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Check the residency patches from one tag during one tide

Source: R/fun_check_res_patch.R
atl_check_res_patch.Rd

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

Usage

atl_check_res_patch(
  data,
  tide_data,
  tide,
  offset = 0,
  buffer_res_patches,
  buffer_bm = 250,
  buffer_overview = 10000,
  point_size = 1,
  point_alpha = 0.5,
  path_linewidth = 0.5,
  path_alpha = 0.2,
  patch_label_size = 4,
  patch_label_padding = 1,
  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,
  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

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.

buffer_res_patches

A numeric value (in meters) specifying the buffer around the polygon of each residency patch, which should be half of lim_spat_indep of the residency patch calculation. If not the function can create MULTIPOLGONS for single residency patches. That will give a warning message, but works if desired.

buffer_bm

Map buffer size (default: 250).

buffer_overview

Overview map buffer size (default: 10000).

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).

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)

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