Check the residence patches from one tag during one tide — atl_check_res

Generates a ggplot2 showing bird residence patches per tideID, including movement paths, patch durations, and an inset overview map.

Usage

atl_check_res_patch(
  data,
  tide_data,
  tide_data_highres,
  tide,
  offset = 0,
  waterlevel_min = -150,
  waterlevel_max = 150,
  waterlevel_line = 60,
  buffer_res_patches,
  buffer_bm = 250,
  buffer_overview = 10000,
  speed_threshold = 3,
  point_size = 1,
  point_alpha = 0.5,
  path_linewidth = 0.5,
  path_alpha = 0.2,
  patch_label_size = 4,
  patch_label_padding = 1,
  patch_alpha = 0.7,
  element_text_size = 11,
  water_fill = "#D7E7FF",
  water_colour = "grey80",
  land_fill = "#faf5ef",
  land_colour = "grey80",
  mudflat_colour = "#faf5ef",
  mudflat_fill = "#faf5ef",
  mudflat_alpha = 0.6,
  roosts = FALSE,
  filename = NULL,
  png_width = 3840,
  png_height = 2160
)

Arguments

data: A data.table containing tracking data of one tag. Must include the columns: tag, x, y, time,datetime, and species and patch, as created by atl_res_patch().
tide_data: Data on the timing (in UTC) of low and high tides.
tide_data_highres: Data on the timing (in UTC) of the waterlevel in small intervals (e.g. every 10 min) as provided from Rijkwaterstaat.
tide: Tide ID to subset.
offset: The offset in minutes between the location of the tidal gauge and the tracking area. This value will be added to the timing of the water data.
waterlevel_min: Numeric in cmNAP. Minimum water level to fix the axis, if NA (default) it uses the minimum of the provided water level data. water level to the duration range (default: NA, which uses the minimum of the provided water level data).
waterlevel_max: Numeric in cmNAP. Maximum water level to fix the axis, if NA (default) it uses the minimum of the provided water level data.
waterlevel_line: Numeric in cmNAP. The water level to add as a dotted line to the plot (default: 60 cmNAP).
buffer_res_patches: A numeric value (in meters) specifying the buffer around the polygon of each residence patch. If set to half of lim_spat_indep of the residence patch calculation it reflects the distance used to determine spatial independence of patches.
buffer_bm: Map buffer size (default: 250).
buffer_overview: Overview map buffer size (default: 10000).
speed_threshold: Speed threshold in m/s for colour scale of movement speed (default: 3 m/s).
point_size: Size of plotted points (default: 1).
point_alpha: Transparency of points (default: 0.5).
path_linewidth: Line width of movement paths (default: 0.5).
path_alpha: Transparency of movement paths (default: 0.2).
patch_label_size: Font size for patch labels (default: 4).
patch_label_padding: Padding for patch labels (default: 1).
patch_alpha: Alpha for patch polygons (default: 0.7).
element_text_size: Font size for axis and legend text (default: 11).
water_fill: Water fill (default "#D7E7FF")
water_colour: Water coulour (default "grey80")
land_fill: Land fill (default "#faf5ef")
land_colour: Land colour (default "grey80")
mudflat_colour: Mudflat colour (default "#faf5ef")
mudflat_fill: Mudflat fill (default "#faf5ef")
mudflat_alpha: Mudflat alpha (default 0.6)
roosts: Logical. Whether to add the roost polygon around Griend or not (default: FALSE).
filename: Character (or NULL). If provided, the plot is saved as a .png file to this path and with this name; otherwise, the function returns the plot.
png_width: Width of saved PNG (default: 3840).
png_height: Height of saved PNG (default: 2160).

Value

A ggplot object or a saved PNG file.

Author

Johannes Krietsch

Examples

# packages
library(tools4watlas)

# load example data
data <- data_example

# load example tide pattern and waterlevel data
tidal_pattern_fp <- system.file(
  "extdata", "example-tidalPattern-west_terschelling-UTC.csv",
  package = "tools4watlas"
)
measured_water_height_fp <- system.file(
  "extdata", "example-gemeten_waterhoogte-west_terschelling-clean-UTC.csv",
  package = "tools4watlas"
)
tidal_pattern <- fread(tidal_pattern_fp, yaml = TRUE)
measured_water_height <- fread(measured_water_height_fp)

# calculate residence patches for one red knot
data <- atl_res_patch(
  data[tag == "3038"],
  max_speed = 3, lim_spat_indep = 75, lim_time_indep = 180,
  min_fixes = 3, min_duration = 120
)

# plot example
atl_check_res_patch(
  data[tag == "3038"],
  tide_data = tidal_pattern, tide_data_highres = measured_water_height,
  tide = "2023513", offset = 30,
  buffer_res_patches = 75 / 2
)