dist.3col

Transform a distance matrix to a 3-column matrix in which the first 2 columns indicate the pairwised samples/species names.

tool

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).

Daliang Ning

iCAMP

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

dist.3col function

<dl> <dt>dist</dt>
<dd>a square matrix or distance object with column names and row names.</dd></dl>

Arguments

Author

Transform distance matrix to 3-column matrix — dist.3col

<dl>

 <dt>dist</dt>
<dd>a square matrix or distance object with column names and row names.</dd>

</dl>

dist.3col: Transform distance matrix to 3-column matrix

Description

Usage

Value

Arguments

Author

Details

Examples