-
Notifications
You must be signed in to change notification settings - Fork 63
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
68 additions
and
66 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| # NEON Forecast Challenge Workshop Pre-Workshop Instructions | ||
| This is a repository for materials to complete the NEON Ecological Forecasting Challenge workshop. The main branch focuses on forecasts for the aquatics theme forecast production. Select a different branch of the repository to complete the workshop for other theme forecasts. | ||
|
|
||
| This workshop repository is a dynamic repository and may change in future iterations. | ||
| This is a repository for materials to complete the NEON Ecological Forecasting Challenge workshop. The main branch focuses on forecasts for the aquatics theme forecast production. Select a different branch of the repository to complete the workshop for other theme forecasts. | ||
|
|
||
| This workshop repository is a dynamic repository and may change in future iterations. | ||
|
|
||
| The materials are split into three sections: | ||
|
|
||
| * `Submit_forecast` - want to get started with making and submitting forecasts to the Challenge - start here! | ||
| * `Automate_forecasts` - you've made a model and submitted a forecast successfully? Automate your workflow to submit a new forecacst every day | ||
| * `Analyse_scores` - interested in knowing how different forecasts are performing within the Challenge? This is a brief introduction in how to access the scored forecasts and do some simple analyses. | ||
| 1. `Submit_forecast` - want to get started with making and submitting forecasts to the Challenge - start here! | ||
| 2. `Automate_forecasts` - you've made a model and submitted a forecast successfully? Automate your workflow to submit a new forecast every day | ||
| 3. `Analyse_scores` - interested in knowing how different forecasts are performing within the Challenge? This is a brief introduction in how to access the scored forecasts and do some simple analyses. | ||
|
|
||
| Below are some pre-workshop instructions to make sure you are ready to go! | ||
|
|
||
| __Any questions, email [[email protected]](mailto:[email protected]) before the workshop!__ | ||
| **Any questions, email [freyao\@vt.edu](mailto:[email protected]) before the workshop!** | ||
|
|
||
| ## 1. Setting up your R environment | ||
|
|
||
| R version 4.2 is required to run the code in this workshop. You should also check that your Rtools is up to date and compatible with R 4.2, see (https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html). | ||
| R version 4.2 is required to run the code in this workshop. You should also check that your Rtools is up to date and compatible with R 4.2, see (<https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html>). | ||
|
|
||
| The following packages need to be installed using the following code. | ||
|
|
||
|
|
@@ -30,55 +31,56 @@ remotes::install_github('eco4cast/neon4cast') # package from NEON4cast challenge | |
|
|
||
| There are 3 options for getting the code locally so that you can run it, depending on your experience with Github/Git you can do one of the following: | ||
|
|
||
| 1. __Fork (recommended)__ the repository to your Github and then clone the repository from your Github repository to a local RStudio project. This will allow you to modify the scripts and push it back to your Github. | ||
| 1. **Fork (recommended)** the repository to your Github and then clone the repository from your Github repository to a local RStudio project. This will allow you to modify the scripts and push it back to your Github. | ||
|
|
||
| - Find the fork button in the top right of the webpage --> Create Fork. This will generate a copy of this repository in your Github. | ||
| - Then use the <> Code button to copy the HTTPS link (from you Github!). | ||
| - In RStudio, go to New Project --> Version Control --> Git. | ||
| - Paste the HTTPS link in the Repository URL space, and choose a suitable location for your local repository --> Create Project. | ||
| - Open the .Rmd file | ||
| - Find the fork button in the top right of the webpage --\> Create Fork. This will generate a copy of this repository in your Github. | ||
| - Then use the \<\> Code button to copy the HTTPS link (from you Github!). | ||
| - In RStudio, go to New Project --\> Version Control --\> Git. | ||
| - Paste the HTTPS link in the Repository URL space, and choose a suitable location for your local repository --\> Create Project. | ||
| - Open the .Rmd file | ||
|
|
||
| 2. __Clone__ the workshop repository to a local RStudio project. Your local workspace will be set up and you can commit changes locally but they won't be pushed back to the Github repository. | ||
| - Find the fork button in the top left of the webpage --> Create Fork. | ||
| - Then use the <> Code button to copy the HTTPS link. | ||
| - In RStudio go to New Project --> Version Control --> Git. | ||
| - Paste the HTTPS link in the Repository URL space, and choose a suitable location for your local repository --> Create Project. | ||
| - Open the .Rmd file | ||
| 2. **Clone** the workshop repository to a local RStudio project. Your local workspace will be set up and you can commit changes locally but they won't be pushed back to the Github repository. | ||
|
|
||
| 3. __Download__ the zip file of the repository code. You can save changes (without version control) locally. | ||
