FishDiveR (version 1.1.0)

plot_cluster_TDR: Plot the time-series depth records of the selected tag. Colour days by cluster

Description

plot_cluster_TDR plots the time-series depth record of the selected archival tag. Each day of data is coloured by the assigned cluster, this helps to visualise changes in vertical movement behaviour over time.

Usage

plot_cluster_TDR(
  tag_ID,
  data_folder = NULL,
  kmeans_result,
  every_nth = 10,
  every_s = 0,
  X_lim = NULL,
  Y_lim = c(0, 250, 50),
  date_breaks = "14 day",
  legend = TRUE,
  plot_size = c(12, 6),
  dpi = 300,
  output = FALSE,
  output_folder = NULL,
  verbose = FALSE
)

Value

Returns the cluster TDR plot. Additionally prints to file the TDR plot. Additionally outputs a facet plot of all tag_IDs.

Arguments

tag_ID

Unique tag identification number in a vector of characters. E.g. "123456".

data_folder

Parent folder path with separate folders for each tag data. E.g. "C:/Tag data". Defaults to 'data_dir'

kmeans_result

An object of class 'kmeans' containing the k-means clustering data. Output of 'k_clustering()' function.

every_nth

Numerical. Optional down-sampling of data points to plot. Defaults to 10, plotting every 10th record.

every_s

Numerical. Alternative to every_nth. Optional down-sampling of data points to plot by number of seconds, as opposed to records. E.g. plots every 60th second, rather than 10th row of data. Must be a multiple of the sampling frequency. Overrides every_nth if != 0.

X_lim

Optional. Vector with two dates delimiting the time-depth record to plot. E.g. c("2000-01-01", "2000-11-23")

Y_lim

Character vector with minimum depth, maximum depth, and sequence for ticks on Y-axis. Must be numeric, positive and 3 elements long. E.g. c(0,1500,100).

date_breaks

X-axis ggplot2 date breaks. E.g, "24 hour, "3 day", "2 week".

legend

TRUE or FALSE. Whether or not to plot the figure legend. Defaults to TRUE.

plot_size

ggSave height and width for saving the output plot. Must be numeric, positive and 2 elements long. Default to 'c(12,6)'

dpi

Numerical. DPI to use for 'ggsave()' output. E.g, 600

output

Logical. If TRUE, output is saved to output_folder. Defaults to FALSE.

output_folder

Output folder path. If output = TRUE, output_folder must be provided. Defaults to NULL.

verbose

Logical. If TRUE, progress messages are shown. Defaults to FALSE.

Examples

# Set file path
filepath <- system.file("extdata", package = "FishDiveR")

# Load kmeans_result
kmeans_result <- readRDS(file.path(filepath, "data/5_k-means/kmeans_result.rds"))

# Run plot_clusters function
plot_cluster_TDR(
  tag_ID = "data",
  data_folder = filepath,
  kmeans_result = kmeans_result,
  every_nth = 10,
  every_s = 0,
  X_lim = NULL,
  Y_lim = c(0, 300, 50),
  date_breaks = "1 day",
  legend = TRUE,
  plot_size = c(12, 6),
  dpi = 100,
  output = TRUE,
  output_folder = tempdir(),
  verbose = TRUE
)