iCAMP

1.5.12

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

1packages depend

11.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Daliang NingFirst published 2020-09-094 releasesCRAN page ↗GitHub ↗

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).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("iCAMP", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("DaliangNing/iCAMP1")

Development version from DaliangNing/iCAMP1. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-icamp

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-iCAMP

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-iCAMP

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 87%

Downloads

11.7K

CRAN downloads in the past year

Rank #3,377 · ~32/day · ~976/mo

Releases R versions

Daily download trend is not available in this view yet.

88330 days

3.4K90 days

11.7K1 year

Compare downloads with other packages →

Also on110 r2u32 autocran

Repository

GitHub ↗ daliangning/icamp1

95Stars

30Forks

5Open issues

0Open PRs

0Releases

291Commits

1Contributors

License GPL-2.0 · 291 commits · Last activity 2025-10-01 · 0% stars, 30d

Stars over time

2025-07-09 · 812026-07-07 · 95

Repository practices

Upstream repositoryBeta

Checks run against github.com/daliangning/icamp1 on 2026-07-30.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (11)

veganparallelpermute ape bigmemory nortest minpack.lm Hmiscstats4DirichletReg data.table

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

NST

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Daliang Ning

no longer listed · 1.2.8 to 1.5.12

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.5.12Latest
2022-06-01 · current release · diff ↗
unarchivedReturned to CRAN
2022-06-01
archivedRemoved from CRAN
2022-04-24
check problems were not corrected in time
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.4
2021-01-09 · diff ↗
1.2.9
2020-09-19 · diff ↗
1.2.8
2020-09-09
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-09
Total releases: 4 / 6 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5
Bundled data: 381 KB / 2 files
Download size: 544 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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