internals: App Specific Functions and Internals
In ABbiodiversity/cure4insect: Custom Reporting for Intactness and Sector Effects

internals

R Documentation

App Specific Functions and Internals

Description

These functions are needed by OpenCPU apps in the package, or needed to be exported by the package but not intended to be used by users.

Usage

app_read_csv(...)
app_test(...)

.load_species_data(species, boot=NULL, path=NULL, version=NULL,
    taxon, model_north, model_south)
.calculate_results(y, level=0.9, .c4is)
.calculate_limit(y, limit=NULL)
.report_all_by1(boot=NULL, path=NULL, version=NULL, level=0.9, cores=NULL)
.read_raster_template()
.make_raster(value, rc, rt)
.rasterize_multi(y, type=c("richness", "intactness"), rt)
.verbose()
.get_cores(cores=NULL)
.check(x, ref)
.combine_veg_soil(w, veg, soil)
.validate_id(id, type=c("km", "qs"))
.verbose()
.select_id(mregion="both", nr=NULL, nsr=NULL, luf=NULL)
p_bird(D, area=c("ha", "km"), pair_adj=2)
.truncate(x, trunc=NULL)

Arguments

`species, boot, path, version`	arguments passed to `load_species_data` and other functions.
`taxon, model_north, model_south`	taxonomic group required for the correct path, and logical values indicating north and south model results.
`y, level`	arguments passed to `calculate_results` and other functions.
`.c4is`	the subset environment `as.list(.c4is)`.
`cores`	desired number of cores to use.
`value, rc, rt`	call `value`, `rc` is data frame with `Row` and `Col` indices for `value`, `rt` is raster template from `.read_raster_template`.
`id`	spatial IDs.
`type`	type of multi-species map (richness or intactness) or spatial ID (km or QS).
`limit`	abundance threshold for multi-species intactness reporting.
`x`	input object.
`ref`	checking the validity of land cover classes in `x` against the `ref`erence list of possible values.
`w, veg, soil`	calculates a weighted average of `veg` and `soil` based models based on weights for the vegetation models (`w`).
`mregion, nr, nsr, luf`	regions.
`D, area, pair_adj`	density, scale, and pair adjustment to turn bird densities into probability of observing non-zero count.
`trunc`	quantile for truncating values of `x`, usually a vector or a raster object.
`...`	arguments passed to underlying functions.