animation_expression: Animation Expression

Description Usage Arguments Value

View source: R/animation_expression.R

Description

Animation Expression

Usage

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animation_expression(
  bg,
  bg.axes,
  bg.misc,
  bg.opts,
  blur.size,
  cliques,
  color_covariate_function,
  coord,
  covariate,
  covariate.factors,
  covariate.interp,
  covariate.legend.loc,
  covariate.name,
  covariate.range,
  covariate.thresh,
  covariate.ticks,
  crawl.mu.color,
  crawl.plot.type,
  cur.time,
  date.col,
  delta.t,
  dev.opts,
  dimmed,
  ID_names,
  interpolation_type,
  interval,
  legend.loc,
  main,
  method,
  n.frames,
  network,
  network.interp,
  network.ring.trans,
  network.ring.wt,
  network.segment.trans,
  network.thresh,
  network.segment.wt,
  par.opts,
  paths,
  paths.interp,
  plot.date,
  pt.alpha,
  pt.cex,
  pt.colors,
  pt.wd,
  res,
  scale,
  simulation,
  simulation.iter,
  tail.alpha,
  tail.colors,
  tail.length,
  tail.wd,
  theme_map,
  time.grid,
  Time.name,
  uncertainty.level,
  whole.path,
  xlim,
  ylim,
  ...
)

Arguments

bg

a list object for the ggmap background if background object is supplied

bg.axes

logical: should animation place axis labels when using a background image (default is TRUE). If RGoogleMaps is used to produce background, labels will be "northing" and "easting". Otherwise, the strings given to coord will be used.

bg.misc

Character string which will be executed as R code after generating the background, and before adding trajectories, etc.

bg.opts

Options passed to plot() function call that makes background in each frame. For example, this could be used to specify blue ocean and gray landcover if background is a SpatialPolygonsDataFrame and bg.opts = list(bg = "dodgerblue4", col = "gray", border = "gray").

blur.size

a integer of the size for blur points; default is 8

cliques

A list of colors for network projections

color_covariate_function

a function to generate color for coraviate interpolation

coord

A character vector of length 2 giving the names of the longitude/easting and latitude/northing columns in the paths data.frame (in that order). This is required if paths is not a SpatialPointsDataFrame.

covariate

The name of the column in paths that identifies the covariate to be mapped to a ring of color around each point.

covariate.factors

factor levels for covariate interpolation

covariate.interp

interpolation for covariate projections

covariate.legend.loc

either the location of the covariate legend, or NA if no legend is desired

covariate.name

name of covariate interpolation

covariate.range

the range of covaraite interpolation

covariate.thresh

if changed from its default value of NULL, the interpolated value of the covariate will be binarized based on this numeric value.

covariate.ticks
crawl.mu.color

color for the main predictions for crawl interpolation; default is black

crawl.plot.type

a character string of what type of the plot you wish to generate when interpolation_type = "crawl". Default is "point.tail" for points with tails; input "point" for point plot and input "blur" for blur point plot; input "blur.point" for blur point with tails

cur.time

start time of animation

date.col

default is "black"

delta.t

The gap in time between each frame in the animation. Specify one of delta.t or n.frames. If both are specified, delta.t is used.

dev.opts

Options passed to png() before creating each frame.

dimmed

Numeric vector of individuals to "dim" in the animation. Order corresponds to the order of the ID.name variable, or order of paths list.

ID_names

a list of names for each animal in the data

interpolation_type

a character string of the type of interpolation. Default is "gam" for a generalized addictive model. Input "crawl" to interpolate using crawl package

interval

Seconds per frame in animation. Default is 1/12 (or 12 frames per second).

legend.loc

passed to first argument of legend() function. Default is "topright". NA removes legend.

main

Title for each frame. SOON: support for changing titles to allow for, say, dates.

method

either "html" (default) or "mp4". The latter requires the user has installed ffmpeg (see ?animation::saveVideo()).

n.frames

The number of frames used to animate the complete time domain of the data.

network

Array of dimensions (# individuals, # individuals, n.frames) that gives a dyanmic network structure among the individuals.

network.interp

interpolated network of dimension (n.indiv, n.indiv, n.frames)

network.ring.trans

transparency of network segments (default is 1)

network.ring.wt

thickness of network rings (default is 3)

network.segment.trans
network.thresh
network.segment.wt

thickness of network segments (default is 3)

par.opts

Options passed to par() before creating each frame.

paths

A list of all paths from each animals stored in a data.frame or SpatialPointsDataFrame object.

paths.interp

a path animation object that contains all predicted and simulated paths for all animals

plot.date

Logical variable toggling date text at the time center of the animation.

pt.alpha

alpha value for the points

pt.cex

A numeric value giving the character expansion (size) of the points for each individual. Default is 1.

pt.colors

A vector of colors to be used for each individual in the animation. Default values come from Color Brewer palettes. When a network is provided, this is ignored and individuals are all colored black. If NA, no plot colors are chosen to distinguish individuals. This can be useful when making animations involving a covariate. Consider also setting legend.loc to NA in this case.

pt.wd

size of the points; default is 1

res

Resolution of images in animation. Increase this for higher quality (and larger) images.

scale
simulation

logical. Generate simulation predictions to have multiple projects for the animal paths

simulation.iter

an integer of how many paths the crawl model will generate

tail.alpha

alpha value for the tails

tail.colors

default is "gray87". Can be single color or vector of colors.

tail.length

Length of the tail trailing each individual.

tail.wd

Thickness of tail trailing behind each individual. Default is 1.

theme_map

plot theme for ggplot, default is NULL

time.grid

A vector of time interval.

Time.name

The name of the columns in paths gving the observation times. This column must be of class POSIXt, or numeric.

uncertainty.level

value in (0, 1) corresponding to level at which to draw uncertainty ellipses. NA (default) results in no ellipses.

whole.path

logical. If TRUE (default = FALSE), the complete interpolated trajectories will be plotted in the background of the animation. If whole.path = TRUE, consider also setting tail.length = 0.

xlim

Boundaries for plotting. If left undefined, the range of the data will be used.

ylim

Boundaries for plotting. If left undefined, the range of the data will be used.

...

other arguments to be passed to ani.options to animation options such as the time interval between image frames.

Value

animation for different methods and different interpolation types


anipaths documentation built on May 17, 2021, 5:07 p.m.