fmap: fmap

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

fmap

Description

map aniMotum fitted or predicted locations, with or without Argos observations, optionally apply a different projection

Usage

fmap(
  x,
  y = NULL,
  what = c("fitted", "predicted", "rerouted"),
  conf = TRUE,
  obs = FALSE,
  obs.shp = 17,
  by.id = TRUE,
  by.date = TRUE,
  crs = NULL,
  ext.rng = c(0.05, 0.05),
  size = 0.25,
  col.ssm = "dodgerblue",
  col.obs = "black",
  lines = FALSE,
  landfill = grey(0.6),
  map_type = "default",
  pal = "Cividis",
  rev = FALSE,
  last_loc = NULL,
  ...
)

Arguments

x	a aniMotum ssm fit object with class ssm_df
y	optionally, a aniMotum mpm fit object with class mpm_df; default is NULL
what	specify which location estimates to map: fitted, predicted or rerouted
conf	include confidence regions around estimated location (logical; default = TRUE, unless y is an mpm fit object then conf is FALSE)
obs	include Argos observations on map (logical; default = FALSE)
obs.shp	point shape for observations (default = 17)
by.id	when mapping multiple tracks, should locations be coloured by id (logical; default = TRUE if nrow(x) > 1 else FALSE)
by.date	when mapping single tracks, should locations be coloured by date (logical; default = TRUE if nrow(x) == 1 else FALSE)
crs	proj4string for re-projecting locations, if NULL the default projection ("+proj=merc") for the fitting the SSM will be used
ext.rng	factors to extend the plot range in x and y dimensions (can exceed 1)
size	size of estimated location points (size = NA will draw no points). Optionally, a vector of length 2 with size of observed locations given by 2nd value (ignored if obs = FALSE)
col.ssm	colour of ssm-fitted or ssm-predicted locations (ignored if by.id = TRUE)
col.obs	colour of observed locations (ignored if obs = FALSE)
lines	logical indicating if lines are added to connect estimated locations (default = FALSE)
landfill	colour to use for land (default = grey(0.6))
map_type	background map type (default = NULL, which uses rnaturalearth to add landmasses); if packages ggspatial & rosm are installed then any map type returned by rosm::osm.types can be used for a more detailed map background.
pal	hcl.colors palette to use (default: "Cividis"; type hcl.pals() for options)
rev	reverse colour palette (logical)
last_loc	colour to render last location of each track (default = NULL)
...	additional arguments passed to ggspatial::annotation_map_tile

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