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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.