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AdrienneMendrik authored Apr 2, 2024
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Expand Up @@ -12,7 +12,7 @@ This is a template repository to prepare your submission for phase 1 of the Pred

## Prerequisites

1. Make a copy of [this](https://github.com/eyra/fertility-prediction-challenge) template repository, by forking and cloning as explained [here](https://github.com/eyra/fertility-prediction-challenge/wiki#how-to-fork-and-clone-this-repository). Use your own copy of the repository to prepare your method for submission as explained [here](https://github.com/eyra/fertility-prediction-challenge/tree/master#prepare-your-method).
1. Make a copy of [this](https://github.com/eyra/fertility-prediction-challenge) template repository, by forking and cloning as explained [here](https://github.com/eyra/fertility-prediction-challenge/wiki/PreFer-Challenge-Wiki#how-to-fork-and-clone-this-repository). Use your own copy of the repository to prepare your method for submission as explained [here](https://github.com/eyra/fertility-prediction-challenge/tree/master#prepare-your-method).
2. Make sure to allow Github Actions on your own repository: Go to the “Actions” tab and click “I understand my workflows, go ahead and enable them.”
3. If you have not already done so, download the training data and codebooks via the "Download Data" task on the Next platform.❗️**Important**: you are not allowed to share these datasets and you **may not** upload them to your Github repository!

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4. **Train, tune, and save your model**: any steps to train your model need to be added to the `training.py`/`training.R` script with documentation (e.g., code for the model, number of folds, set seed). The only function in this script is `train_save_model` in which you can add the steps needed to run the model. The output of this script is your saved model, either ```model.joblib``` for Python or ```model.rds``` for R. Make sure that your model is saved in the same folder as `submission.py`/`submission.R` under the name `model.joblib` for Python or `model.rds` for R. The model will be applied to the holdout data when you submit your method.

5. **Test your model on fake data**: you can test your ```clean_df``` function and your model (stored in: ```model.joblib```/```model.rds```) on the fake data (`PreFer_fake_data.csv`) with the ```predict_outcomes``` function. The the ```predict_outcomes``` function in `submission.py`/`submission.R` will be run on the holdout data to generate your challenge submission result on the leaderboard. Make sure that the outputs of your model are predicted classes (i.e. 0s and 1s) rather than, for example, probabilities and to add or edit dependencies when required as described [here](https://github.com/eyra/fertility-prediction-challenge/wiki#how-to-add-or-edit-dependencies-librariespackages). If your method does not run on the "fake data", it will not run on the holdout data. If you passed the test (i.e.```predict_outcomes``` led to predictions rather than errors), you can start [submitting your method](https://github.com/eyra/fertility-prediction-challenge/tree/master#submit-your-method).
5. **Test your model on fake data**: you can test your ```clean_df``` function and your model (stored in: ```model.joblib```/```model.rds```) on the fake data (`PreFer_fake_data.csv`) with the ```predict_outcomes``` function. The ```predict_outcomes``` function in `submission.py`/`submission.R` will be run on the holdout data to generate your challenge submission result on the leaderboard. Make sure that the outputs of your model are predicted classes (i.e. 0s and 1s) rather than, for example, probabilities and to add or edit dependencies when required as described [here](https://github.com/eyra/fertility-prediction-challenge/wiki/PreFer-Challenge-Wiki#how-to-add-or-edit-dependencies-librariespackages). If your method does not run on the "fake data", it will not run on the holdout data. If you passed the test (i.e.```predict_outcomes``` led to predictions rather than errors), you can start [submitting your method](https://github.com/eyra/fertility-prediction-challenge/tree/master#submit-your-method).

ℹ️ Check out [this website](https://preferdatachallenge.nl/posts) for guides, notebooks, and blogs to guide you through this process.

Expand All @@ -44,7 +44,7 @@ Submit your method via the "Submit Method" task on the Next platform by providin

![](https://github.com/eyra/fertility-prediction-challenge/blob/master/images/Checks%20passed.png)

ℹ️ If the check fails go to [FAQ](https://github.com/eyra/fertility-prediction-challenge/wiki#frequently-asked-questions). You might need to add dependencies as described [here](https://github.com/eyra/fertility-prediction-challenge/wiki#how-to-add-or-edit-dependencies-librariespackages).
ℹ️ If the check fails go to [FAQ](https://github.com/eyra/fertility-prediction-challenge/wiki/PreFer-Challenge-Wiki#frequently-asked-questions). You might need to add dependencies as described [here](https://github.com/eyra/fertility-prediction-challenge/wiki/PreFer-Challenge-Wiki#how-to-add-or-edit-dependencies-librariespackages).

4. On the main page of your repository, above the file list, click commits to view a list of commits, as described [here](https://docs.github.com/en/pull-requests/committing-changes-to-your-project/creating-and-editing-commits/about-commits#about-commit-branches-and-tag-labels)
5. Go to the commit that you want to submit and right click on view commit details, then click "Copy Link Address", see example below:
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