animate_move animates movement data provided as move class objects or a list of them. The function creates an animated GIF or video file and saves it into the output directory. animate_move can be operated in different timing modes (see paths_mode) and with different background layer types (see layer, layer_type and map_type).

animate_move(m, out_dir, conv_dir = "", paths_mode = "true_data",
  paths_na.hold = TRUE, paths_col = "auto", paths_alpha = 1,
  indi_names = NA, layer = "basemap", layer_dt = "basemap",
  layer_int = FALSE, layer_type = "", layer_stretch = "none",
  layer_col = c("sandybrown", "white", "darkgreen"), layer_nacol = "white",
  map_type = "satellite", stats_create = FALSE, static_data = NA,
  static_gg = NA, extent_factor = 1e-04, tail_elements = 10,
  tail_size = 4, img_title = "title", img_sub = "subtitle",
  img_caption = "caption", img_labs = "labs", legend_title = "",
  legend_limits = NA, legend_labels = "auto", map_elements = TRUE,
  time_bar_col = "grey", time_scale = TRUE, time_pos_x = 0.5,
  time_pos_y = 0.05, time_size = 3, scalebar_col = "white",
  scalebar_dist = "auto", north_col = "white", frames_layout = 0,
  frames_nmax = 0, frames_fps = 25, frames_nres = 1, frames_tres = 0,
  frames_width = NA, frames_height = NA, frames_pixres = 80,
  out_name = "moveVis", out_format = "gif", overwrite = FALSE,
  log_level = 1, log_logical = FALSE, ..., conv_cmd = "",
  conv_frames = 100)

Arguments

m

list or moveStack class object. Needs to contain one or several move class objects (one for each individual path to be displayed) containing point coordinates, timestamps, projection and individual ID.

out_dir

character. Output directory of the output file.

conv_dir

character. Command of or path to required image/video converter tool. Depends on, what is specified for out_format. If out_format = "gif", animate_move() works with the ImageMagick convert tool. In this case, specify command of or path to the convert tool. You can use get_libraries to find or download/install convert. If out_format is a video format (e.g. "mp4", "mov" ...), animate_move() works with either the FFmpeg ffmepg tool or the libav avconv tool. In this case, specify command of or path to the ffmpeg or avconv tool. See also get_libraries. If not specified, animate_move() trys to find libraries automatically.

paths_mode

character vector. Mode to be used for dealing with time information when displaying multiple individual paths. If set to "true_data", paths are displayed based on true coverage times, showing only time periods that are covered. Time gaps will be skipped. Each frame is linked to a specific true time. If set to "true_time", paths are displayed based on true coverage times. Time gaps will be filled with non-movement frames. This mode is only recommended, if the dataset has no time gaps. Each frame is linked to a specific, true time. If set to "simple", all movement paths are displayed individually with no regard to the true coverage times. Time gaps will be skipped. Each frame displays several times at once, since each individual path has its own time. Default is "true_data".

paths_na.hold

logical. If TRUE, last path location is being hold on frame for NA path locations. If FALSE, path disappears until next path non-NA location. Default is TRUE.

paths_col

character vector. Colours of the individual animation paths. If set to "auto", a predfined colour set will be used. If single colour, all paths will be displayed by the same colour. If more individuals then colours, the colours are repeated.

paths_alpha

numeric. Set transparency of pathes. If set to 0, path is invisible. Default is 1.

indi_names

character. Optional vector of individual names. Length has to be equal to number of individuals in m. If NA, individual names are tried to be extracted from m using idData. Default is NA.

layer

raster, list or character "basemap". Single raster object or list of raster objects to be used as (dynamically changing) basemap layer. Default is "basemap" to download a static basemap layer. Use a rasterBrick class object and set layer_type to "RGB" to compute a RGB basemap.

layer_dt

POSIXct vector or list. Single POSIXct date/time stamp or list of POSIXct date/time stamps representing the acquisition dates of the layer raster objects.

layer_int

logical. Whether to interpolate the basemap layer objects over time, if several are provided (TRUE), or to display them one after another depending on the animation time frame that is displayed (FALSE). Default is FALSE.

layer_type

charachter. Layer type. Either "RGB" (if layer is a rasterBrick class onejct), "gradient" or "discrete". Default is "RGB". Ignored, if layer = "basemap".

layer_stretch

character. Ignored, if layer_type is not "RGB". Either "none", "lin", "hist", "sqrt" or "log" for no stretch, linear, histogram, square-root or logarithmic stretch. Default is "none".

layer_col

character vector. Two or more colours to be used for displaying the background layer. If layer_type = "gradient", a colour ramp between the colous is calcualted. If layer_type = "discrete", the colours will be used per value range. Ignored, if layer_type = "RGB".

layer_nacol

character. Colour to be displayed for NA values. Default is "white".

map_type

character. Static basemap type. Chosse from "roadmap", "satellite", "hybrid", "terrain".

stats_create

logical. TRUE to create statistic plots side by side with the spatial plot. Use the arguments explained for animate_stats to adjust the plotting behaviour. Default is FALSE.

