plot.osmose.config: Plot method for `osmose.config` objects

Description

This method takes a osmose.config object and produce useful plots.

This function implements a plot method for different osmose classes.

Usage

# S3 method for osmose.config
plot(x, what = "predation", ...)
# S3 method for osmose.config.reproduction
plot(
  x,
  type = 1,
  species = 0,
  speciesNames = NULL,
  start = NULL,
  end = NULL,
  initialYear = NULL,
  freq = 12,
  xlim = NULL,
  ylim = NULL,
  col = "black",
  axes = TRUE,
  border = NA,
  legend = TRUE,
  ...
)
# S3 method for osmose.config.species
plot(
  x,
  n = 100,
  type = 1,
  species = 0,
  speciesNames = NULL,
  addElements = c("segments", "points", "polygon", "text"),
  axes = TRUE,
  border = NA,
  xlim = NULL,
  ylim = NULL,
  legend = TRUE,
  col = "black",
  ...
)
# S3 method for osmose.config.predation
plot(
  x,
  type = 1,
  species = 0,
  speciesNames = NULL,
  addElements = c("segments", "points", "text"),
  axes = TRUE,
  border = NA,
  xlim = NULL,
  ylim = NULL,
  col = "gray70",
  legend = TRUE,
  ...
)

Arguments

osmose like object.

what

Variable name to plot. By default is what = "predation". See Details.

...

Extra arguments of the function.

type

A numeric value, indicating the type of plot to be used (type = 1, by default). See Details.

species

A numeric vector specifying the species that will be showed. If NULL (default), all the available species time series will be plotted. See Details.

speciesNames

A vector with the names for each species. If NULL (default) the names of x will be used.

start

A numeric value indicating the first element of the time indexation of the object x is specified with this parameter. By default start = NULL and the time indexation start with the first element of x.

end

A numeric value. The last element of the time indexation of the object x is specified with this parameter. By default end = NULL and the time indexation finish with the last element of x.

initialYear

A numeric value. It specifies the first element that is going to be used on the x axis for the plots.

freq

A numeric value to indicate the steps by year used in the time series. Default values, see Details.

xlim, ylim

numeric vectors of length 2, giving the x and y coordinates ranges.

col

A vector with the color names for the plots. By default col = NULL and the colors will be chosen by the function.

axes

a logical value indicating whether both axes should be drawn on the plot.

border

the color to draw the border of CI polygons, bar plots and box plots. By default, border = NA, which means that no border will be drawn.

legend

logical do you want to show a legend of species? (valid only for those plot types TS-2)

numeric value indicating the number of steps that are going to be used to plot the growth curve (n = 100 as default). The larger is n, the more resolution the curve will have.

addElements

A character vector indicating extra graphical elements that can be included.

Details

Plot types will depend on the class of x, which is defined by what. Thereby,

what = predation: Generates a plot of size range as shadows for a selected species .
what = reproduction: Generates a single plots of seasonality of reproduction whether as lines (type = 1) or bars (type = 2)
what = species: Generates a plot of growth curve following the VB parameters defined on configuration files (type = 1).

species argument follows the indexation way of java: starting in zero, as osmose-java returns species outputs.

Default value for freq will be calculated from x: $freq = 1/x$model$start$.

Extra arguments can be passed using ... and depending on the type, you can modify arguments like: cex, cex.axis, border (useful for polygon and barplots), etc.