wingen function to do everything (preview and generate moving window maps, krige, and mask)
wingen_do_everything.Rd
wingen function to do everything (preview and generate moving window maps, krige, and mask)
Usage
wingen_do_everything(
gen,
lyr,
coords,
wdim = 3,
fact = 0,
sample_count = TRUE,
min_n = 2,
preview = FALSE,
stat = "pi",
rarify = FALSE,
kriged = FALSE,
grd = NULL,
index = 1,
agg_grd = NULL,
disagg_grd = NULL,
agg_r = NULL,
disagg_r = NULL,
masked = FALSE,
mask = NULL,
bkg = NULL,
plot_count = FALSE,
quiet = FALSE
)
Arguments
- gen
genetic data either as an object of type vcf or a path to a vcf file (note: order matters! The coordinate and genetic data should be in the same order; there are currently no checks for this)
- lyr
SpatRaster or RasterLayer to slide the window across (see Details for important information about projections). For
method = "resist"
this should also be the conductivity layer (see resist_gd)- coords
coordinates of samples as sf points, a two-column matrix, or a data.frame representing x and y coordinates (see Details for important information about projections)
- wdim
if
method = "window"
, dimensions (height x width) of window; if only one value is provided, a square window is created (defaults to 3 x 3 window)- fact
aggregation factor to apply to
lyr
(defaults to 0; note: increasing this value reduces computational time)- sample_count
whether to create plot of sample counts for each cell (defaults to TRUE)
- min_n
minimum number of samples to use in calculations (any focal cell with a window containing less than this number of samples will be assigned a value of NA)
- preview
whether to produce preview of raster layer, window and focal cell size using preview_gd (default = FALSE)
- stat
genetic diversity statistic(s) to calculate (see Details, defaults to
"pi"
). Can be a single statistic or a vector of statistics- rarify
if rarify = TRUE, rarefaction is performed (defaults to FALSE)
- kriged
whether to smooth out mapped values using kriging using krig_gd (default = FALSE)
- grd
object to create grid for kriging; can be a SpatRaster or RasterLayer. If undefined, will use
r
to create a grid.- index
integer indices of layers in raster stack to krige (defaults to 1; i.e., the first layer)
- agg_grd
factor to use for aggregation of
grd
, if provided (this will decrease the resolution of the final kriged raster; defaults to NULL)- disagg_grd
factor to use for disaggregation of
grd
, if provided (this will increase the resolution of the final kriged raster; defaults to NULL)- agg_r
factor to use for aggregation of
r
, if provided (this will decrease the number of points used in the kriging model; defaults to NULL)- disagg_r
factor to use for disaggregation, of
r
if provided (this will increase the number of points used in the kriging model; defaults to NULL)- masked
whether to mask out areas outside region of interest using mask_gd (default = FALSE)
- plot_count
if TRUE, whether to visualize sample counts using plot_count (default = FALSE)
- quiet
whether to operate quietly and suppress the output of tables and figures (defaults to FALSE)
Details
When using wingen, please cite the original citation: Bishop, A.P., Chambers, E.A., Wang, I.J. (2023). Generating continuous maps of genetic diversity using moving windows. Methods Ecol. Evol. doi: https://doi.org/10.1111/2041-210X.14090 N.B.: Be aware that this function sets many of the wingen function arguments to defaults, which my result in sub optimal results. We highly advise researchers to run each wingen function separately for best results.
See also
Other wingen functions:
krig_agg_helper()
,
krig_helper()