static_data

data.frame. Data (e.g. static points) to be displayed within the spatial plot of the output animation. At least, "x", "y" columns for the coordinates and "names" for the naming of the point have to be included. If "static_gg" remains unspecified, "static_data" is plottet as points to the output map, annotated with their namings. Points outside the frame extent are not displayed. See "static_gg" for further options.

static_gg

character. One or several ggplot2 functions, concatenated by "+" specifying how "static_data" should be displayed, e.g. using geom_point and geom_text for displaying points annotated with text. ggplot2 data and aes, aes_ arguments etc. need to referr to the columns specified in "static_data". As default, "static_data" is plotted as geom_point and geom_label.

extent_factor

numeric. Defines the distance between the spatial extents of the movement data set and the basemap as proportion of the axis distance. Default is 0.0001. The higher the value, the larger the basemap extent. Ignored, if layer = "basemap".

tail_elements

numeric. Number of points to be displayed as path tail of the animation paths. Default is 10.

tail_size

numeric. Size of the first tail element. Default is 4.

img_title

character. Titel to be displayed above the animated plot. If not specified, no title will be displayed.

img_sub

character. Subtitel to be displayed underneath the title. If not specified, no subtitle will be displayed.

img_caption

character. Caption to be displayed underneath the plot. If not specified, no caption will be displayed.

img_labs

character. Axis titles to be displayed at the x and y axis of the plot. If not specified, labs will be computed depending on the projection or will be "x" and "y".

legend_title

character. Title to be displayed above the basemap layer legend (if layer_type is not "RGB"). Ignored, if layer = "basemap".

legend_limits

numeric vector. Fixed minimum and maximum limit values of the legend (gradient layer type). Default is NA for data-depending minimum and maximum values. Ignored, if layer_type is "discrete" or "RGB".

legend_labels

character vectors. Label for each legend break class. If set to "auto", values are displayed. Default is "auto".

map_elements

logical. If FALSE, map elements (north arrow and scale bar) are hidden. Default is TRUE.

time_bar_col

character. Colour of the time progress bar on the top edge of the map. Default is "grey".

time_scale

logical. If FALSE, time scale is hidden. Default is TRUE.

time_pos_x

numeric between 0 and 1, defines the relative position of the time scale display in the x direction. Default is 0.5 (centered).

time_pos_y

numeric between 0 and 1, defines the relative position of the time scale display in the y direction. Default is 0.06 (top).

time_size

numeric. Defines the font size of the time scale display. Default is 3.

scalebar_col

character. Colour of the scalebar text. Default is "white".

scalebar_dist

numeric. Distance represented by the scalebar in kilometers.

north_col

character. Colour of the north arrow. Default is "white".

frames_layout

matrix. Optional layout. Define, which plots should be placed where using a matrix representing the GIF/video frame. Matrix elements can be the following plot identifiers: "map" for the spatial plot, "st_all", "st_per" for the overall and periodic stats plot or "st_allR", "st_perR", "st_allG", "st_perG", "st_allB", "st_perB" for the overall and periodic stats plots per band, when using layer_type = "RGB", and 'st_leg' for a stats legend. Alternatively, integers from 1 to 8 corresponding to the described order can be used. Plots not mentioned using frames_layout identifiers are not displayed. If set to 0, layout is generated automatically. Default is 0.

frames_nmax

numeric. Number of maximum frames. If set, the animation will be stopped, after the specified number of frames is reached. Default is 0 (displaying all frames).

frames_fps

numeric. Frames to display per second (FPS). Note that the gif format only can handle FPS out of 100, e.g. 25. In that case, frames_fps input is rounded. Default is 25.

frames_nres

numeric. Interval of which frames of all frames should be used (nth elements). Default is 1 (every frame is used). If set to 2, only every second frame is used.

frames_tres

numeric. Defines temporal output resolution in seconds, 'm' should be interpolated to (linear interpolation). If 0, temporal resolution is detected automatically. Default is 0.

frames_width

numeric. Number of pixels of frame width. Default is 600 (with stats plots 1000).

frames_height

numeric. Number of pixels of frame height. Defualt is 600.

frames_pixres

numeric. Resolution of output file in pixel in ppi. The higher the ppi, the higher frames_height and frames_width should be to avoid large fonts and overlaps. Default is 80.

out_name

character. Name of the output file. Default is "moveVis".

out_format

character. Output format, e.g. "gif", "avi", "3gp", "mov", "mpeg", "mp4". Use get_formats to get all supported file formats on your system. "gif" is recommended for short animations only (recommended max. frame number around 200 frames; GIF frames are unlimited, but compution time will be very long). Use a video format for long animations. Format "gif" requires ImageMagick, all other video formats require FFmpeg ('ffmpeg') or libav ('avconv') to be installed. For that, also see get_libraries.

overwrite

logical. If TRUE, files with equal file names to out_name will be overwritten. Default is FALSE.

log_level

numeric. Level of console output given by the function. There are three log levels. If set to 3, no messages will be displayed except erros that caused an abortion of the process. If set to 2, warnings and errors will be displayed. If set to 1, a log showing the process activity, wanrnings ans errors will be displayed.

log_logical

logical. For large processing schemes. If TRUE, the function returns TRUE when finished processing succesfully.