| - Find the <> Code button --> Download ZIP. | ||
| - Unzip this to a location on your PC and open the `ESA2023_neon4cast_workshop.Rproj` file in RStudio. | ||
| - Find the fork button in the top left of the webpage --\> Create Fork. | ||
| - Then use the \<\> Code button to copy the HTTPS link. | ||
| - In RStudio go to New Project --\> Version Control --\> Git. | ||
| - Paste the HTTPS link in the Repository URL space, and choose a suitable location for your local repository --\> Create Project. | ||
| - Open the .Rmd file | ||
|
|
||
| More information on forking and cloning in R can be found at [happygitwithr](https://happygitwithr.com/fork-and-clone.html), a great resource to get you started using version control with RStudio. | ||
| 3. **Download** the zip file of the repository code. You can save changes (without version control) locally. | ||
|
|
||
| - Find the \<\> Code button --\> Download ZIP. | ||
| - Unzip this to a location on your PC and open the `NEON-forecast-challenge-workshop.Rproj` file in RStudio. | ||
|
|
||
| For the workshop you can follow along via the rmarkdown document (`Submit_forecast/NEON_forecast_challenge_workshop_aquatics.Rmd`) or the md (`Submit_forecast/NEON_forecast_challenge_workshop_aquatics.md`), both of which can be downloaded here or you can fork the whole repository. | ||
| More information on forking and cloning in R can be found at [happygitwithr](https://happygitwithr.com/fork-and-clone.html), a great resource to get you started using version control with RStudio. | ||
|
|
||
| For the workshop you can follow along via the rmarkdown document (`Submit_forecast/NEON_forecast_challenge_workshop_aquatics.Rmd`) or the md (`Submit_forecast/NEON_forecast_challenge_workshop_aquatics.md`), both of which can be downloaded here or you can fork the whole repository. | ||
|
|
||
| ## Optional: Use Docker | ||
|
|
||
| Another option to running the materials locally is to use a Docker container that has all the packages pre-installed. | ||
| Another option to running the materials locally is to use a Docker container that has all the packages pre-installed. | ||
|
|
||
| ### Installing Docker | ||
| Go to [https://docs.docker.com/get-docker/](https://docs.docker.com/get-docker/) to install the relevant install for your platform (available for PC, Mac and Linux). Also see [https://docs.docker.com/desktop/](https://docs.docker.com/desktop/). | ||
|
|
||
| NOTE: | ||
| * If you're running Windows, you will need WSL (Windows Subsystem for Linux) | ||
| * If you're running a Linux distribution, you may have to enable Viritualization on your computer (see [here](https://stackoverflow.com/questions/76646465/unable-to-launch-docker-desktop-on-ubuntu/76655270#76655270)) | ||
| Go to <https://docs.docker.com/get-docker/> to install the relevant install for your platform (available for PC, Mac and Linux). Also see <https://docs.docker.com/desktop/>. | ||
|
|
||
| NOTE: \* If you're running Windows, you will need WSL (Windows Subsystem for Linux) \* If you're running a Linux distribution, you may have to enable Viritualization on your computer (see [here](https://stackoverflow.com/questions/76646465/unable-to-launch-docker-desktop-on-ubuntu/76655270#76655270)) | ||
|
|
||
| ### Running a docker container | ||
|
|
||
| 1. Launch Docker Desktop (either from the Command Line or by starting the GUI) | ||
| 2. At the command line run the following command which tells docker to `run` the container with the name `eco4cast/rocker-neon4cast` that has all the packages and libraries installed already. The `PASSWORD=yourpassword` sets a simple password that you will use to open the container. The `-ti` option starts both a terminal and an interactive session. | ||
| ``` | ||
| 1. Launch Docker Desktop (either from the Command Line or by starting the GUI) | ||
| 2. At the command line run the following command which tells docker to `run` the container with the name `eco4cast/rocker-neon4cast` that has all the packages and libraries installed already. The `PASSWORD=yourpassword` sets a simple password that you will use to open the container. The `-ti` option starts both a terminal and an interactive session. | ||
|
|
||
| ``` | ||
| docker run --rm -ti -e PASSWORD=yourpassword -p 8787:8787 eco4cast/rocker-neon4cast | ||
| ``` | ||
| This can take a few minutes to download and install. It will be quicker the next time you launch it. | ||
|
|
||
| 3. Open up a web browser and navigate to `http://localhost:8787/` | ||
| 4. Enter the username: `rstudio` and password: `yourpassword` | ||
| 5. You should see a R Studio interface with all the packages etc. pre-installed and ready to go. | ||
| This can take a few minutes to download and install. It will be quicker the next time you launch it. | ||
|
|
||
| 3. Open up a web browser and navigate to `http://localhost:8787/` | ||
| 4. Enter the username: `rstudio` and password: `yourpassword` | ||
| 5. You should see a R Studio interface with all the packages etc. pre-installed and ready to go. | ||
|
|
||
| You can close this localhost window (and then come back to it) but if you close the container from Docker (turn off your computer etc.) any changes will be lost unless you push them to Github or exported to your local environment. | ||
|
|
||
| Then follow the instructions for Getting the Code above (`2. Get the Code`). | ||
| Then follow the instructions for Getting the Code above (`2. Get the Code`). | ||
Oops, something went wrong.