wkrig_gd()
for improved kriging performance.krig_gd()
: This legacy function now gives a
deprecation warning and requires manual installation of the automap
package.Patch to fix L
argument defaults and improve
documentation.
The wingen default for all functions is now
L = "nvariants"
, which sets L
to the number of
variants in the VCF when calculating pi. This was already the default in
the original window_gd()
function, but
circle_gd()
and resist_gd()
had
L = NULL
as the default, which returns the sum over SNPs of
nucleotide diversity. We have also improved documentation for
L
.
Minor changes for CRAN
ggplot()
in examples and preview_gd()
plot_gd()
/plot_count()
to ggplot plotting with
ggplot_gd()
/ggplot_count()
in the README,
vignette, andpreview_gd()
functionspar()
plot_gd()
and plot_count()
can still be
used...
There was a bug that resulted in arguments not being passed
to*_general()
/*_gd()
functions; this has been
fixed for *_general()
and deprecated for *gd()
(see below)
...
for
window_gd()
/circle_gd()
/resist_gd()
and addition of sig
argument...
has been deprecated for these functions
because it wasn’t actually passing the ...
arguments to
anywhere in the first place, so this should hopefully not affect any
users...
is
sig
which is used to set the alpha threshold when
stat = "hwe"
. We have addressed this issue by adding
sig
as an argument to all of the functions.parallel
and ncores
argumentsparallelization must now be set up outside of functions, as described in the vignette
The sp package is no longer imported by wingen
The grd
argument in krig_gd()
now only
accepts SpatRaster and Raster objects
parallel
and ncores
argumentsThe parallel
and ncores
arguments have been
deprecated for all functions.
Instead, future::plan()
should be used to setup
parallelization (see the package vignette for more details).
circle_gd()
/circle_general()
and
resist_gd()
/resist_general()
( functionspreview_gd()
takes a new argument (method
)
to specify which method to generate a preview of ("window"
,
"circle"
, or "resist"
)maxdist
for
circle_gd()
/resist_gd()
stat
)ggplot_gd()
and
ggplot_count()
plot_gd()
will now generate plots for all layers except
the sample count layer and vise versa for plot_count()
window_gd()
is now called
gen
instead of vcf
. The argument is otherwise
the same (i.e., takes the same input), however the name was generalized
such that future versions could potentially take different types of
genetic data without confusion.mask_gd()
is now called
y
instead of mask
to avoid conflation with the
function mask()
mask_gd()
will longer provide the option to resample
rasters, rasters must be transformed before the function is usedInitial release of the wingen R package