sdm_thresh: SDM Leaflet map with different thresholds

In silasprincipe/sdmvis: Interactive tools for visualizing SDM/ENM results

Description

Create a Leaflet map with the results of an SDM and draw how different thresholds will result. This map can be explored interactively in the viewer, so its possible to have a better comprehension of the outcomes of your SDM.

Usage

sdm_thresh(
  sdm,
  thresh,
  tname = NULL,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE,
  thresh.color = NULL
)

## S4 method for signature 'Raster'
sdm_thresh(
  sdm,
  thresh,
  tname = NULL,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE,
  thresh.color = NULL
)

## S4 method for signature 'data.frame'
sdm_thresh(
  sdm,
  thresh,
  tname = NULL,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE,
  thresh.color = NULL
)

Arguments

sdm	The SDM/ENM result. Should be in the Raster* format.
thresh	A vector containing the thresholds to be applied (numeric values).
tname	An optional character vector containing the names of the thresholds to be used in the legend. If not supplied, numerals will be used instead.
pts	A data frame containing the presence or presence/absence points (optional). The first column should be longitude (x) and the sencond latitude (y). In the case of presence/absence data, an additional collumn should be provided, coded as 0 (absence) and 1 (presence).
pal	Character string indicating the name of the continuous mode palette (see gen_pal). If not supplied, the default will be used.
crs	Enables to change the default projection used in the Leaflet package. For now, not functional.
cluster	Should the points be clustered (i.e., aggregated)? Only valid if 'pts' is supplied. Default is FALSE.
simplify	Should the polygons be simplified? If TRUE, the output became lighter.
thresh.color	Vector of color(s) to be used for the threshold(s) polygon(s)

Value

A Leaflet map.

Functions

• sdm_thresh,Raster-method: Method for Raster*

• sdm_thresh,data.frame-method: Method for data frames

Examples

library(sdmvis)
# Load data
data("original_sdm")
data("pa_data")

# Plot
sdm_thresh(sdm = original_sdm[[1]],
           thresh = -2,
           tname = "TSS",
           pts = pa_data)

silasprincipe/sdmvis documentation built on Dec. 23, 2021, 2:22 a.m.