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[![DOI](https://zenodo.org/badge/1.svg)](https://zenodo.org/badge/latestdoi/)

# Mapping oak wilt disease using phenological observations from space
# Mapping oak wilt disease from space using land surface phenology

<br />

These codes are used to predict the present of symptomatic oak trees to oak
wilt using land surface phenology (LSP) metrics (Fig 1). LSP metrics are derived from
Analysis Ready Data (ARD) of Sentinel-2 using the processing workflow of [FORCE](https://force-eo.readthedocs.io/en/latest/).
These codes are used to predict the present of symptomatic oak trees to oak wilt
disease using land surface phenology (LSP) metrics (Fig 1). LSP metrics are
derived from Analysis Ready Data (ARD) of Sentinel-2 using the processing
workflow of [FORCE](https://force-eo.readthedocs.io/en/latest/) (Fig. 2).

The data used in this manuscript that accompany these codes are available at the
[DRUM](https://doi.org). Please follow the instructions described there for proper
citation of the data.
<p align="center">
<img src="https://github.com/ASCEND-BII/Oak-wilt/blob/main/inst/Figure_1.png?raw=true" align="center" alt="500" width="500"/>
<br>
<em>Fig 1. Temporal changes in the Chlorophyll/Carotenoid Index (CCI) of a pixel from an oak tree
that died from oak wilt disease (a) and the expected behavior of land surface phenology metrics
when oak tree conditions are compared with the surrounding healthy vegetation for a given
phenological year (b).</em>
</p>

<br />

<p align="center">
<img src="https://github.com/ASCEND-BII/Oak-wilt/blob/main/inst/workflow.png?raw=true" align="center" alt="720" width="720"/>
<br>
<em>Fig 1. Schematic workflow description.</em>
<em>Fig 2. Schematic workflow description.</em>
</p>

<br />

#### Code structure
Most of the data used in our manuscript that accompany these codes are available
at the [DRUM](https://doi.org). Please follow the instructions described there for
proper citation of the data if used.

<br />

#### Products available

We made available all the scenes of [LSP](https://app.globus.org/file-manager?origin_id=d5f9b461-7d6e-442b-87ed-be8aa2ca6763&origin_path=%2F)
(L3) and the predicted [maps of probabilities](https://app.globus.org/file-manager?origin_id=2ad70821-cc5a-424e-aa72-8553d2bb45eb&origin_path=%2F) (L4) for both states (i.e., Minnesota and Wisconsin). These can be accessible
using a free [Globus](https://www.globus.org/) account.

#### Citing codes, manuscript, and data.

Expand All @@ -42,10 +58,6 @@ citation of the data.
```


J. Antonio Guzmán Q. 1* , Jesús N. Pinto-Ledezma 1 , David Frantz 2 , Philip A. Townsend 3 , Jennifer
Juzwik 4 , Jeannine Cavender-Bares 1

##### Manuscript

```
Expand All @@ -60,7 +72,3 @@ Juzwik 4 , Jeannine Cavender-Bares 1
}
```

##### Data

Please follow the instructions from [Data Repository for U of M](https://doi.org)

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