feat: landscape-species and land use regression examples

Author: martibosch

docs/api.md

@@ -1,20 +1,6 @@
 # API
 
-## Computing features
-
 ```{eval-rst}
-.. autoclass:: focalpy.MultiScaleFeatureComputer
+.. autoclass:: focalpy.FocalAnalysis
    :members:
 ```
-
-## Standalone topographic functions
-
-```{eval-rst}
-.. autofunction:: focalpy.topo.compute_terrain_attribute
-
-.. autofunction:: focalpy.topo.northness
-
-.. autofunction:: focalpy.topo.comparative_height_at_center
-
-.. autofunction:: focalpy.topo.flow_accumulation_at_center
-```

docs/conf.py

@@ -76,6 +76,9 @@ def run(self, **kwargs):
 
 # do NOT execute notebooks
 nbsphinx_execute = "never"
+# do NOT add ".ipynb" to source suffixes
+# see https://github.com/spatialaudio/nbsphinx/issues/310
+source_suffix = [".md", ".rst"]
 
 # theme
 html_theme = "pydata_sphinx_theme"

docs/index.md

@@ -4,7 +4,6 @@ hidden:
 maxdepth: 1
 ---
 
-overview
 user-guide/introduction
 api
 contributing

docs/references.bib

@@ -6,6 +6,26 @@ @article{brennen2002focal
   year={2002}
 }
 
+@incollection{band2005heterogeneity,
+  title={Heterogeneity in urban ecosystems: patterns and process},
+  author={Band, Larry E and Cadenasso, Mary L and Grimmond, C Susan and Grove, J Morgan and Pickett, Steward TA},
+  booktitle={Ecosystem function in heterogeneous landscapes},
+  pages={257--278},
+  year={2005},
+  publisher={Springer}
+}
+
+@article{cadenasso2007spatial,
+  title={Spatial heterogeneity in urban ecosystems: reconceptualizing land cover and a framework for classification},
+  author={Cadenasso, Mary L and Pickett, Steward TA and Schwarz, Kirsten},
+  journal={Frontiers in Ecology and the Environment},
+  volume={5},
+  number={2},
+  pages={80--88},
+  year={2007},
+  publisher={Wiley Online Library}
+}
+
 @article{hoek2008review,
   title={A review of land-use regression models to assess spatial variation of outdoor air pollution},
   author={Hoek, Gerard and Beelen, Rob and De Hoogh, Kees and Vienneau, Danielle and Gulliver, John and Fischer, Paul and Briggs, David},
@@ -28,6 +48,17 @@ @article{jackson2012size
   publisher={Springer}
 }
 
+@article{dormann2013collinearity,
+  title={Collinearity: a review of methods to deal with it and a simulation study evaluating their performance},
+  author={Dormann, Carsten F and Elith, Jane and Bacher, Sven and Buchmann, Carsten and Carl, Gudrun and Carr{\'e}, Gabriel and Marqu{\'e}z, Jaime R Garc{\'\i}a and Gruber, Bernd and Lafourcade, Bruno and Leit{\~a}o, Pedro J and others},
+  journal={Ecography},
+  volume={36},
+  number={1},
+  pages={27--46},
+  year={2013},
+  publisher={Wiley Online Library}
+}
+
 @article{pasher2013optimizing,
   title={Optimizing landscape selection for estimating relative effects of landscape variables on ecological responses},
   author={Pasher, Jon and Mitchell, Scott W and King, Douglas J and Fahrig, Lenore and Smith, Adam C and Lindsay, Kathryn E},
@@ -39,6 +70,16 @@ @article{pasher2013optimizing
   publisher={Springer}
 }
 
+@article{zhang2013hierarchical,
+  title={A hierarchical patch mosaic ecosystem model for urban landscapes: model development and evaluation},
+  author={Zhang, Chi and Wu, Jianguo and Grimm, Nancy B and McHale, Melissa and Buyantuyev, Alexander},
+  journal={Ecological modelling},
+  volume={250},
+  pages={81--100},
+  year={2013},
+  publisher={Elsevier}
+}
+
 @misc{jackson2015ecologists,
   title={Are ecologists conducting research at the optimal scale?},
   author={Jackson, Heather Bird and Fahrig, Lenore},
@@ -50,6 +91,69 @@ @misc{jackson2015ecologists
   publisher={Wiley Online Library}
 }
 
+@article{schindler2015performance,
+  title={Performance of methods to select landscape metrics for modelling species richness},
+  author={Schindler, Stefan and von Wehrden, Henrik and Poirazidis, Kostas and Hochachka, Wesley M and Wrbka, Thomas and Kati, Vassiliki},
+  journal={Ecological Modelling},
+  volume={295},
+  pages={107--112},
+  year={2015},
+  publisher={Elsevier}
+}
+
+@article{aronson2017biodiversity,
+  title={Biodiversity in the city: key challenges for urban green space management},
+  author={Aronson, Myla FJ and Lepczyk, Christopher A and Evans, Karl L and Goddard, Mark A and Lerman, Susannah B and MacIvor, J Scott and Nilon, Charles H and Vargo, Timothy},
+  journal={Frontiers in Ecology and the Environment},
+  volume={15},
+  number={4},
+  pages={189--196},
+  year={2017},
+  publisher={Wiley Online Library}
+}
+
+@article{riitters2019pattern,
+  title={Pattern metrics for a transdisciplinary landscape ecology},
+  author={Riitters, Kurt},
+  journal={Landscape Ecology},
+  volume={34},
+  number={9},
+  pages={2057--2063},
+  year={2019},
+  publisher={Springer}
+}
+
+@article{fournier2020origin,
+  title={The origin of urban communities: From the regional species pool to community assemblages in city},
+  author={Fournier, Bertrand and Frey, David and Moretti, Marco},
+  journal={Journal of Biogeography},
+  volume={47},
+  number={3},
+  pages={615--629},
+  year={2020},
+  publisher={Wiley Online Library}
+}
+
+@article{casanelles2021applying,
+  title={Applying predictive models to study the ecological properties of urban ecosystems: A case study in Z{\"u}rich, Switzerland},
+  author={Casanelles-Abella, Joan and Chauvier, Yohann and Zellweger, Florian and Villiger, Petrissa and Frey, David and Ginzler, Christian and Moretti, Marco and Pellissier, Lo{\"\i}c},
+  journal={Landscape and Urban Planning},
+  volume={214},
+  pages={104137},
+  year={2021},
+  publisher={Elsevier}
+}
+
+@article{effrosynidis2021evaluation,
+  title={An evaluation of feature selection methods for environmental data},
+  author={Effrosynidis, Dimitrios and Arampatzis, Avi},
+  journal={Ecological Informatics},
+  volume={61},
+  pages={101224},
+  year={2021},
+  publisher={Elsevier}
+}
+
 @article{giuliani2022downscaling,
   title={Downscaling Switzerland land use/land cover data using nearest neighbors and an expert system},
   author={Giuliani, Gregory and Rodila, Denisa and K{\"u}lling, Nathan and Maggini, Ramona and Lehmann, Anthony},

docs/user-guide/a01-data.ipynb

@@ -0,0 +1,13 @@
+# User guide
+
+```{toctree}
+---
+hidden:
+maxdepth: 1
+---
+
+landscape-species-inference
+land-use-regression
+spatial-predictors
+a01-data
+```