Changes in version 1.4.4 (2026-04-25) Major changes - None. Minor changes - Resolved Rcpp Rf_error() issue by adding Rcpp::stop() calls. Changes in version 1.4.3.9000 Major changes - None Minor changes - Started using Github Actions for continuous integration testing. Changes in version 1.4.3 (2020-12-02) Major changes - None Minor changes - Updated RcppExports.cpp and deleted C++ test files that aren't used. Changes in version 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 Changes in version 1.4.1 (2020-10-29) Major changes - None Minor changes - Added vignette to .Rbuildignore to ease CRAN submission. Changes in version 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. Changes in version 1.3.0 (2020-06-30) 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. Changes in version 1.2.4 Major changes - None Minor changes - Updated calc_lrt_tib function to accommodate d-dimensional, d-variate scans Changes in version 1.2.3 (2019-11-05) Major changes - None Minor changes - I shortened title per CRAN recommendation - I added \value tags to document functions' outputs Changes in version 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. Changes in version 1.2.1 Major changes - none Minor changes - removed examples' and vignettes' dependencies on qtl2 R package. Changes in version 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. Changes in version 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 Changes in version 1.0.7 Major changes - None Minor changes - fixed Description field of DESCRIPTION file per feedback from CRAN Changes in version 1.0.6 Major changes - None Minor changes - removed Additional_repositories field from DESCRIPTION Changes in version 1.0.5 Major changes - None Minor changes - added cran-comments.md file via devtools & added it to .Rbuildignore Changes in version 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. Changes in version 1.0.3 Major changes - Revisions per peer review at Journal of Open Source Software Minor changes - None Changes in version 0.1.3 Major changes - Submitted paper.md to JOSS Minor changes - Minor updates to recla vignette to download precalculated founder allele dosages Changes in version 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. Changes in version 0.1.2.9001 Major changes - added a vignette for HTCondor & bootstrap analysis - updated README.Rmd and README.md (per suggestions & PR of @kbroman) Changes in version 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 Changes in version 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 Changes in version 0.1.1 Major changes - restructured scan_pvl to allow for more than two phenotypes. Now output is a dataframe. Changes in version 0.1.0 Major changes - Added a NEWS.md file to track changes to the package.