ecos_plot_pie: Produces ecological pie chart representations of...

In kkdey/ecostructure: Visualizing Structure in ecological site-species abundance data

Description

Make a pie chart representation of the membership probabilities omega output from the ecos_fit model.

Usage

ecos_plot_pie(
  omega = NULL,
  coords = NULL,
  bgmap_path = NULL,
  adjust = FALSE,
  thresh = 0.7,
  long_lim = c(-180, 180),
  lat_lim = c(-60, 90),
  coastline_lwd = 10,
  intensity = 1,
  radius = 0.5,
  color = c("dodgerblue2", "#E31A1C", "green4", "#6A3D9A", "#FF7F00", "black", "gold1",
    "skyblue2", "#FB9A99", "palegreen2", "#CAB2D6", "#FDBF6F", "gray70", "khaki2",
    "maroon", "orchid1", "deeppink1", "blue1", "steelblue4", "darkturquoise", "green1",
    "yellow4", "yellow3", "darkorange4", "brown", "red", "cornflowerblue", "cyan",
    "brown4", "burlywood", "darkgoldenrod1", "azure4", "green", "deepskyblue", "yellow",
    "azure1"),
  pie_control = list(),
  image_width = 1000,
  image_height = 800,
  path = "geostructure_plot.tiff"
)

Arguments

omega	Matrix of Cluster membership probabilities of each sample obtained from ecos_fit(). The row sums sum to 1 for each sample.
coords	a matrix of latitude and longitude entries for each site (row) of the omega matrix.This matrix has as many rows as the omega matrix and two columns for the latitude and longitude.
bgmap_path	The path to the shapefile to be used for plotting the map data. One can choose a shapefile of their own preference of resolution. If missing, we use a default background map - which is a coarse one.
adjust	A Boolean, indicating whether to adjust for the richness cluster. Defaults to TRUE.
thresh	a numeric value between 0 and 1 indicating the level at which to threshold the richness cluster. Sites represented by member- ship probability above this threshold of the richness cluster are removed.
long_lim	The limits for the longitude in the map plot. The default is c(-180,180) and removes Antarctica from the map.
lat_lim	The limits for the latitude in the map plot. The default is c(-60,90) and removes Antarctica from the map.
coastline_lwd	The line width for the coastline plotted in the map. Defaults to 10.
intensity	The intensity of the colors for the pie chart representation. Lies between 0 and 1. Defaults to 1.
radius	The radius of the pie charts. Defaults to 0.5
color	the vector of colors - of same size or more than the number of clusters. If missing, we use a default set of colors- chosen so that they are distinct from one another.
pie_control	The list of control parameters to be passed into the add.pie function of the package maptools.
image_width	The width of the image output. Defaults to 1000.
image_height	The height of the image output. Defaults to 800.
path	The path where the output image is saved.

Value

Returns a pie chart representation of the memberships obtained from ecos_fit on a global species presence-absence/counts data

Examples

 data("australia_birds")
 data("australia_model")
 ecos_plot_pie(omega = australia_model$omega,
                     coords = australia_birds$latlong, 
                     long_lim = c(110,160),
                     lat_lim = c(-50,-10),
                     color= c("orange", "red", "yellow", "deepskyblue", 
                              "chartreuse", "blue"))

kkdey/ecostructure documentation built on Jan. 26, 2021, 4:10 p.m.