microeco

2.3.0

Microbial Community Ecology Data Analysis

5packages depend

39.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Chi LiuFirst published 2020-11-1249 releasesCRAN page ↗GitHub ↗

A series of data analysis approaches for microbiome data based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.

Install

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

install.packages("microeco", 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("ChiLiubio/microeco")

Development version from ChiLiubio/microeco. 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-microeco

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

# 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-microeco

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

39.8K

CRAN downloads in the past year

Rank #2,304 · ~109/day · ~3.3K/mo

microeco Releases R versions

Daily download trend is not available in this view yet.

2.8K30 days

9.8K90 days

39.8K1 year

Compare downloads with other packages →

Also on268 r2u31 autocran

Repository

GitHub ↗ chiliubio/microeco

286Stars

80Forks

40Open issues

0Open PRs

52Releases

1,142Commits

4Contributors

License GPL-3.0 · 1,142 commits · Last activity 2026-07-11 · +2.1% stars, 30d

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/chiliubio/microeco on 2026-07-19.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0ggplot2

Imports (15)

R6statsape vegan rlang data.table magrittr dplyr tibble scalesgridRColorBrewer reshape2 igraph (>= 2.0.0)lifecycle

LinkingTo (0)

none

Suggests (12)

GUniFracMASSggpubr randomForest ggdendro ggrepel agricolae gridExtra picante pheatmap mice GGally

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

file2meco meconetcomp mecoturn LorMe SQMtools

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Chi Liu

Author, Maintainer

Authors (1)

Chi Liu

Author, Maintainer

Contributors (3)

Xiangzhen Li

Contributor

Felipe R. P. Mansoldo

Contributor · added in 0.6.0

Minjie Yao

Contributor

Listed in earlier versions (8)

Yang Cao

no longer listed · 0.2.1 to 1.6.0

Stilianos Louca

no longer listed · 0.2.1 to 0.3.3

Paul J. McMurdie

no longer listed · 0.2.1 to 0.3.1

Nhu H. Nguyen

no longer listed · 0.2.1 to 0.3.3

James Robert White

no longer listed · 0.2.1 to 0.3.1

Umer Zeeshan Ijaz

no longer listed · 0.5.1 to 1.6.0

Chenhao Li

no longer listed · 0.5.1 to 1.6.0

Felipe Mansoldo

no longer listed · 0.5.1

Package Timeline

49 releases. R releases are shown for context.

2.3.0Latest
2026-07-07 · current release · diff ↗
2.2.0
2026-05-14 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.1.0
2026-04-10 · diff ↗
2.0.0
2026-01-27 · diff ↗
1.16.0
2025-10-31 · diff ↗
1.15.0
2025-05-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.14.0
2025-03-28 · diff ↗
1.13.0
2025-02-08 · diff ↗
1.12.0
2025-01-07 · diff ↗
1.11.0
2024-12-15 · diff ↗
1.10.0
2024-10-29 · diff ↗
1.9.1
2024-08-23 · diff ↗
1.9.0
2024-08-18 · diff ↗
1.8.0
2024-06-28 · diff ↗

Show 40 earlier events

1.7.1
2024-05-23 · diff ↗
1.7.0
2024-05-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.0
2024-03-31 · diff ↗
1.5.0
2024-03-04 · diff ↗
1.4.0
2024-01-22 · diff ↗
1.3.0
2023-12-11 · diff ↗
1.2.2
2023-11-18 · diff ↗
1.2.0
2023-11-08 · diff ↗
1.1.0
2023-09-14 · diff ↗
1.0.0
2023-09-06 · diff ↗
0.20.0
2023-06-27 · diff ↗
0.19.5
2023-06-09 · diff ↗
0.19.0
2023-05-25 · diff ↗
0.17.0
2023-05-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.16.0
2023-04-14 · diff ↗
0.15.0
2023-03-27 · diff ↗
0.14.1
2023-02-20 · diff ↗
0.14.0
2023-02-10 · diff ↗
0.13.0
2022-11-15 · diff ↗
0.12.0
2022-10-04 · diff ↗
0.11.0
2022-06-22 · diff ↗
0.10.1
2022-05-30 · diff ↗
0.10.0
2022-05-27 · diff ↗
0.9.0
2022-05-17 · diff ↗
0.8.0
2022-05-03 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.7.5
2022-04-20 · diff ↗
0.7.1
2022-03-19 · diff ↗
0.6.5
2022-01-07 · diff ↗
0.6.0
2021-11-16 · diff ↗
0.5.1
2021-09-01 · diff ↗
0.4.0
2021-05-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.3
2021-03-27 · diff ↗
0.3.1
2020-11-24 · diff ↗
0.3.0
2020-11-15 · diff ↗
0.2.1
2020-11-12
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-12
Total releases: 49 / 6 yrs
License: GPL-3 OSI
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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