If needed directory doesn't exist, create it rather than stopping
with an error (fst_genoprob() and bind_fst() and functions that
call them). Fixes Issue #17.
Fix some URLs in Readme, News, and vignette.
Have fst_genoprob() and genoprob_to_alleleprob_fst() check that
input is of class "calc_genoprob".
Fix index entry in vignette
Added tests for qtl2::calc_het() (which previously wasn't working
with qtl2fst-based probabilities). Also added tests of
qtl2::calc_entropy(), qtl2::calc_geno_freq(), and qtl2::compare_genoprob().
These tests fail without qtl2 >= 0.24, so added that in Imports in
the description file.
Removed LazyData field from DESCRIPTION file
Added calc_genoprob_fst() which combines calc_genoprob() and
fst_genoprob() to save use of RAM when calculating genotype
probabilities.
Added genoprob_to_alleleprob_fst() which combines
genoprob_to_alleleprob() and fst_genoprob() to save use of RAM
when converting genotype probabilities to allele dosages.
Added summary() and print() functions for "fst_genoprob"
objects.
Rewrote the vignette using the iron dataset, so that it's faster to build.
class(), avoiding constructions like
"blah" %in% class(object) and instead using
inherits(object, "blah").Renumbering to match R/qtl2 version
Use Markdown for function documentation, throughout
fst_genoprob(): added quiet argument, to replace verbose which
we'll ultimately remove. Also added an argument overwrite; if
FALSE (the default), refuse to overwrite the .fst files.
Renamed fst2calc_genoprob() as fst_extract(). The function with
the original name will remain for a while, but will give a warning.
Renamed fst_genoprob_restore() as `fst_restore(). The function with
the original name will remain for a while, but will give a warning.
When fst_genoprob() creates the set of .fst files with the
genotype probabilities, it also creates a .rds file with the index
object. Load this object with readRDS(). cbind.fst_genoprob() and
rbind.fst_genoprob() will write the index .fst file for the new
object.
Added overwrite and quiet arguments to cbind.fst_genoprob()
and rbind.fst_genoprob().
Added a function fst_path() for viewing the path to the files behind
an "fst_genoprob" database.
Added a function fst_files() for viewing the set of files behind an
"fst_genoprob" database.
Added a function replace_path() for replacing the file path within a
"fst_genoprob" object.