RShiny_Microclim

The repo reproduces the figures in this manuscript: Meyer, Abigail V., Yutaro Sakairi, Michael R. Kearney, and Lauren B. Buckley. 2023. “A Guide and Tools for Selecting and Accessing Microclimate Data for Mechanistic Niche Modeling.” Ecosphere14(4): e4506.

Ecosphere manuscript version of code

RShiny_MicroclimGuide is an interactive shiny app that facilitates the selection of microclimate datasets. The app compares 8 different datasets (SCAN, ERA5-Land, GLDAS, gridMET, NOAA NCDC, microclim, microclimUS, USCRN) both temporally and spatially. Once users selects a dataset, we offer this user guide, which explains how to access and download each dataset.

An archive Docker Azure version of the app is in this repo. The app is now published on Shiny Apps from this repo.

Prerequisites for opening in Rstudio

Git and Rstudio (Instructions)
Installation of the following R packages: shiny, raster, ggplot2, leaflet, shinyWidgets, shinythemes, shinycssloaders, magrittr, shinyBS, shinyjs, climateR, AOI, plotly, data.table, viridis, cicerone, utils, MALDIquant, ncdf4, rnoaa

pkgs <- c("shiny", "raster", "ggplot2", "leaflet", "shinyWidgets", "shinythemes", "shinycssloaders", "magrittr", "shinyBS", "shinyjs", "climateR", "AOI", "plotly", "data.table", "viridis", "cicerone", "utils", "MALDIquant", "ncdf4", "rnoaa")
lapply(pkgs, FUN = function(x) {
    if (!require(x, character.only = TRUE)) {
      install.packages(x, dependencies = TRUE)
    }
  }
)

devtools::install_github(c("mikejohnson51/AOI", "mikejohnson51/climateR"))

Using RShiny_Microclim

• Opening in Rstudio:
  Click on "Code" on the top right to copy the link to this repository.
  Click File, New Project, Version Control, Git
  Paste the repository URL and click Create Project.

• Alternatively, go to this link.

Contributing to RShiny_Microclim

To contribute to RShiny_Microclim, follow these steps:

1. Fork this repository.
2. Create a branch: git checkout -b <branch_name>.
3. Make your changes and commit them: git commit -m '<commit_message>'
4. Push to the original branch: git push origin <project_name>/<location>
5. Create the pull request.

Alternatively see the GitHub documentation on creating a pull request.