Plot COSEWIC IAO and EOO — cosewic

Creates a plot of COSEWIC ranges for illustration and checking. Note: If using maptiles from OpenStreetMap ("osm", the default) in a public document/website/etc., you must attribute OpenStreetMap.

Usage

cosewic_plot(
  ranges,
  which = c("eoo", "iao"),
  points = NULL,
  grid = NULL,
  map = "osm",
  iao_prop = FALSE,
  crs = NULL,
  group = "species_id",
  title = "",
  zoomin = -1,
  arrow_location = "tr",
  scale_location = "br",
  verbose = TRUE,
  species
)

Arguments

ranges: List. Output of cosewic_ranges() with spatial = TRUE.
which: Character vector. Which range types to calculate. Any combination of "eoo" and "iao", default is both.
points: Data frame. Optional raw data points to add to the plot (are not filtered, regardless if a prop_include < 1 was used in cosewic_ranges().
grid: sf data frame. Optional grid over which to summarize IAO values (useful for species with many points over a broad distribution).
map: Character or sf data frame. Underlying base map over which to plot the values.. "osm" by default to use OpenStreetMap base maps via ggspatial::annotation_map_tile(). Can be one of rosm::osm.types(), a sf polygon base map, or NULL for no base map.
iao_prop: Logical. Whether to show IAO as a proportion for easier plotting of multiple groups (allows collecting legends by the patchwork package).
crs: A coordinate reference system (see ?sf::st_transform()). Defaults to Albers Equal-Area for Canada (ESRI:102001) for area calculations. Note that it must be a projection (i.e. not simply a reference system like 4326 used for GPS) for area calculations. If NULL for plots, uses the CRS of the base map or of the IAO/EOO data.
group: Character. Name of the column containing group identification. By default this is species_id in NatureCounts data.
title: Character. Optional title to add to the map. Can be a named by group vector to supply different titles for different groups.
zoomin: Numeric. Zoom adjustment for ggspatial::annotation_map_tile(). Only applies if map defines a map tile (e.g., "osm")
arrow_location: Character. Location for the North arrow, one of 'tr', 'tl', 'br', or 'bl', for top right, top left, etc. NULL omits the arrow.
scale_location: Character. Location for the map scale, one of 'tr', 'tl', 'br', or 'bl', for top right, top left, etc. NULL omits the scale.
verbose: Logical. Show messages?
species: Deprecated. Use groups.

Value

ggplot2 map

Examples

r <- cosewic_ranges(bcch)
#> (This message is shown once per session)
#> As of naturecounts v0.5.0 `cosewic_ranges()` now uses `prop_include = 1` instead of `eoo_p = 0.95`. 
#> This defines the proportion of observations used in both IAO and EOO calculations.
#> The default is `prop_include = 1` (include all observations).
#> This message is displayed once per session.
cosewic_plot(r)
#> Zoom: 9
#> Fetching 9 missing tiles
#> 
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#> ...complete!

cosewic_plot(r, points = bcch)
#> Zoom: 9


# Only one or the other
cosewic_plot(r, which = "eoo", points = bcch)
#> Zoom: 9

cosewic_plot(r, which = "iao")
#> Zoom: 9


# Use a different CRS for the map (only applies if not using map tiles)
cosewic_plot(r, crs = 3347) # No change
#> 'crs' is only applicable when not using map tiles. Map tiles always use CRS of EPSG:3857.
#> Loading required namespace: raster
#> Zoom: 9

cosewic_plot(r, map = map_canada(), crs = 3347)


# Summarize IAO over larger grid
cosewic_plot(
  r,
  grid = grid_canada(50),
  map = map_canada(),
  title = "Black-capped chickadees"
)


# Plot multiple groups - separate plots
m <- rbind(bcch, hofi)
r <- cosewic_ranges(m)
p <- cosewic_plot(r)
p[[1]]
#> Zoom: 9

p[[2]]
#> Zoom: 6
#> Fetching 4 missing tiles
#> 
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#> ...complete!


# Plot multiple groups - Use IAO as a proportion for identical legends
p <- cosewic_plot(
  r,
  iao_prop = TRUE,
  title = c("14280" = "Black-capped chickadees", "20350" = "House Finches")
)

# Use patchwork to combine into a single figure
if(requireNamespace("patchwork", quietly = TRUE)) {
  library(patchwork)
  wrap_plots(p) +
    plot_layout(guides = "collect")
}
#> Zoom: 9
#> Zoom: 6