ConDivSim | R Documentation |

Simulate expectations (under a null model) of mean pairwise distance for a set of communities with different species richness.

ConDivSim(object, type = "traits", n.sim = 100, plot = TRUE, disp99 = FALSE)

`object` |
a |

`type` |
character string giving the type of distance matrix on
which the mean pairwise distance is based. Either "trait" or "phy"
to a phylogenetic or trait-based distance matrix, or an actual
matrix to use (e.g., one from |

`n.sim` |
The number of permutations of the presence vector used to make the estimations. |

`plot` |
TRUE or FALSE to make the plot of the expected average mean pairwise distance, and the 5-95% confidence interval. |

`disp99` |
Display the 99% interval? |

If `plot == TRUE`

, then a surface is drawn giving the
null distribution. Lighter shades of gray give larger intervals
with categories: 0.005-0.995 = 99%, 0.025-0.975 = 95%, 0.05-0.95
= 90%, 0.25-0.75 = 50%.

`matrix`

with quantiles of mean pairwise distances for
all quantiles of of mean pairwise distance, with one row for the
range of species richnesses in the data (see column SpRich).

No serious checking of user-provided matrices is performed; this is both useful and dangerous!

Steve Walker, wrappers by Will Pearse

`sim.phy`

`scape`

data(laja) data <- comparative.comm(invert.tree, river.sites, invert.traits) #Must have all species present in at least one community! #...and must be presence-absence data data <- data[,colSums(data$comm) > 0] data$comm[data$comm>1] <- 1 sims <- ConDivSim(data) #...without traits... sims.phy <- ConDivSim(data, type="phy")

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