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index.qmd
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---
title: "Summarizing bird migration and stopovers within urbanized landscapes using Motus data"
---
__*Pilot Phase*__
Principal Investigators: **[Barbara Frei](https://www.thebirdsthetrees.com/), [Elizabeth Gow](https://www.elizabethgow.com/) and Krista De Groot**
Workflow design: [Steffi LaZerte](https://steffilazerte.ca)
**The code in this workflow is released under GPL3.**
## Getting Started
This site contains the workflow for obtaining and filtering Motus track data
for the analysis of Urban/Rural stopovers during avian migration.
This website contains the full annotated code and outputs run as of the dates
on each page.
There are two ways to use this workflow
1. **Walk through this website**, familiarize yourself with the code and outputs [Most users]
2. **Modify this workflow** by working directly in the qmd scripts used to create
this workflow [Some users]
- To do this, you can either create a [PR](https://happygitwithr.com/big-picture.html?q=pull%20request#special-features-of-github)
to the workflow or [clone](https://happygitwithr.com/push-pull-github.html?q=clone#git-clone-command-line)
it and work on your own copy.
- Each qmd file is setup to be run interactively (i.e. in an R session) as well
as to be compiled non-interactively to create this script
- Be warned that compiling the whole site can take a long time, especially if
new data is being downloaded!
- Use `renv::restore()` to ensure you have the same packages and versions
installed in this project to reproduce this workflow.
## Packages and Reproducibility
All R packages used in this workflow are loaded by the `XX_setup.R` (see the
Appendix [Setup](XX_setup.html)).
We use [renv](https://rstudio.github.io/renv/) to keep track of the packages used
and their versions. Use `renv::restore()` to double check that your version of
this project has the correct packages ready to go.
If all goes as planned renv should install the packages for you if you're missing any.
Each script ends with a "Reproducibility" block which includes the session information
with specific packages used when that page was last compiled.
For publication, check the [Citations](XX_citations.R) Appendix to ensure we use proper citations.
## Understanding outputs
Each page performs a different step in the workflow (in order), from downloading the data,
to filtering, to summarizing.
#### Hidden Code
All code to illustrate these steps is included in the documents, however, it may
sometimes be 'folded'. To show this code, click on the "Code" button below.
```{r}
#| code-fold: true
# Folded code!
```
#### Hidden Tables
Note that many tables are actually much longer (and/or wider) than they appear.
If you hover the mouse over a table, scroll bars should appear (or you can use the
mouse roller button).
```{r}
#| echo: false
#| message: false
source("XX_setup.R")
read_csv("Data/03_Final/transitions_final.csv") |>
gt() |>
gt_theme() |>
tab_options(container.height = px(200),
container.overflow.y = "auto")
```
#### Data
All the datasets created by this workflow are documented in the Appendix [Datasets](XX_data.html).
#### More details please!
- The [Notes & Details](XX_details.html) Appendix explains some of the more technical
aspects and general coding design and decisions made.
- The [Setup](XX_setup.html) Appendix explains the setup and defaults as well as
sharing the fuctions used in this workflow.
- If you have questions about a particular step in the workflow, contact Steffi
or consider opening an issue in the repository.