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1 change: 1 addition & 0 deletions docs/Makefile
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clean:
rm -rf $(BUILDDIR)/*
rm -rf .jupyter_cache

html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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# Community

```{toctree}
:caption: CLAM Community
:maxdepth: 1
:hidden:

Website <https://clam-community.github.io/>
```

```{toctree}
:caption: GitHub
:maxdepth: 1
:hidden:

Discussions <https://github.com/Parcels-code/parcels/discussions>
Issues <https://github.com/Parcels-code/parcels/issues>
```

```{toctree}
:caption: Community examples
:maxdepth: 1
:hidden:

Repository <https://github.com/Parcels-code/parcels_contributions>
```

Parcels users and developers interact in a vibrant community on a few different platforms. Check out the cards below to see how you can interact with us.

`````{grid} 1 2 2 2
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Curious to see if someone has already written the custom `Kernel` you are thinking of or runs **Parcels** with the same hydrodynamic data? Check out the parcels_contributions repository and share examples with other users!

```{image} https://img.shields.io/badge/maintainer_needed-red
:width: 40%
```

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```{button-link} https://github.com/Parcels-code/parcels_contributions
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Share custom Parcels code
```
````
````{grid-item-card} Lagrangian Diagnostics
:img-top: ../_static/LAdiag-logo.svg
:shadow: md
`````

Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses.
(analysis-code)=

+++
## Analysis code

```{button-link} https://lagrangian-diags.readthedocs.io/en/latest/
:click-parent:
:color: secondary
:expand:
The following is an alphabetically sorted list of tools for analysing Lagrangian trajectory output:

Visit Lagrangian Diagnostics
```
````
`````
- [Lagrangian Diagnostics](https://lagrangian-diags.readthedocs.io/en/latest/) (![maintainer needed](https://img.shields.io/badge/maintainer_needed-red)): Are you interested in advanced analysis and diagnostics of Parcels output or Lagrangian trajectories in general? The Lagrangian Diagnostics project provides code and descriptions of different analyses.
- [Lagrangian Trajectories Toolbox](https://github.com/oj-tooth/lt_toolbox): A Python library dedicated to the post-processing, visualisation and analysis of Lagrangian particle trajectories. This library assumes trajectories are stored as tabular output (e..g, Parquet or CSV).
- [TrajAn](https://github.com/OpenDrift/trajan): A Python package for analysing and plotting ocean drifter and trajectory data stored, developed as part of the OpenDrift project. This library assumes trajectories are stored as CF-compliant Netcdf/Zarr output.

## Projects that use Parcels

The following is an alphabetically sorted list of projects that use Parcels:

- [LOCATE](https://github.com/UPC-LOCATE/LOCATE/): A collection of numerical tools developed within LOCATE ESA-funded project to build simulations of plastic particle dispersion in nearshore water.
- [PlasticParcels](https://github.com/Parcels-code/plasticparcels): A tool - based on Parcels - providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties.
- [pyPlume](https://github.com/jerukan/PyPlume): A collection of notebooks and methods made unifying the process of loading two-dimensional oceanic current vector fields from models and observations, simulating trajectory models, and analyzing and visualizing particle trajectories.
- [VirtualFleet](https://github.com/euroargodev/VirtualFleet): Make and analyse simulations of virtual Argo float trajectories
- [VirtualShip](https://virtualship.parcels-code.org/): A framework to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments.

## Other Lagrangian software

The following is an alphabetically sorted list of other Lagrangian ocean modelling and analysis software:
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Again, make these cards?


- [connectivity-modeling-system (CMS)](https://github.com/beatrixparis/connectivity-modeling-system)
- [Drifters.jl](https://github.com/JuliaClimate/Drifters.jl)
- [oceantracker](https://github.com/oceantracker/oceantracker)
- [OpenDrift](https://github.com/OpenDrift/opendrift)
- [TrackMPD](https://github.com/IJalonRojas/TrackMPD)
- [TRACMASS](https://www.tracmass.org/)
2 changes: 1 addition & 1 deletion docs/getting_started/explanation_concepts.md
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To analyse the particle data generated in the simulation, we need to define a `parcels.ParticleFile` and add it as an argument to `parcels.ParticleSet.execute()`. The output will be written in a [zarr format](https://zarr.readthedocs.io/en/stable/), which can be opened as an `xarray.Dataset`. The dataset will contain the particle data with at least `time`, `z`, `lat` and `lon`, for each particle at timesteps defined by the `outputdt` argument.

There are many ways to analyze particle output, and although we provide [a short tutorial to get started](./tutorial_output.ipynb), we recommend writing your own analysis code and checking out other projects such as [trajan](https://opendrift.github.io/trajan/index.html) and [Lagrangian Diagnostics](https://lagrangian-diags.readthedocs.io/en/latest/).
There are many ways to analyze particle output, and although we provide [a short tutorial to get started](./tutorial_output.ipynb), we recommend writing your own analysis code and checking out [related Lagrangian analysis projects in our community page](../community/index.md#analysis-code).

```{admonition} 🖥️ Learn how to run a simulation
:class: seealso
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