QCMI

An R package for easy modeling, filtering, and quantifying putative biotic interactions of microbial communities.

Overview

qcmi calculates the strength of biotic associations and quantifies the contributions on microbial diversity.

qcmi provides some convenient verbs to make it easy to process data and results:

Pipeline

Step 1. Construct ecological networks for microbial communities. 📜
Step 2. Assign the ecological assembly processes to each significantly pair ASVs. 📈
Step 3. Quantify the strength of biotic associations to each local site. 📊
Step 4. Calculate the effects of biotic associations on alpha and beta diversity of microbial communities. ❤️

Function

trans_ps() converts the data to phyloseq format.
filter_ps() filters OTU table by occurrence and abundance.
cal_network() infers ecological networks.
test_link_env() classifies the ecological associations to environmental filtering
test_link_dl() classifies the ecological associations to dispersal limitation
assigned_process() identifies ecological associations as environmental filtering and dispersal limitation
qcmi() quantifies the local intensity of microbial biotic interaction.
cal_alphacon() calculates the contributions of microbial interaction on alpha diversity
cal_betacon() calculates the contributions of microbial interaction on beta diversity

For a detailed introduction, please see qcmi.test.r.

Installation

to get the development version from GitHub:

# If devtools package is not installed, first install it
install.packages("devtools")
devtools::install_github("joshualiuxu/qcmi")

load the package:

library(“qcmi”)

If you find a bug, please file a minimal reproducible example in the issues

Usage

Please see the document of qcmi.test.r

Contributing

I’m happy to receive bug reports, suggestions, questions, and (most of all) contributions to fix problems and add features. I personally prefer using the GitHub issues system over trying to reach out to me in other ways (personal e-mail, Twitter, etc.). Pull Requests for contributions are encouraged.

Here are some simple ways in which you can contribute (in the increasing order of commitment):

Read and correct any inconsistencies in the documentation
Raise issues about bugs or wanted features
Review code
Add new functionality (in the form of new plotting functions or helpers for preparing subtitles)

Citation

Not yet QAQ 👻👻👻

AnyiHu / qcmi