App Specific Functions and Internals

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.

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 reference 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.

Details

app_read_csv wraps read.csv.

app_test mimics custom_report.

Interface for internal functions might change and usage is not recommended.