Package: iCAMP 1.5.12

Daliang Ning

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

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).

Authors:Daliang Ning

iCAMP_1.5.12.tar.gz
iCAMP_1.5.12.tar.gz(r-4.5-noble)iCAMP_1.5.12.tar.gz(r-4.4-noble)
iCAMP_1.5.12.tgz(r-4.4-emscripten)iCAMP_1.5.12.tgz(r-4.3-emscripten)
iCAMP.pdf |iCAMP.html✨
iCAMP/json (API)

# Install 'iCAMP' in R:
install.packages('iCAMP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/daliangning/icamp1/issues

Datasets:

52 exports 1 stars 1.24 score 81 dependencies 1 dependents 3 mentions 37 scripts 697 downloads

Last updated 2 years agofrom:e9566a8dc1. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-linuxOKSep 08 2024

Exports:bmntdbmntd.bigbmpdbNRI.bin.bigbNRI.bin.cmbNRI.cmbNRIn.pbNTI.bigbNTI.big.cmbNTI.bin.bigbNTI.bin.cmbNTI.cmbNTIn.pchange.sigindexcohenddist.3coldist.bin.3coldnicheicamp.bigicamp.binsicamp.booticamp.cateicamp.cmicamp.cm2match.2colmatch.namemaxbigmmidpoint.root.bigmntdnmpdnNRI.cmNRI.pNTI.cmNTI.pnull.normpdist.bigpdist.pps.binqp.bin.jsqpenqpen.cmqpen.testRC.bin.bigcRC.bin.cmRC.cmRC.pcsnmsnm.bootsnm.commtaxa.binphy.bigtree.droottree.path

Dependencies:apebackportsbase64encBHbigmemorybigmemory.sribslibcachemcheckmatecliclustercolorspacedata.tabledigestDirichletRegevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmaxLikmemoisemgcvmimeminpack.lmmiscToolsmunsellnlmennetnortestpermutepillarpkgconfigR6rappdirsRColorBrewerRcpprlangrmarkdownrpartrstudioapisandwichsassscalesstringistringrtibbletinytexutf8uuidvctrsveganviridisviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysisiCAMP-package iCAMP
beta mean nearest taxon distance (betaMNTD)bmntd
beta mean nearest taxon distance (betaMNTD) from big databmntd.big
Beta mean pairwise distance (betaMPD)bmpd
Calculate beta net relatedness index (betaNRI) for each phylogenetic binbNRI.bin.big
Calculate beta net relatedness index (betaNRI) for each phylogenetic bin under multiple metacommunitiesbNRI.bin.cm
Calculate beta net relatedness index with parallel computing under multiple metacommunitiesbNRI.cm
Calculate beta net relatedness index with parallel computingbNRIn.p
Beta nearest taxon index (betaNTI) from big databNTI.big
Beta nearest taxon index (betaNTI) from big data and under multiple metacommunitiesbNTI.big.cm
Calculate beta nearest taxon index (betaNTI) for each phylogenetic binbNTI.bin.big
Calculate beta nearest taxon index (betaNTI) for each phylogenetic bin under multiple metacommunitiesbNTI.bin.cm
Calculate beta nearest taxon index (betaNTI) with parallel computing under multiple metacommunitiesbNTI.cm
Calculate beta nearest taxon index (betaNTI) with parallel computingbNTIn.p
Change significance index option in iCAMP analysischange.sigindex
Cohen's d effect sizecohend
Transform distance matrix to 3-column matrixdist.3col
Convert a list of dist (or matrixes) to a matrixdist.bin.3col
Calculate niche difference between speciesdniche
A simple example dataset for testexample.data
Infer community assembly mechanism by phylogenetic-bin-based null model analysisicamp.big
Summarize iCAMP result in each binicamp.bins
Bootstrapping analysis of icamp resultsicamp.boot
Summarize iCAMP result for different categories of taxaicamp.cate
Infer community assembly mechanism by phylogenetic-bin-based null model analysis under multiple metacommunitiesicamp.cm
Phylogenetic-bin-based null model analysis under different metacommunity settings for phylogenetic and taxonomic null modelsicamp.cm2
Example output of function icamp.bigicamp.out
Check the consistency of the first two columns of different matrixesmatch.2col
Check and ensure the consistency of IDs in different objects.match.name
Find maximum value in a big matrixmaxbigm
Midpoint root a large phylogenymidpoint.root.big
Mean nearest taxon distance (MNTD)mntdn
Mean pairwise distance (MPD)mpdn
Calculate net relatedness index (NRI) under multiple metacommunitiesNRI.cm
Calculate net relatedness index (NRI) by parallel computing.NRI.p
Calculate nearest taxon index (NTI) under multiple metacommunitiesNTI.cm
Calculate nearest taxon index (NTI) with parallel computingNTI.p
Normality test for null valuesnull.norm
Pairwise phylogenetic distance matrix from big treepdist.big
Pairwise phylogenetic distance matrix from small treepdist.p
Test within-bin phylogenetic signalps.bin
Calculate relative importance of community assembly processesqp.bin.js
Quantifying assembly processes based on entire-community null model analysisqpen
Quantifying assembly processes based on entire-community null model analysis under multiple metacommunitiesqpen.cm
Summary and comparison of QPEN results based on bootstrappingqpen.test
Calculate modified Roup-Crick index based on Bray-Curtis similarity for each phylogenetic binRC.bin.bigc
Calculate modified Roup-Crick index based on Bray-Curtis similarity for each phylogenetic bin under multiple metacommunitiesRC.bin.cm
Modified Raup-Crick index based on Bray-Curtis similarity under multiple metacommunitiesRC.cm
Modified Raup-Crick index based on Bray-Curtis similarityRC.pc
Estimation of neutral taxa percentae and dispersal ratesnm snm.boot snm.comm
Phylogenetic binning based on phylogenetic treetaxa.binphy.big
Distance from root to tip(s) and node(s) on phylogenetic treetree.droot
List nodes and edge lengthes from root to each tip and/or nodetree.path