mortsplot: Plot residence events

In mort: Identifying Potential Mortalities and Expelled Tags in Aquatic Acoustic Telemetry Arrays

Plot residence events

Description

Plot residence events, with the option of plotting identified mortalities. Plotting uses ggplot2. Interactive option also uses plotly.

Usage

mortsplot(
  data,
  type,
  ID,
  station,
  res.start = "auto",
  res.end = "auto",
  morts = NULL,
  singles = TRUE,
  interactive = FALSE,
  residences = NULL,
  units = NULL,
  season.start = NULL,
  season.end = NULL,
  facet = FALSE,
  facet.axis = "x",
  facet.by = "season",
  verbose = TRUE
)

Arguments

data	a dataframe of residence events. Residence events must include tag ID, location name, start time, and end time.
type	the method used to generate the residence events. Options are "mort", "actel", "glatos", "vtrack", or "manual".
ID	a string of the name of the column in data that holds the tag or sample IDs.
station	a string of the name of the column in data that holds the station name or receiver location.
res.start	a string of the name of the column in data that holds the start date and time. Must be specified and in POSIXt or character in the format YYYY-mm-dd HH:MM:SS if type="manual".
res.end	a string of the name of the column in data that holds the end date and time. Must be specified and in POSIXt or character in the format YYYY-mm-dd HH:MM:SS if type="manual".
morts	a dataframe containing potential mortalities. The dataframe must have the same ID, station, res.start, res.end, and residences column names as data.
singles	option to adjust the end times of residence events so single detection events are visible. Adjustment is for visualization purposes only and should not obscure or impact the visualization of other residence events.
interactive	option to generate an interactive plot.
residences	an optional character string with the name of the column in data that holds the duration of the residence events. Required if generating an interactive plot or applying season.
units	units of the duration of the residence events in data. Required if applying season.
season.start	the start date/time(s) of the period of interest. If the period of interest is the same in all study years, must be a character string in format "dd-mm". Otherwise, must be in POSIXt, or a character string in format YYYY-mm-dd HH:MM:SS.
season.end	the end date/time(s) of the period of interest. If the period of interest is the same in all study years, must be a character string in format "dd-mm". Otherwise, must be in POSIXt, or a character string in format YYYY-mm-dd HH:MM:SS.
facet	option to facet by year or season. If TRUE, then season.start and season.end must be provided.
facet.axis	option to position facets along x or y axis. Options are "x" and "y". Default is "x". Note that facet.axis can only be "y" if facet.by="year".
facet.by	option to facet by "season" (as defined with season.start and season.end) or "year". Default is "season".
verbose	option to display updates and progress bar as function is run. Default is TRUE.

Value

a ggplot2 plot. Additional arguments (e.g., formatting axes, legend, aes, manual colour scales) can be added as for any ggplot2 plot. If interactive=TRUE, returns a plotly plot.

Examples

plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name")
plot

# With mortalities plotted over residences:
morts<-morts(data=events,type="mort",ID="ID",station="Station.Name",
method="any",verbose=FALSE)

plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",
morts=morts)
plot

mort documentation built on Sept. 4, 2023, 9:06 a.m.