Resolved Rcpp Rf_error() issue by adding Rcpp::stop() calls.
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 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.