Skip to content

Commit 555dc81

Browse files
chenyangkangchenyangkang
committed
update mkdocs #33 
1 parent 67f7efd commit 555dc81

32 files changed

+208
-56
lines changed

‎docs/API_Documentation/stemflow.gridding.QTree.md ‎docs/API_Documentation/gridding/stemflow.gridding.QTree.md

File renamed without changes.

‎docs/API_Documentation/stemflow.gridding.Q_blocks.md ‎docs/API_Documentation/gridding/stemflow.gridding.Q_blocks.md

File renamed without changes.

‎docs/API_Documentation/stemflow.gridding.QuadGrid.md ‎docs/API_Documentation/gridding/stemflow.gridding.QuadGrid.md

File renamed without changes.

‎docs/API_Documentation/gridding/stemflow.gridding.Sphere_QTree.md

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# stemflow.gridding.Sphere_QTree
2+
3+
::: stemflow.gridding.Sphere_QTree

‎docs/API_Documentation/stemflow.model.AdaSTEM.md ‎docs/API_Documentation/model/stemflow.model.AdaSTEM.md

File renamed without changes.

‎docs/API_Documentation/stemflow.model.Hurdle.md ‎docs/API_Documentation/model/stemflow.model.Hurdle.md

File renamed without changes.

‎docs/API_Documentation/stemflow.model.STEM.md ‎docs/API_Documentation/model/stemflow.model.STEM.md

File renamed without changes.

‎docs/API_Documentation/model/stemflow.model.SphereAdaSTEM.md

+4
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
# stemflow.model.SphereAdaSTEM
2+
---
3+
::: stemflow.model.SphereAdaSTEM
4+
---

‎docs/API_Documentation/stemflow.model.dummy_model.md ‎docs/API_Documentation/model/stemflow.model.dummy_model.md

File renamed without changes.

‎docs/API_Documentation/stemflow.model.special_hurdle.md ‎docs/API_Documentation/model/stemflow.model.special_hurdle.md

File renamed without changes.

‎docs/API_Documentation/stemflow.model.static_func_AdaSTEM.md ‎docs/API_Documentation/model/stemflow.model.static_func_AdaSTEM.md

File renamed without changes.

‎docs/API_Documentation/utils/jitterrotation/stemflow.utils.jitterrotation.jitterrotator.md

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
# stemflow.utils.jitterrotation.jitterrotator
2+
3+
---
4+
::: stemflow.utils.jitterrotation.jitterrotator
5+
---

‎docs/API_Documentation/utils/sphere/stemflow.utils.sphere.Icosahedron.md

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
# stemflow.utils.sphere.Icosahedron
2+
3+
---
4+
::: stemflow.utils.sphere.Icosahedron
5+
---

‎docs/API_Documentation/utils/sphere/stemflow.utils.sphere.coordinate_transform.md

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# stemflow.utils.sphere.coordinate_transform
2+
3+
::: stemflow.utils.sphere.coordinate_transform

‎docs/API_Documentation/utils/sphere/stemflow.utils.sphere.discriminant_formula.md

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# stemflow.utils.sphere.discriminant_formula
2+
3+
::: stemflow.utils.sphere.discriminant_formula

‎docs/API_Documentation/utils/sphere/stemflow.utils.sphere.distance.md

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# stemflow.utils.sphere.distance
2+
3+
::: stemflow.utils.sphere.distance

‎docs/API_Documentation/stemflow.utils.generate_soft_colors.md ‎docs/API_Documentation/utils/stemflow.utils.generate_soft_colors.md

File renamed without changes.

‎docs/API_Documentation/stemflow.utils.plot_gif.md ‎docs/API_Documentation/utils/stemflow.utils.plot_gif.md

File renamed without changes.

‎docs/API_Documentation/stemflow.utils.quadtree.md ‎docs/API_Documentation/utils/stemflow.utils.quadtree.md

File renamed without changes.

‎docs/API_Documentation/utils/stemflow.utils.sphere_quadtree.md

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
# stemflow.utils.sphere_quadtree
2+
3+
---
4+
::: stemflow.utils.sphere_quadtree
5+
---

‎docs/API_Documentation/utils/stemflow.utils.validation.md

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
# stemflow.utils.validation
2+
3+
---
4+
::: stemflow.utils.validation
5+
---

‎docs/API_Documentation/utils/stemflow.utils.wrapper.md

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
# stemflow.utils.wrapper
2+
3+
---
4+
::: stemflow.utils.wrapper
5+
---

‎docs/Sphere_gridding.html

+71
Large diffs are not rendered by default.

‎docs/Sphere_gridding.png

272 KB
Loading

‎docs/index.md

+69-43
Original file line numberDiff line numberDiff line change
@@ -57,57 +57,75 @@ For more information, please see [an introduction to stemflow](https://chenyangk
5757
-----
5858

