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

## Documentation for package ‘iCAMP’ version 1.8.6

- DESCRIPTION file.

## Help Pages

iCAMP-package | Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis
big.mantel.correlog | Mantel Correlogram and stepwise Mantel test for big data
bmntd | beta mean nearest taxon distance (betaMNTD)
bmntd.big | beta mean nearest taxon distance (betaMNTD) from big data
bmpd | Beta mean pairwise distance (betaMPD)
bmpd.big | Beta mean pairwise distance (betaMPD) for big data
bNRI.big.cm | Calculate beta net relatedness index under multiple metacommunities for big data
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
metaset | Metacommunity settings
midpoint.root.big | Midpoint root a large phylogeny
mntd.big | Mean nearest taxon distance (MNTD) for big data
mntdn | Mean nearest taxon distance (MNTD)
mpd.big | Mean pairwise distance (MPD) from big data.
mpdn | Mean pairwise distance (MPD)
NRI.cm | Calculate net relatedness index (NRI) under multiple metacommunities
NRI.cm.big | Calculate net relatedness index (NRI) under multiple metacommunities for big data
NRI.p | Calculate net relatedness index (NRI) by parallel computing.
NTI.cm | Calculate nearest taxon index (NTI) under multiple metacommunities
NTI.cm.big | Calculate nearest taxon index (NTI) under multiple metacommunities for big data
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
taxa.binphy.big.cm | Phylogenetic binning based on phylogenetic tree for multi-metacommunity data
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