...

optional arguments. All arguments taken by animate_stats can be handed over to animate_move as well to create sidy-by-side spatial and statistic plot animations (see animate_stats).

conv_cmd

character. Recommended for expert use only. Passes additional command line options to the conversion command, e.g. with a convert call adding '-limit' for memory ressource handling. For details, see check the documentations of ImageMagick convert, FFmpeg ffmpeg and libav avconv.

conv_frames

numeric. Recommended for expert use only. Only used, if out_format = "gif". Number of frames to be used for creating GIF segments that will be assembled to a final GIF file. Correct number depends on system performance and total frames number. Default is 100. Ignored, if out_format is not "gif".

Value

None or logical (see log_logical). The output file is written to the ouput directory.

Details

Make sure you have run get_libraries before you use moveVis for the first time: Depending on the selected output format (out_format, animate_move either needs the convert tool of the ImageMagick software package (.gif format) or either ffmpeg from FFmpeg or avconv from libav (video formats). The command or directory to the convert tool needs to be provided with conv_dir. Please use get_libraries to search for the needed libraries and command/tool directories on your system or to automatically download and install the required software. See get_libraries and out_format and conv_dir for details.

animate_move preprocesses your move data depending on the state of the data (see paths_mode and frames_tres). animate_move is based on ggplot2.

See also

Examples

# NOT RUN { #Load move and moveVis packages library(move) library(moveVis) #Get the sample data from the moveVis package (a data.frame) data("move_data") move_data$dt <- as.POSIXct(strptime(move_data$dt, "%Y-%m-%d %H:%M:%S", tz = "UTC")) #Create moveStack object including multiple individuals from the data.frame #alternatively, use the move package to download data directly from movebank.org m <- move(move_data$lon, move_data$lat, proj=CRS("+proj=longlat +ellps=WGS84"), time = move_data$dt, animal=move_data$individual, data=move_data) #Find the command or directory to convert tool of ImageMagick conv_dir <- get_libraries() #Specify the output directory, e.g. out_dir <- paste0(getwd(),"/test") #Specify some optional appearance variables img_title <- "Movement of the white stork population at Lake Constance, Germany" img_sub <- paste0("including individuals ",paste(rownames(idData(m)), collapse=', ')) img_caption <- "Projection: Geographical, WGS84; Sources: Movebank 2013; Google Maps" #Call animate_move() with an automatic basemap from Google, maximum frames at 50 #output format "gif" animate_move(m, out_dir, conv_dir, tail_elements = 10, paths_mode = "true_data", frames_nmax = 50, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002, out_format = "gif") #Improve your animation by adding a static points layer static_data <- data.frame(x = c(8.94,8.943), y = c(47.75,47.753), names = c("Site 1","Site 2")) #Call animate_move() with "static_data" added #use another output format, e.g. "mov" animate_move(m, out_dir, conv_dir, tail_elements = 10, paths_mode = "true_data", frames_nmax = 50, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002, static_data=static_data, out_format = "mov") #Try a different paths_mode: Instead of "true_data" use "simple" #output format "mp4". Longer videos then 100-200 frames should not be GIFs animate_move(m, out_dir, conv_dir, tail_elements = 10, paths_mode = "simple", frames_nmax = 50, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002, static_data=static_data, out_format = "mp4") #Use your own basemap by adding lists of rasters and of timestamps data("basemap_data") layer = basemap_data[[1]] #this is a example MODIS NDVI dataset layer_dt = basemap_data[[2]] #this is a corresponding date/time list #Call animate_move with NDVI data as basemap #layer_type is "gradient", since NDVI values are continuous animate_move(m, out_dir, conv_dir, tail_elements = 10, layer_type = "gradient", paths_mode = "true_data", frames_nmax = 50, layer =layer, layer_dt = layer_dt, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002) #How do your moving individuals interact with their environments? #Use "stats_create" to create statistics plots animate_move(m, out_dir, conv_dir, tail_elements = 10, layer_type = "gradient", paths_mode = "true_data", frames_nmax = 50, layer =layer, layer_dt = layer_dt, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002, stats_create = TRUE) #If you just want those stats plots, use animate_stats() #Use "frames_layout" to change the layout of your animation #e.g. change the position of st_all and st_per frames_layout <- rbind(c("map","map","map","st_all","st_leg"), c("map","map","map","st_per","st_leg")) #or equalize the sizes of spatial map and stats plots frames_layout <- rbind(c("map","st_all","st_per","st_leg")) animate_move(m, out_dir, conv_dir, tail_elements = 10, layer_type = "gradient", paths_mode = "true_data", frames_nmax = 50, layer =layer, layer_dt = layer_dt, img_caption = img_caption, img_title = img_title, img_sub = img_sub, log_level = 1, extent_factor = 0.0002, stats_create = TRUE, frames_layout=frames_layout) # }