Package index • comdynamite

Simulate metacommunities

The process-based model, from landscape and traits to abundances.

simulate_metacommunity(): Simulate a metacommunity
simulate_static(): Simulate a static metacommunity
simulate_logistic(): Simulate presences and absences from logistic responses
logistic_gradients(): Gradients of the seven scenarios of Peres-Neto et al. (2012)
mc_dynamics(): Metacommunity dynamics from growth rates
growth_rates(): Growth rates of each species at each site

Spatially implicit and grid landscapes, dispersal and environment.

landscape_implicit(): Spatially implicit landscape
landscape_grid(): Spatially explicit landscape on a square grid
dispersal_kernel(): Exponential dispersal kernel
env_over_time(): Environment that changes over time
torus_permutations(): Site permutations that keep the structure of a torus

Traits with phylogenetic signal and evolutionary regimes.

species_traits(): Species traits, with or without phylogenetic signal
trait_bm(): Trait evolution by Brownian motion with Pagel's lambda
traits_ou(): Traits evolving by an Ornstein-Uhlenbeck process with one or several optima
paint_regimes(): Assign selective regimes to clades

Interspecific competition, optionally structured by relatedness.

Analyses of phylogenetic community structure.

pcc_test(): Test phylogenetic community composition against the environment
phylo_eigenvectors(): Phylogenetic eigenvectors
phylo_beta_test(): Test phylogenetic beta diversity against the environment
phylo_beta(): Phylogenetic beta diversity between communities
node_test(): Test clades against the environment, node by node
biogeography_matrix(): Matrix of biogeographic events
node_contrasts(): Node contrasts of a phylogeny
plot_node_test(): Plot the results of a node test on the phylogeny
plot_node_heatmap(): Plot the semipartial correlations of a node test
phylo_vector(): Represent a phylogeny by one vector related to a predictor
trait_partition(): Partition trait or phylogenetic variation between environment and space
plot_trait_partition(): Plot the fractions of a trait partition

Community assembly without population dynamics.

assemble_community(): Assemble a local community from a regional pool by rules