Package index • tools4watlas

Load and check data

Functions to load data from SQLlite or remote SQL database

atl_get_data(): Get data from a SQLite-database

atl_summary(): Summary of localization data

atl_format_time(): Format time in easy readable interval

atl_check_data(): Check data has required columns

atl_full_tag_id(): Create full tag ID or tag ID with specific length

atl_file_path(): Get the file path for WATLAS or GIS data based on the user's name.

Filter data

Fuctions to filter data

atl_filter_covariates(): Filter data by position covariates

atl_filter_bounds(): Filter positions by an area

atl_within_polygon(): Detect position intersections with a polygon

Track characteristics

Functions to calculate speed and turning angle

atl_simple_dist(): Calculate distances between successive localizations

atl_get_speed(): Calculate instantaneous speed

atl_turning_angle(): Get the turning angle between points

Smooth or thin track

Functions to calculate speed and turning angle

atl_median_smooth(): Apply a median smooth to coordinates

atl_thin_data(): Thin tracking data by resampling or aggregation

Residency patch functions

Functions to calculate residency patches

atl_res_patch(): Construct residence patches from position data

atl_patch_dist(): Get the distance between patches

atl_res_patch_summary(): Summary of patch data

atl_check_res_patch(): Check the residency patches from one tag during one tide

Spatial functions

Transform data to sf object and get a bounding box

atl_as_sf(): Convert a data.frame or data.table to an simple feature (sf) object

atl_bbox(): Create a bounding box with specified aspect ratio and buffer

Plotting functions

Functions to plot the data

atl_create_bm(): Create a basemap with customised bounding box

atl_check_tag(): Check the data from one tag on a map

atl_check_res_patch(): Check the residency patches from one tag during one tide

atl_t_col(): Make a colour transparent

atl_spec_cols(): WATLAS species colours

atl_spec_labs(): WATLAS species labels

atl_tag_cols(): Assign colours to tag ID's

atl_tag_labs(): Create unique labels for tags by combining specified columns

Animation functions

Functions to animate the data

atl_time_steps(): Generate time steps and file names for an animation of movements

atl_progress_bar(): Display a live progress bar for PNG file generation in a directory

atl_alpha_along(): Creates different alpha values along a vector

atl_size_along(): Creates different size values along a vector

atl_ffmpeg_pattern(): Generate ffmpeg filename pattern

Add enviromental data

Functions to add tidal data and other SpatRaster data

atl_add_tidal_data(): Add tidal data to tracking data

atl_add_raster_data(): Add raster data to tracking data

Data

Example and map data provided with the package

data_example: Data from two red knots and one redshank

land: Land polygon around the Dutch Wadden Sea

mudflats: Mudflats polygons within the Dutch Wadden Sea

lakes: Lake on Griend

Deprecated

Functions that a not further developed

atl_plot_tag(): Plot track for one individual on a simple background

atl_plot_tag_osm(): Plot track for one individual on a OpenStreetMap satellite map

atl_plot_map_osm(): Plot a map downloaded with OpenStreetMap

atl_plot_rpatches(): Add residence patches to a plot

atl_plot_add_track(): Add tracks to plot from list