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Check the data from one tag on a map

Source: R/fun_check_tag.R
atl_check_tag.Rd

This function processes tracking data for a specific tag and generates a visualization using ggplot2. It allows customization of colors, point sizes, and track styles, and supports various display options such as datetime, nbs (number of base stations / receivers), standard deviation, speed_in and gap. The function can either return the plot or save it as an png file.

Usage

atl_check_tag(
  data,
  buffer = 1000,
  asp = "16:9",
  option = "datetime",
  scale_option = "A",
  scale_direction = -1,
  scale_trans = "identity",
  scale_max = NULL,
  first_n = NULL,
  last_n = NULL,
  highlight_first = FALSE,
  highlight_last = FALSE,
  highlight_outliers = FALSE,
  point_size = 0.5,
  point_alpha = 1,
  path_linewidth = 0.5,
  path_alpha = 0.1,
  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. Must include the columns: "tag", "x", "y", "time", and "datetime".

buffer

Numeric. The buffer size in meters around the data points in the plot (default: 1000).

asp

The aspect ratio of the plot (default: "16:9").

option

Determines the color mapping variable. Options are:

  • "datetime": Datetime along the track

  • "nbs": Number of receiver (base) stations that contributed to the localization

  • "var": Error as maximal variance of varx and vary

  • "speed_in": Speed in m/s

  • "gap": Gaps coloured by time and as point size

scale_option

Character. The color scheme option from viridis (default: "A"). See https://search.r-project.org/CRAN/refmans/viridisLite/html/viridis.html for all options (A-H).

scale_direction

Numeric. Direction of the color scale (-1 reverses, default: -1).

scale_trans

Transformation of the scale. Default is "identity", (no transformation), could be e.g. "log", "log10" or "sqrt". See scale_*_trans() for all options.

scale_max

If set, determines the max value of the scale for options: nbs (numeric), var (numberic), speed_in (numeric m/s), gap (numeric in seconds). Everything above the max value will get the max color.

first_n

Numeric (or NULL). If provided, only the first n locations are shown.

last_n

Numeric (or NULL). If provided, only the last n locations are shown.

highlight_first

Logical. If TRUE, highlights the first point in the track (default: FALSE).

highlight_last

Logical. If TRUE, highlights the last point in the track (default: FALSE).

highlight_outliers

Logical. If TRUE, highlights all points that are flagged as outliers (needs preassigned column with outlier TRUE or FALSE) track (default: FALSE).

point_size

The size of the data points (default: 0.5).

point_alpha

Numeric. Transparency of the data points (default: 1).

path_linewidth

Numeric. The width of the connecting track lines (default: 0.5).

path_alpha

Transparency of the track lines (default: 0.1).

element_text_size

Adjust size of the text.

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 ggplot2 object with the specified option and adjustments. If filename is provided, the plot is saved as a .png file instead of being returned.

Author

Johannes Krietsch

Examples

# packages
library(tools4watlas)

# path to csv with filtered data
data_path <- system.file(
  "extdata", "watlas_data_filtered.csv",
  package = "tools4watlas"
)

# load data
data <- fread(data_path, yaml = TRUE)

# subset bar-tailed godwit
data <- data[species == "bar-tailed godwit"]

# plot different options
atl_check_tag(
  data,
  option = "datetime",
  highlight_first = TRUE, highlight_last = TRUE
)

atl_check_tag(data, option = "nbs")

atl_check_tag(data, option = "var")

atl_check_tag(data, option = "speed_in")

atl_check_tag(data, option = "gap")