animation_expression function

Animation Expression

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.

Returns

animation for different methods and different interpolation types