map: map

In ianjonsen/foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement

map

Description

map aniMotum-estimated locations and behavioural indices with coastline and projection options

Usage

map(
  x,
  y = NULL,
  what = c("fitted", "predicted", "rerouted"),
  aes = aes_lst(),
  by.id = TRUE,
  by.date = FALSE,
  crs = NULL,
  ext.rng = c(0.05, 0.05),
  buffer = 10000,
  map_type = "default",
  normalise = TRUE,
  group = FALSE,
  silent = FALSE,
  ...
)

Arguments

x	a aniMotum ssm fit object with class ssm_df or (old) fG_ssm
y	optionally, a aniMotum mpm fit object with class mpm_df or (old) fG_mpm
what	specify which location estimates to map: fitted, predicted or rerouted
aes	a list of map controls and aesthetics (shape, size, col, fill, alpha) for each map feature (estimated locations, confidence ellipses, track lines, observed locations, land masses, water bodies). Constructed by aes_lst() and can be modified for custom maps (see examples)
by.id	when mapping multiple tracks, should locations be coloured by id (logical; default = TRUE if nrow(x) > 1 else FALSE; ignored if behavioural index provided)
by.date	when mapping single tracks, should locations be coloured by date (logical; default = FALSE; ignored if behavioural index provided)
crs	proj4string for re-projecting locations, if NULL the default projection (Mercator) for the fitting the SSM will be used
ext.rng	proportion (can exceed 1) to extend the plot range in x and y dimensions
buffer	distance (in km) to buffer locations for subsetting land polygons (default = 10000). If map extents are expanded by many factors then the buffer distance may need to be increased, otherwise this should not be used. Ignored if map_type != "default".
map_type	background map type ("default" uses rnaturalearth::ne_countries to add land polygons). If the rnaturalearthdata package is installed then high-resolution land polygons will be used. If the ggspatial and rosm packages are installed then any tile map type returned by rosm::osm.types can be used for a potentially more detailed coastline at fine spatial scales, given appropriate zoom settings (see ggspatial::annotation_map_tile for details).
normalise	logical; if output includes a move persistence estimate, should g (the move persistence index) be normalised to have minimum = 0 and maximum = 1 (default = TRUE).
group	logical; should g be normalised among individuals as a group, a 'relative g', or separately to highlight regions of lowest and highest move persistence along a track (default = FALSE).
silent	logical; generate maps silently (default = FALSE).
...	additional arguments passed to ggspatial::annotation_map_tile

Value

a map as a ggplot2 object

Examples

# create an ssm fit object

fit <- fit_ssm(ellie, model = "rw", time.step = 24, control = ssm_control(verbose = 0))

# render default map

map(fit, what = "p")

ianjonsen/foieGras documentation built on Jan. 17, 2025, 11:15 p.m.