https://github.com/ebedthan/midas-pub-micro
Analysis Code of MIDAS scientific article #1
https://github.com/ebedthan/midas-pub-micro
microbiome-analysis
Last synced: 3 months ago
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Analysis Code of MIDAS scientific article #1
- Host: GitHub
- URL: https://github.com/ebedthan/midas-pub-micro
- Owner: Ebedthan
- Created: 2025-03-10T09:50:30.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2025-03-10T10:07:02.000Z (3 months ago)
- Last Synced: 2025-03-10T11:23:07.632Z (3 months ago)
- Topics: microbiome-analysis
- Language: R
- Homepage:
- Size: 5.78 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## Analysis Code of MIDAS scientific article #1
### Overview
We used `R` to analyse microbiome data. To facilitate reproducibility, `renv`
package was used to bundle everything needed to reproduce results.
### How to reproduce the results ?
1. Download the data folder
The data folder was not added to GitHub (because of its size) but is publicly
available on Zenodo at this link .
**Important**: Note that the `data` folder in this repo is not complete and should be
replaced by the folder on Zenodo (that contains the CHELSA tiff files) also.
2. Check you have the exact version of R used
We used **R version 4.4.3 (2025-02-28)** on a `x86_64-pc-linux-gnu` PC.
3. Download the repository
Using the CLI you can use:
``` bash
git clone https://github.com/Ebedthan/midas-pub-micro.git
```
or directly download the zipped file from GitHub.
After downloading, decompress the folder if needed and navigate into the folder.
4. Reproduce the results
First open `R` and then install `renv`:
``` r
install.packages("renv")
```
Then restore the project state as defined in the lockfile by using
``` r
renv::restore()
```
Then you can run the analysis in the `diversity_analysis.R` and get the results.
Enjoy!