#### **READ ME FIRST**
This is a public repository for materials associated with the following publication:
**Potential for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage**
Faye Manning, Jeff Curtis, Ian R. Walker, and Jason Pither
The final published version is available at this DOI: [https://doi.org/10.1111/fwb.13706](https://doi.org/10.1111/fwb.13706)
A preprint of the manuscript is available [here](https://ecoevorxiv.org/h97pw/).
***
#### **Contents**
The key contents are:
1. The Supporting Information file called ["Manning_et_all_suppinfo.pdf"](https://osf.io/d7sxp/), to accompany the main manuscript linked as a preprint [here](https://ecoevorxiv.org/h97pw).
2. The R Markdown script for all analyses, also available as PDF document. The RMD file is in the "scripts" folder that comes with the archived (zip) file, and the rendered PDF document is available on the main OSF page and is called ["Manning_et_al_full_script.pdf"](https://osf.io/59j4b/). This script includes:
- all R code (annotated) for all analyses
- descriptions of all raw data files
- descriptions of all data sources
3. A video file "duck_video.MOV" showing the procedure for processing ducks
#### **Instructions:**
1. To reproduce all analyses, download the ZIP file "diatom.zip" from [here](https://osf.io/ujnw2/files/) and unzip to your local storage.
2. Open the RStudio project called "diatom.Rproj"
3. If you do not already have the `renv` package installed, install the latest development version using the following commands in the console:
```
if (!requireNamespace("remotes"))
install.packages("remotes")
remotes::install_github("rstudio/renv")
```
4. Once `renv` is installed, you can restore the project with all its required libraries using the following command in the console:
```
renv::restore()
```
5. If you encounter problems when restoring, consult this [webpage](https://rstudio.github.io/renv/) for assistance.
6. Open the RMD script "Manning_et_al_full_script.Rmd", which is located in the "scripts" subdirectory.
7. You can then optionally run the entire script by pressing command+option+r (Mac) or ctrl+alt+r (Windows), or you can work through chunks yourself.
**NOTE**: The script has only been vetted on MacOS thus far. Vetting for reproducibility with Microsoft Windows is in progress.
8. For ease of reading, you can "knit" the RMD script to HTML or PDF using the knit function in RStudio.
9. If you use the code or data in any capacity, please cite this repository as follows:
>Pither, J. & Manning, F.S. (2021). Data and scripts for: Potential for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage. Retrieved from: osf.io/ujnw2
