Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis
beta mean nearest taxon distance (betaMNTD) from big data
beta mean nearest taxon distance (betaMNTD)
Beta mean pairwise distance (betaMPD)
Calculate beta net relatedness index (betaNRI) for each phylogenetic b...
Calculate beta net relatedness index (betaNRI) for each phylogenetic b...
Calculate beta net relatedness index with parallel computing under mul...
Calculate beta net relatedness index with parallel computing
Beta nearest taxon index (betaNTI) from big data and under multiple me...
Beta nearest taxon index (betaNTI) from big data
Calculate beta nearest taxon index (betaNTI) for each phylogenetic bin
Calculate beta nearest taxon index (betaNTI) for each phylogenetic bin...
Calculate beta nearest taxon index (betaNTI) with parallel computing u...
Calculate beta nearest taxon index (betaNTI) with parallel computing
Change significance index option in iCAMP analysis
Cohen's d effect size
Transform distance matrix to 3-column matrix
Convert a list of dist (or matrixes) to a matrix
Calculate niche difference between species
Infer Community Assembly Mechanisms by Phylogenetic-bin-based null mod...
Infer community assembly mechanism by phylogenetic-bin-based null mode...
Summarize iCAMP result in each bin
Bootstrapping analysis of icamp results
Summarize iCAMP result for different categories of taxa
Infer community assembly mechanism by phylogenetic-bin-based null mode...
Phylogenetic-bin-based null model analysis under different metacommuni...
Check the consistency of the first two columns of different matrixes
Check and ensure the consistency of IDs in different objects.
Find maximum value in a big matrix
Midpoint root a large phylogeny
Mean nearest taxon distance (MNTD)
Mean pairwise distance (MPD)
Calculate net relatedness index (NRI) under multiple metacommunities
Calculate net relatedness index (NRI) by parallel computing.
Calculate nearest taxon index (NTI) under multiple metacommunities
Calculate nearest taxon index (NTI) with parallel computing
Normality test for null values
Pairwise phylogenetic distance matrix from big tree
Pairwise phylogenetic distance matrix from small tree
Test within-bin phylogenetic signal
Calculate relative importance of community assembly processes
Quantifying assembly processes based on entire-community null model an...
Quantifying assembly processes based on entire-community null model an...
Summary and comparison of QPEN results based on bootstrapping
Calculate modified Roup-Crick index based on Bray-Curtis similarity fo...
Calculate modified Roup-Crick index based on Bray-Curtis similarity fo...
Modified Raup-Crick index based on Bray-Curtis similarity under multip...
Modified Raup-Crick index based on Bray-Curtis similarity
Estimation of neutral taxa percentae and dispersal rate
Phylogenetic binning based on phylogenetic tree
Distance from root to tip(s) and node(s) on phylogenetic tree
List nodes and edge lengthes from root to each tip and/or node
To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc. Version 1.3.x mainly improved the function for 'QPEN' and added function 'icamp.cate()' to summarize 'iCAMP' results for different categories of taxa (e.g. core versus rare taxa).