"plot"(x, type = "hist", ...)The "hist" plot type is common to all EcoSimR modules. The blue histogram represents the NRep values of the metric for the simulated assemblages. The red vertical line represents the metric value for the real assemblage. The two pairs of vertical dashed black lines represent the one-tailed (long dash) and two-tailed (short dash) 95
The "cooc" plot type illustrates the binary presence-absence data (observed = red, simulated = blue). Each row in the grid is a species, each column is a site, and the entries represent the presence (color-filled) or absence (empty) of a species in a site. The rows and columns are illustrated with the same ordering as the original data matrix.
The "burn_in" plot type illustrates the trace values of the metric generated for sim9 during the burn-in period. The x axis is the replicate number and the y axis is the value of the metric. The metric for the original data matrix is illustrated as a horizontal red line. Consecutive simulated metric values are illustrated with a blue line, and the gray line is a simple loess fit to the simulated values. If the burn_in period is sufficiently long, the trace should be stable, indicating that a stationary distribution has probably been reached.