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 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

• Added Additional_repositories field to DESCRIPTION file per https://cran.r-project.org/submit.html in preparation for CRAN submission.
  
• Added url for Jiang and Zeng 1995 GENETICS article, per https://cran.r-project.org/submit.html.

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.