convert_to_scan1_output to convert
multivariate, one-QTL lods to output format of qtl2::scan1,
for use in qtl2::bayes_int.scan_pvl and boot_pvl to reduce
duplicated codeparallel.cores value to
parallelly::availableCores() for compatibility with job
schedulers.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.boot_pvl, changing
nboot_per_job to nboot.scan_pvl_clean to be called in both
scan_pvl and boot_pvl. This change shouldn’t
affect most users’ experiences.calc_lrt_tib function to accommodate
d-dimensional, d-variate scansI shortened title per CRAN recommendation
I added tags to document functions’ outputs
Per CRAN submission feedback, I spelled out QTL in DESCRIPTION file and upon first use in vignettes.
Added citations with references to vignettes.
plot_pvl to not indicate
univariate peak positions.Re-created profile LOD plots for vignettes and README without indicating univariate peak positions.
Added line type arguments to plot_pvl.
boot_pvl and scan_pvlboot_pvlboot_pvl and
scan_pvlscan_pvlscan_pvl to a tibbleboot_n function for use in bootstrap
analysescalc_covs. Note
that we still don’t use genetic data when calling
calc_covs.calc_loglik_bvlmmscan_pvl to allow for more than two
phenotypes. Now output is a dataframe.NEWS.md file to track changes to the
package.