simulateHubbell {miaSim} | R Documentation |
Neutral species abundances simulation according to the Hubbell model.
simulateHubbell( n.species, M, I = 1000, d = 10, m = 0.02, tskip = 0, tend, norm = FALSE )
n.species |
Integer: the amount of different species initially in the local community |
M |
Integer: amount of different species in the metacommunity,including those of the local community |
I |
Integer: fixed amount of individuals in the
local community (default: |
d |
Integer: fixed amount of deaths of local community
individuals in each generation (default: |
m |
Numeric: immigration rate: the probability that a
death in the local community is replaced by a migrant of the metacommunity
rather than by the birth of a local community member
(default: |
tskip |
Integer: number of generations that should
not be included in the outputted species abundance matrix.
(default: |
tend |
Integer: number of simulations to be simulated |
norm |
Logical: whether the time series should
be returned with the abundances as proportions ( |
simulateHubbell
returns a SummarizedExperiment
class object containing matrix with species abundance as rows and
time points as columns
Rosindell, James et al. "The unified neutral theory of biodiversity and biogeography at age ten." Trends in ecology & evolution vol. 26,7 (2011).
colData <- DataFrame(sampleID = c(seq_len(100)), time = as.Date(100, origin = "2000-01-01")) rowData <- data.frame(Kingdom = "Animalia", Phylum = rep(c("Platyhelminthes", "Mollusca"), c(50, 50)), Class = rep(c("Turbellaria", "Polyplacophora"), each = 50), ASV1 = paste0("D", seq_len(100)), ASV2 = paste0("E", seq_len(100)), ASV3 = paste0("F", seq_len(100)), ASV4 = paste0("G", seq_len(100)), ASV5 = paste0("H", seq_len(100)), ASV6 = paste0("J", seq_len(100)), ASV7 = paste0("K", seq_len(100)), row.names = rownames(paste0("species", seq_len(10))), stringsAsFactors = FALSE) rowData <- t(rowData) ExampleHubbell <- simulateHubbell(n.species = 8, M = 10, I = 1000, d = 50, m = 0.02, tend = 100) rowData(ExampleHubbell) <- rowData colData(ExampleHubbell) <- colData