Create country-level summary maps of species and occurrence numbers

Source: R/summaryMaps.R

Builds an output figure that shows the number of species and the number of occurrences per country. Breaks the data into classes for visualisation. Users may filter data to their taxa of interest to produce figures of interest.

summaryMaps(
  data = NULL,
  class_n = 15,
  class_Style = "fisher",
  outPath = NULL,
  fileName = NULL,
  width = 10,
  height = 5,
  dpi = 300,
  returnPlot = FALSE,
  scale = 110,
  pointBuffer = 0.01
)

Arguments

data

A data frame or tibble. Occurrence records as input.

class_n

Numeric. The number of categories to break the data into.

class_Style

Character. The class style passed to classInt::classIntervals(). Options are chosen style: one of "fixed", "sd", "equal", "pretty", "quantile", "kmeans", "hclust", "bclust", "fisher", "jenks", "dpih", "headtails", or "maximum". Default = "fisher"

outPath

A character vector the path to the save location for the output figure.

fileName

A character vector with file name for the output figure, ending with '.pdf'.

width

Numeric. The width, in inches, of the resulting figure. Default = 10.

height

Numeric. The height, in inches, of the resulting figure. Default = 5.

dpi

Numeric. The resolution of the resulting plot. Default = 300.

returnPlot

Logical. If TRUE, return the plot to the environment. Default = FALSE.

scale

Numeric or character. Passed to rnaturalearth's ne_countries(). Scale of map to return, one of 110, 50, 10 or 'small', 'medium', 'large'. Default = 110.

pointBuffer

Numeric. Amount to buffer points, in decimal degrees. If the point is outside of a country, but within this point buffer, it will count towards that country. It's a good idea to keep this value consistent with the prior flags applied. Default = 0.01.

Value

Saves a figure to the user-specified outpath and name with a global map of bee occurrence species and count data from the input dataset.

Examples

# Read in data
data(beesFlagged)
OutPath_Figures <- tempdir()
# This simple example using the test data has very few classes due to the small amount of input 
# data.
summaryMaps(
data = beesFlagged,
width = 10, height = 10,
class_n = 4,
class_Style = "fisher",
outPath = OutPath_Figures,
fileName = paste0("CountryMaps_fisher_TEST.pdf"),
)
#> Spherical geometry (s2) switched off
#>  - Extracting country data from points...
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> Extraction complete.
#>  - Buffering naturalearth map by pointBuffer...
#> dist is assumed to be in decimal degrees (arc_degrees).
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar