README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# HydroSurvDOYTEMP

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<!-- badges: end -->

<!-- lastcommit: start -->
[![Last Commit](https://img.shields.io/github/last-commit/caitobrien/HydroSurvSizePred)](https://github.com/caitobrien/HydroSurvSizePred/commits/main)
<!-- lastcommit: end -->

**HydroSurvDOYTEMP** an interactive visualization tool based on the models adapted from Scheuerell et al. (2009) and Gosselin et al. (2018). 

The goal of **HydroSurvDOYTEMP** is to showcase predicted survival for Chinook salmon, *Oncorhynchus tshawytscha*, and Steelhead, *Oncorhynchus mykiss*, influenced by seasonal changes experienced during downstream migration through the Federal Columbia River Power System Hydrosystem (FCRPS), Pacific Northwest, USA.

*Please note that this shiny app is currently under development*

## Installation

**Option 1:** You can install the development version of *HydroSurvDOYTEMP* from [GitHub](https://github.com/) with:

``` r
# Install the developmental version of the HydroSurvSizePred package from GitHub
devtools::install_github("caitobrien/HydroSurvDOYTEMP")

# Load the package
library(HydroSurvDOYTEMP)

# Run the app
run_app()

#if needed, detach the package workspace and repeat above lines of code
detach("package:HydroSurvDOYTEMP", unload=TRUE)
```

*HydroSurvDOYTEMP* is currently in development and changes are continuously being made. If you have already imported to R studio, please rerun `install_github("caitobrien/HydroSurvDOYTEMP")` to see latest changes in the developmental version. If no changes have been made since last import, a warning will appear: `Skipping install of 'HydroSurvSizePred' from a github remote, the SHAX (XXXXXX) has not changed since last install. Use 'force = TRUE' to force installation` and you have the latest developmental version imported. Use `detach()` if not working properly and reinstall. 

This option will run the Shiny App within you RStudio environment but will not download the background files necessary to run. 

**Option 2:** If you are interested in the files that support the development version, please see: [https://github.com/caitobrien/HydroSurvDOYTEMP](https://github.com/caitobrien/HydroSurvDOYTEMP) to clone the repository. Alternatively, within Rstudio, use the following steps: 

1. Start a new project with  `File > New Project > Version Control > Git` 

2. In the repository URL field, paste `https://github.com/caitobrien/HydroSurvDOYTEMP.git`

3. Once project is created, and the repository is cloned, you can run the app within R environment by going to the folder: `dev > run_dev.R` and loading lines of code, with the final `run_app()` to launch the app.


*Possible download error with GitHubs security settings:*

If you receive an error associated with github_PAT credentials, you may need to setup a GitHub Personal Access Token (PAT) for authentication when you try to install a package from GitHub using `devtools::install_github()`. Here are the steps to resolve this issue:

1. **Generate a new GitHub PAT**: Go to your GitHub account settings, then to Developer settings -> Personal access tokens -> Generate new token (classic or fine-grained). Set expiration date and save token. Token will disappear if not saved.

2. **Set the new PAT in your R environment**: You can use the `usethis` package to set the PAT in your R environment. Here's how:

```r
# Install the usethis package if you haven't already
install.packages("usethis")

# Use usethis to set the GITHUB_PAT environment variable
usethis::edit_r_environ()

# This will open your .Renviron file in a text editor. Add the following line to the file, replacing "your_new_pat" with your actual PAT:
GITHUB_PAT=your_new_pat

# Save and close the file. Then, restart your R session to make sure the new environment variable takes effect.
```

3. **Try installing the package again**: Now, you should be able to install the package from GitHub without encountering the authentication error. Follow steps in Option 1.


The app structure follows a Golem framework described in [Engineering Production-Grade Shiny Apps](https://engineering-shiny.org/setting-up-for-success.html) by Colin Fay, Sébastien Rochette, Vincent Guyader and Cervan Girard.

## Contact

This app is being developed by Caitlin O'Brien, Research Scientist, Columbia Basin Research, SAFS, University of Washington. Please reach out with questions/concerns via csobrien@uw.edu.

```{r update_readme, eval=FALSE, include=FALSE}
#You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this.
devtools::build_readme()
```