Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

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Documentation for package ‘iCAMP’ version 1.5.12

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iCAMP-package Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis
bmntd beta mean nearest taxon distance (betaMNTD)
bmntd.big beta mean nearest taxon distance (betaMNTD) from big data
bmpd Beta mean pairwise distance (betaMPD)
bNRI.bin.big Calculate beta net relatedness index (betaNRI) for each phylogenetic bin
bNRI.bin.cm Calculate beta net relatedness index (betaNRI) for each phylogenetic bin under multiple metacommunities
bNRI.cm Calculate beta net relatedness index with parallel computing under multiple metacommunities
bNRIn.p Calculate beta net relatedness index with parallel computing
bNTI.big Beta nearest taxon index (betaNTI) from big data
bNTI.big.cm Beta nearest taxon index (betaNTI) from big data and under multiple metacommunities
bNTI.bin.big Calculate beta nearest taxon index (betaNTI) for each phylogenetic bin
bNTI.bin.cm Calculate beta nearest taxon index (betaNTI) for each phylogenetic bin under multiple metacommunities
bNTI.cm Calculate beta nearest taxon index (betaNTI) with parallel computing under multiple metacommunities
bNTIn.p Calculate beta nearest taxon index (betaNTI) with parallel computing
change.sigindex Change significance index option in iCAMP analysis
cohend Cohen's d effect size
dist.3col Transform distance matrix to 3-column matrix
dist.bin.3col Convert a list of dist (or matrixes) to a matrix
dniche Calculate niche difference between species
example.data A simple example dataset for test
iCAMP Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis
icamp.big Infer community assembly mechanism by phylogenetic-bin-based null model analysis
icamp.bins Summarize iCAMP result in each bin
icamp.boot Bootstrapping analysis of icamp results
icamp.cate Summarize iCAMP result for different categories of taxa
icamp.cm Infer community assembly mechanism by phylogenetic-bin-based null model analysis under multiple metacommunities
icamp.cm2 Phylogenetic-bin-based null model analysis under different metacommunity settings for phylogenetic and taxonomic null models
icamp.out Example output of function icamp.big
match.2col Check the consistency of the first two columns of different matrixes
match.name Check and ensure the consistency of IDs in different objects.
maxbigm Find maximum value in a big matrix
midpoint.root.big Midpoint root a large phylogeny
mntdn Mean nearest taxon distance (MNTD)
mpdn Mean pairwise distance (MPD)
NRI.cm Calculate net relatedness index (NRI) under multiple metacommunities
NRI.p Calculate net relatedness index (NRI) by parallel computing.
NTI.cm Calculate nearest taxon index (NTI) under multiple metacommunities
NTI.p Calculate nearest taxon index (NTI) with parallel computing
null.norm Normality test for null values
pdist.big Pairwise phylogenetic distance matrix from big tree
pdist.p Pairwise phylogenetic distance matrix from small tree
ps.bin Test within-bin phylogenetic signal
qp.bin.js Calculate relative importance of community assembly processes
qpen Quantifying assembly processes based on entire-community null model analysis
qpen.cm Quantifying assembly processes based on entire-community null model analysis under multiple metacommunities
qpen.test Summary and comparison of QPEN results based on bootstrapping
RC.bin.bigc Calculate modified Roup-Crick index based on Bray-Curtis similarity for each phylogenetic bin
RC.bin.cm Calculate modified Roup-Crick index based on Bray-Curtis similarity for each phylogenetic bin under multiple metacommunities
RC.cm Modified Raup-Crick index based on Bray-Curtis similarity under multiple metacommunities
RC.pc Modified Raup-Crick index based on Bray-Curtis similarity
snm Estimation of neutral taxa percentae and dispersal rate
snm.boot Estimation of neutral taxa percentae and dispersal rate
snm.comm Estimation of neutral taxa percentae and dispersal rate
taxa.binphy.big Phylogenetic binning based on phylogenetic tree
tree.droot Distance from root to tip(s) and node(s) on phylogenetic tree
tree.path List nodes and edge lengthes from root to each tip and/or node