plot.osmose.config: Plot method for 'osmose.config' objects
In osmose-model/osmose: Object Oriented Simulator of Marine Ecosystems

plot.osmose.config

R Documentation

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 class 'osmose.config'
plot(x, what = "predation", ...)

## S3 method for class '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 class '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 class '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

`x`	`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)
`n`	`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.

Note

Ellipsis (...) must be used carefully, since it will pass the arguments to different generic plot functions. For instance, type = 2 of osmose.config.reproduction method will use ... to pass arguments to barplot, so some arguments like cex may match with many formal arguments (e.g. cex.axis and cex.names), so it may cause errors.