Plots of species ranges on maps of environmental variables

Source: R/ranges_emaps.R

ranges_emaps plots one or more ranges of the same species on various maps of environmental factors (e.g. climatic variables) to detect implications of using one or other type of range regarding the environmental conditions in the areas.

ranges_emaps(..., variables, add_occurrences = FALSE,
             range_colors = NULL, color_variables = NULL,
             ranges_legend = TRUE, legend_position = "bottomright",
             legend_cex = 0.7, zoom = 0.7, verbose = TRUE)

Arguments

...

one or more objects of class sp_range produced with any of the following functions: rangemap_buffer, rangemap_boundaries, rangemap_hull, rangemap_enm, and/or rangemap_tsa. Using up to three or four ranges is recommended for more precise comparisons.
variables

a RasterLayer or RasterStack object of environmental variables that will be used as the base for maps. Projection is assumed to be WGS84 (EPSG:4326). Consider that depending on the species range, using more than 9 variables creates a plot that may not fit in an A4 paper sheet. A maximum of 21 variables is allowed, if this limit is surpassed, other variables will be ignored.
add_occurrences

(logical) if TRUE, species occurrences contained in sp_range objects will be added to the figure. Default = FALSE. If the none of the objects contains occurrences, this argument will be ignored.
range_colors

vector of colors for borders of species ranges. If NULL, the default, distinct levels of gray will be used. If more than 3 sp_range objects are included, defining your own colors is recommended.
color_variables

a color palette (a vector of continuous colors generated by functions like heat.colors). If NULL, the default, rev(terrain.colors(255)) will be used.
ranges_legend

(logical) if TRUE, a legend of the plotted ranges will be added to the last panel of the plot at legend_position. Default = TRUE.
legend_position

(numeric or character) location where the legend will be placed in the plot. If numeric, vector of length = 2 indicating x and y coordinates to position the legend. See details in legend for character options of position. Default = "bottomright".
legend_cex

(numeric) size of the legend with respect to cex option in par. Default = 0.7.
zoom

(numeric) zoom factor when plotting the species range in a map (based on the largest range). Default = 1.3. Larger values will zoom in into the species range and smaller values will zoom out. A value of 0.5 will duplicate the area that the biggest range is covering.
verbose

(logical) whether or not to print messages about the process. Default = TRUE.

Value

A plot showing species ranges on top of maps of environmental variables.

Details

Position of distinct elements depend on the spatial configuration of the species range. Therefore, their position may need to be changed if such elements are needed (e.g., legend). Current character options available for position are: "bottomright", "bottomleft", "topleft", and "topright".

Examples

# example data
data("buffer_range", package = "rangemap")
data("cxhull_range", package = "rangemap")
data("cvehull_range", package = "rangemap")

vars <- raster::stack(system.file("extdata", "variables.tif",
                                  package = "rangemap"))
names(vars) <- c("bio5", "bio6", "bio13", "bio14")

# plotting
ranges_emaps(buffer_range, cxhull_range, cvehull_range, variables = vars)

#> Warning: Discarded datum WGS_1984 in Proj4 definition,
#>  but +towgs84= values preserved