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Add a optimization notebook for phenology #67

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99b38d7
add notebook optimization_phenology
SarahAlidoost Dec 17, 2025
2642e90
fix a test in test_phenology
SarahAlidoost Dec 17, 2025
a6c5460
Merge branch 'main' into pheno_nb_optim
SarahAlidoost Dec 17, 2025
ee057b4
add early stop, fix duration issue
SarahAlidoost Dec 17, 2025
f633aa7
add nb to docs
SarahAlidoost Dec 17, 2025
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14 changes: 8 additions & 6 deletions docs/examples.md
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Expand Up @@ -6,9 +6,10 @@ We provide an example notebook showing optimization of models' parameters with
`diffWOFOST`. To get familiar with the concepts and implementation, check out
[`Introduction`](./index.md) in the documentation.

| Open the notebook | Access the source | View the notebook |
|-------|------------|---------------|
| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization.ipynb) |
| Model | Open the notebook | Access the source | View the notebook |
|---|----|------------|---------------|
| Leaf and Root dynamics| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][leaf_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][leaf_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization.ipynb) |
| Phenology | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)][pheno_colab_link] | [![Access the source code](https://img.shields.io/badge/GitHub_Repository-000.svg?logo=github&labelColor=gray&color=blue)][pheno_source_link] | [![here](https://img.shields.io/badge/View_Notebook-orange.svg?logo=jupyter&labelColor=gray)](./notebooks/optimization_phenology.ipynb) |

!!! note
When calculating gradients, it is important to ensure that the predicted
Expand All @@ -21,6 +22,7 @@ We provide an example notebook showing optimization of models' parameters with
output w.r.t the parameter will be close to zero, which may not provide
useful information for optimization.

[colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb

[source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb
[leaf_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb
[leaf_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization.ipynb
[pheno_colab_link]: https://colab.research.google.com/github/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_phenology.ipynb
[pheno_source_link]: https://github.com/WUR-AI/diffWOFOST/blob/main/docs/notebooks/optimization_phenology.ipynb
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