plots: Plotting functions

In piLaboratory/GillesCom: Gillespie Simulation of Ecological Communities Dynamics

Description

These functions plot relevant information about a simulation

Usage

diagPlots(which = 1:4)

radOverTime(steps, col = c("gray90", "gray10", "blue4"), par.axis = list(),
  ...)

octavOverTime(steps, prop = TRUE, col = c("gray90", "gray10", "blue4"),
  par.axis = list(), ...)

Arguments

which	numerical, may be a single number or a vector: which plots should be done (see Details)
steps	number of intervals in which to cut the trajectories
col	For both radOverTime and octavOverTime, the colors are chosen by three values: [1] the color of the most ancestral rad/octav, [2] the color of the latest rad/octav and [3] a highlight color for the current rad/octav. The colors for the remaining rad/octavs to be plotted are generated with a ramp palette from col[1] to col[2].
par.axis	Additional graphical parameters for handling the axes of the plot.
...	Additional graphical parameters for the plots, such as main title, labels, font size, etc; EXCEPT for the axis.
prop	Logical. Should the octav be plotted using proportions (as opposed to absolute numbers)?

Details

The function diagPlots plots up to four different diagnostic plots (controlled by the parameter "which": 1 - Species richness over time 2 - Total individuals over time 3 - Number of species equivalents calculated from Shannon information index 4 - Kolmogorov-Smirnoff statistic between SADs at each time compared to the SAD at the last time 5 - Estimated Fisher's alpha over time (from a log-series fit) 6 - Estimated sdlog over time (from a lognormal fit)

Notice that the default invocation of this function displays only the plots 1 to 4.

The functions radOverTime and octavOverTime provide a superimposing plot with the rad and octav, respectively, at distinct points in time.

piLaboratory/GillesCom documentation built on May 25, 2019, 6:04 a.m.