Skip to contents

Plot the time-series depth dataset

Source: R/1_import_tag_data.R
plot_TDR.Rd

This function plots the time-series depth data from the imported tag.

Usage

plot_TDR(
  rds_file,
  data_folder = NULL,
  every_nth = 20,
  every_s = 0,
  plot_size = c(12, 6),
  X_lim = NULL,
  Y_lim = c(0, 1500, 100),
  date_breaks = "14 day",
  dpi = 300,
  output = FALSE,
  output_folder = NULL,
  verbose = FALSE,
  minmax_bins = 0,
  colour_temp = FALSE
)

Arguments

rds_file

Character vector file path of rds file. E.g. ("E:/data/archive_days.rds")

data_folder

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

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.

plot_size

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

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".

dpi

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

output

Logical. If TRUE, a plot file is saved to output_folder. Defaults to FALSE.

output_folder

Output folder path used when output = TRUE. Defaults to NULL.

verbose

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

minmax_bins

Numerical. Alternative to every_nth and every_s for fast plotting of large archives. Splits the record into this many equal time bins and plots only the shallowest and deepest record in each, so dive extremes are kept. E.g. 2000. Overrides every_nth and every_s if != 0. Defaults to 0.

colour_temp

Logical. If TRUE, the depth record is coloured by temperature, from blue (cold) to red (warm). Needs a 'temp' column, i.e. the tag imported with temp_col in import_tag_data(). Defaults to FALSE.

Value

A data frame of plot data. The ggplot object is attached as the attribute 'TDR_plot'.

Examples

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

# Run plot_TDR function
TDR_plot <- plot_TDR(
  rds_file = "data/archive_days.rds",
  data_folder = filepath,
  every_nth = 10,
  every_s = 0,
  plot_size = c(12, 6),
  X_lim = NULL,
  Y_lim = c(0, 300, 50),
  date_breaks = "24 hour",
  dpi = 100,
  output = TRUE,
  output_folder = tempdir(),
  verbose = TRUE
)
#> Data sampling interval is 60 seconds
#> Plotting every 10 records 
#> Maximum depth is 256.6 meters
#> Output file:/tmp/RtmpTKWEE7/tag_archive.png