qiime2 plugin for Fido for high dimensional compositional time series analysis
conda install fido r-dplyr r-tidybayes r-tidyr -c mortonjt -c r
conda install -c conda-forge --strict-channel-priority r-arrow feather-format
pip install [email protected]:mortonjt/q2-fido.git
If things break, you may need to install more packages
conda install -c conda-forge r-devtools
In R
library(devtools)
devtools::install_github("jsilve24/driver")
devtools::install_github("wesm/feather/R")
See qiime fido basset --help for more information.
An example run may look as follows. See the examples/alm for relevant files
qiime fido basset --i-table feature-table.qza --m-time-file fecal-metadata.txt --m-time-column collection_day --m-subjects-file fecal-metadata.txt --m-subjects-column host_subject_id --p-host DonorA --p-monte-carlo-samples 1000 --output-dir DonorA --verbose