 instead of log natural base.

qtl2pleio 1.1.0

Major changes

  • rewrites (and deletions) of tibble helper functions
  • major revisions to code in main vignette

Minor changes

  • fixed CITATION after G3 publication

qtl2pleio 1.0.7

Major changes

  • None

Minor changes

  • fixed Description field of DESCRIPTION file per feedback from CRAN

qtl2pleio 1.0.6

Major changes

  • None

Minor changes

  • removed Additional_repositories field from DESCRIPTION

qtl2pleio 1.0.5

Major changes

  • None

Minor changes

  • added cran-comments.md file via devtools & added it to .Rbuildignore

qtl2pleio 1.0.4

Major changes

  • None

Minor changes

qtl2pleio 1.0.3

Major changes

  • Revisions per peer review at Journal of Open Source Software

Minor changes

  • None

qtl2pleio 0.1.3

Major changes

  • Submitted paper.md to JOSS

Minor changes

  • Minor updates to recla vignette to download precalculated founder allele dosages

qtl2pleio 0.1.2.9002

Major changes

  • changed default behavior of plot_pvl to not indicate univariate peak positions.
  • fixed CITATION file to tell users to cite Biorxiv preprint (following CITATION file format of rqtl/qtl2)

Minor changes

  • Removed hex logo file from repo and deleted it from README
  • revised paper.md in preparation for JOSS submission

Bug fixes

  • Re-created profile LOD plots for vignettes and README without indicating univariate peak positions.

  • Added line type arguments to plot_pvl.

qtl2pleio 0.1.2.9001

Major changes

  • added a vignette for HTCondor & bootstrap analysis
  • updated README.Rmd and README.md (per suggestions & PR of @kbroman)

qtl2pleio 0.1.2.9000

Major changes

  • added inst/CITATION file
  • aligned ordering and names of arguments for both boot_pvl and scan_pvl
  • added examples for boot_pvl
  • added literature references to both boot_pvl and scan_pvl

Bug fixes

  • corrected typo in vignette

qtl2pleio 0.1.2

Major changes

  • added tests & examples for scan_pvl
  • changed output of scan_pvl to a tibble
  • added boot_n function for use in bootstrap analyses
  • started using covariates in calls to calc_covs. Note that we still don't use genetic data when calling calc_covs.
  • deprecated calc_loglik_bvlmm

qtl2pleio 0.1.1

Major changes

  • restructured scan_pvl to allow for more than two phenotypes. Now output is a dataframe.

qtl2pleio 0.1.0

Major changes

  • Added a NEWS.md file to track changes to the package.