animation_expression: Animation Expression
In anipaths: Animation of Multiple Trajectories with Uncertainty

animation_expression

R Documentation

Animation Expression

Description

Animation Expression

Usage

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,
  uncertainty.type,
  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 covariate 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 covariate 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.
`uncertainty.type`	State what type of uncertainty plot 1 is default for tails more than 1 is amount of predicted trajectories for each unique individual and blurs for blur plot
`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.