An R package for easy modeling, filtering, and quantifying putative biotic interactions of microbial communities.
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:
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Step 1. Construct ecological networks for microbial communities. π
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Step 2. Assign the ecological assembly processes to each significantly pair ASVs. π
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Step 3. Quantify the strength of biotic associations to each local site. π
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Step 4. Calculate the effects of biotic associations on alpha and beta diversity of microbial communities. β€οΈ
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trans_ps() converts the data to phyloseq format.
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filter_ps() filters OTU table by occurrence and abundance.
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cal_network() infers ecological networks.
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test_link_env() classifies the ecological associations to environmental filtering
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test_link_dl() classifies the ecological associations to dispersal limitation
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assigned_process() identifies ecological associations as environmental filtering and dispersal limitation
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qcmi() quantifies the local intensity of microbial biotic interaction.
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cal_alphacon() calculates the contributions of microbial interaction on alpha diversity
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cal_betacon() calculates the contributions of microbial interaction on beta diversity
For a detailed introduction, please see qcmi.test.r.
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(βqcmiβ)
If you find a bug, please file a minimal reproducible example in the issues
Please see the document of qcmi.test.r
Iβm 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):
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Read and correct any inconsistencies in the documentation
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Raise issues about bugs or wanted features
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Review code
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Add new functionality (in the form of new plotting functions or helpers for preparing subtitles)
Not yet QAQ π»π»π»