radiator is maturing, but in order to make the package better, changes are inevitable. Experimental functions will change, argument names will change.
Below an example of recent changes that are all documented in NEWS and changelog.
DArT users:
filter_dart: is now deprecated. Please use
filter_rad.tidy_dart and tidy_silico_dart: are now
deprecated. Please use read_dart for all the 4 DArT files
recognized by radiator.Missing data: visualization and imputations
Visualizing missing data and it’s imputations requires special
attention that fall outside the scope of radiator.
Inside my package called grur, users can
visualize patterns of missingness associated with
different variables (lanes, chips, sequencers, populations, sample
sites, reads/samples, homozygosity, etc). Several
Map-independent imputations of missing genotypes are
available: Random Forests (on-the-fly-imputations or
predictive modeling), Extreme Gradient Tree Boosting,
Strawman imputations (~ max/mean/mode: the most frequently observed,
non-missing genotypes is used). Imputations can be conducted
overall samples or by
populations/strata/grouping.
radiator::genomic_converter is integrated with the
imputation function of grur.