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Plot Routes

Source: R/plot_routes.R
plot_routes.Rd

Plot Routes and BirdFlowRoutes objects as as lines with color indicating the passage of time. For BirdFlowRoutes the end point of each week is shown as a dot and the size of the dot corresponds to how long the birds stayed at that location.

Usage

plot_routes(
  routes,
  bf,
  facet = FALSE,
  max_stay_len = NULL,
  use_seasonal_colors = TRUE,
  pal = NULL,
  barheight = 8,
  route_linewidth = 0.85,
  dot_sizes = c(1.1, 3.5),
  coast_linewidth = 0.25,
  stay_units = "weeks",
  show_mask = TRUE,
  crs = NULL,
  static = TRUE
)

# S3 method for class 'BirdFlowRoutes'
plot(x, ...)

Arguments

routes, x

An object of class Routes or BirdFlowRoutes. Likely the the output of route(), as_BirdFlowRoutes, or Routes().

bf

A BirdFlow object. Only used if x is a Routes object, in which case it provides the CRS and

facet

If TRUE then use ggplot2::facet_wrap() to show each route out into a separate subplot.

max_stay_len

Used to scale the stay length dots. If NULL (the default) it will be set to the maximum "stay_len" value in routes. Set it manually to keep the dot scaling consistent across multiple plots.

use_seasonal_colors

If TRUE a color scale that uses blues, greens, yellows, reds, for winter, spring, summer, and fall will be used with a consistent mapping of dates to colors regardless of the range of dates plotted. If FALSE then the data will be plotted using the full color scale.

pal

The color palette to use for plotting when use_seasonal_cols is FALSE. Defaults to viridisLite::viridis(n = 5).

barheight

The height of the color gradient legend bar. Passed to ggplot2::guide_colorbar() as barheight argument. Depending on the output resolution and plot size this may need to be adjusted. Can take a number or the output from ggplot2::unit().

route_linewidth

Line width used for routes.

dot_sizes

Two numbers indicating the smallest and largest dot sizes used to represent stay length.

coast_linewidth

Line width used for coastlines.

stay_units

The unit to plot the stay length at each location. Default to weeks. Other options include sec, mins, hours, days and weeks.

show_mask

Should the BirdFlow Model's (bf) static mask be displayed.

crs

Only used when bf is missing. crs sets the Coordinate Reference system used for plotting. See terra::crs().

static

For internal use. It is set to FALSE when plot_routes() is called from animate_routes().

...

Passed to plot_routes() from plot() for Route and BirdFlowRoutes objects.

Value

A ggplot object. Use print() to display it.

Details

plot.BirdFlowRoutes() calls plot_routes().

Examples

bf <- BirdFlowModels::amewoo
n <- 10
rts <- route(bf, n, season = "prebreeding")

# Multiple routes on one plot
plot_routes(rts, bf)


# One panel per route
new_rts <- rts
new_rts$data <- new_rts$data[new_rts$data$route_id %in% 1:4, ]
plot_routes(new_rts, bf, facet = TRUE)


# Returned plot object can be edited
# Here we change the title and add an additional sf
# layer with country boundaries
library(ggplot2)
p <- plot_routes(rts, bf) +
  ggtitle(paste0(species(bf), " (with countries)")) +
  geom_sf(data = get_countries(bf), inherit.aes = FALSE, fill = NA) +
  coord_sf(expand = FALSE)
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
p

if (FALSE) { # \dontrun{
# Use alternate color palettes
plot_routes(rts, bf, use_seasonal_colors = FALSE)

plot_routes(rts, bf,
  use_seasonal_colors = FALSE,
  pal = c("red", "yellow", "blue")
)
} # }