sdm_highlight: SDM Leaflet map highlighting extreme values

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

Description

Create a Leaflet map highlighting extreme values in an SDM output. This can either be minimum, maximum or both values set as a quantile.

Usage

sdm_highlight(
  sdm,
  quantile,
  both.sides = FALSE,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE
)

## S4 method for signature 'Raster'
sdm_highlight(
  sdm,
  quantile,
  both.sides = FALSE,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE
)

## S4 method for signature 'data.frame'
sdm_highlight(
  sdm,
  quantile,
  both.sides = FALSE,
  pts = NULL,
  pal = NULL,
  crs = "standard",
  cluster = FALSE,
  simplify = TRUE
)

Arguments

sdm	The SDM/ENM result. Should be a data.frame (XYZ columns) or in the Raster* format.
quantile	A single numeric value between 0 and 1 indicating which quantile to use (will be the same for both sides, if 'both.sides' set to 'TRUE'). For example, if you want the 25 percent higher values, you can set the quantile to 0.75. If you want both higher and lower 25 percent, just put 0.75, and set 'both.sides = TRUE'. Note: setting quantile 1 makes no sense, as it will be 100 percent. The same for setting it 0.5 and 'both.sides = TRUE'.
both.sides	If set to TRUE, than both the higher and lower values will be ploted.
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.

Value

A Leaflet map.

Functions

• sdm_highlight,Raster-method: Method for Raster*

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

Examples

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

# Plot
sdm_highlight(sdm = original_sdm[[1]],
                quantile = .75,
                pts = pa_data,
                both.sides = TRUE)

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