5959
## Model and data :slot_machine:
60-
60+
<!--
6161
| Main functionality of `stemflow` | Supported data types | Supported tasks | Supported base models |
6262
| -- | -- | -- | -- |
63-
| :white_check_mark: Spatiotemporal modeling & prediction<br> | :white_check_mark: All spatial indexing (CRS)<br> | :white_check_mark: Binary classification task<br> | :white_check_mark: sklearn style `BaseEstimator` classes ([you can make your own base model](https://scikit-learn.org/stable/developers/develop.html)), for example [here](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)<br> |
64-
| :white_check_mark: Calculate overall feature importances<br> | :white_check_mark: All temporal indexing<br> | :white_check_mark: Regression task<br> | :white_check_mark: sklearn style Maxent model. [Example here](https://chenyangkang.github.io/stemflow/Examples/03.Binding_with_Maxent.html). |
63+
| :white_check_mark: Spatiotemporal modeling & prediction<br> | :white_check_mark: User-defined 2D spatial indexing (CRS)<br> | :white_check_mark: Binary classification task<br> | :white_check_mark: sklearn style `BaseEstimator` classes ([you can make your own base model](https://scikit-learn.org/stable/developers/develop.html)), for example [here](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)<br> |
64+
| :white_check_mark: Calculate overall feature importances<br> | :white_check_mark: User-defined temporal indexing<br> | :white_check_mark: Regression task<br> | :white_check_mark: sklearn style Maxent model. [Example here](https://chenyangkang.github.io/stemflow/Examples/03.Binding_with_Maxent.html). |
6565
| :white_check_mark: Plot spatiotemporal dynamics<br> | :white_check_mark: Spatial-only modeling<br> | :white_check_mark: Hurdle task (two step regression – classify then regress the non-zero part)<br> | |
6666
| | :white_check_mark: Both continuous and categorical features (prefer one-hot encoding)<br> | | |
6767
| | :white_check_mark: Both static (e.g., yearly mean temperature) and dynamic features (e.g., daily temperature) | | |
6868
| For details see [AdaSTEM Demo](https://chenyangkang.github.io/stemflow/Examples/01.AdaSTEM_demo.html) | For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html) | For details and tips see [Tips for different tasks](https://chenyangkang.github.io/stemflow/Tips/Tips_for_different_tasks.html) | For details see [Base model choices](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)|
69+
-->
70+
71+
| Main functionality of `stemflow` | Supported indexing | Supported tasks |
72+
| :-- | :-- | :-- |
73+
| :white_check_mark: Spatiotemporal modeling & prediction<br> | :white_check_mark: User-defined 2D spatial indexing (CRS)<br> | :white_check_mark: Binary classification task<br> |
74+
| :white_check_mark: Calculate overall feature importances<br> | :white_check_mark: Spherical indexing <br> | :white_check_mark: Regression task<br> |
75+
| :white_check_mark: Plot spatiotemporal dynamics<br> | :white_check_mark: User-defined temporal indexing<br> | :white_check_mark: Hurdle task (two step regression – classify then regress the non-zero part)<br> |
76+
| | :white_check_mark: Spatial-only modeling<br> | |
77+
| For details see [AdaSTEM Demo](https://chenyangkang.github.io/stemflow/Examples/01.AdaSTEM_demo.html) | For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html) | For details and tips see [Tips for different tasks](https://chenyangkang.github.io/stemflow/Tips/Tips_for_different_tasks.html) |
78+
79+
80+
<!-- column 1 -->
81+
<!-- | Main functionality of `stemflow`
82+
| --
83+
| :white_check_mark: Spatiotemporal modeling & prediction<br>
84+
| :white_check_mark: Calculate overall feature importances<br>
85+
| :white_check_mark: Plot spatiotemporal dynamics<br>
86+
| For details see [AdaSTEM Demo](https://chenyangkang.github.io/stemflow/Examples/01.AdaSTEM_demo.html) -->
87+
88+
89+
<!-- column 2 -->
90+
<!-- | Supported indexing
91+
| --
92+
| :white_check_mark: User-defined 2D spatial indexing (CRS)<br>
93+
| :white_check_mark: Spherical indexing <br>
94+
| :white_check_mark: User-defined temporal indexing<br>
95+
| :white_check_mark: Spatial-only modeling<br>
96+
| For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html) -->
97+
98+
<!-- column 3 -->
99+
<!-- | Supported tasks
100+
| --
101+
| :white_check_mark: Binary classification task<br>
102+
| :white_check_mark: Regression task<br>
103+
| :white_check_mark: Hurdle task (two step regression – classify then regress the non-zero part)<br>
104+
| For details and tips see [Tips for different tasks](https://chenyangkang.github.io/stemflow/Tips/Tips_for_different_tasks.html) -->
105+
106+
107+
| Supported data types | Supported base models |
108+
| -- | -- |
109+
| :white_check_mark: Both continuous and categorical features (prefer one-hot encoding)<br> | :white_check_mark: sklearn style `BaseEstimator` classes ([you can make your own base model](https://scikit-learn.org/stable/developers/develop.html)), for example [here](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)<br> |
110+
| :white_check_mark: Both static (e.g., yearly mean temperature) and dynamic features (e.g., daily temperature)<br> | :white_check_mark: sklearn style Maxent model. [Example here](https://chenyangkang.github.io/stemflow/Examples/03.Binding_with_Maxent.html). |
111+
| For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html) | For details see [Base model choices](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html) |
112+
113+
<!-- column 4 -->
114+
<!-- | Supported data types
115+
| --
116+
| :white_check_mark: Both continuous and categorical features (prefer one-hot encoding)<br>
117+
| :white_check_mark: Both static (e.g., yearly mean temperature) and dynamic features (e.g., daily temperature)<br>
118+
| For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html) -->
119+
120+
121+
<!-- column 5 -->
122+
<!-- | Supported base models
123+
| --
124+
| :white_check_mark: sklearn style `BaseEstimator` classes ([you can make your own base model](https://scikit-learn.org/stable/developers/develop.html)), for example [here](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)<br>
125+
| :white_check_mark: sklearn style Maxent model. [Example here](https://chenyangkang.github.io/stemflow/Examples/03.Binding_with_Maxent.html).
126+
| For details see [Base model choices](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html) -->
69127

70-
<!-- For details see [AdaSTEM Demo](https://chenyangkang.github.io/stemflow/Examples/01.AdaSTEM_demo.html) -->
71-
72-
73-
<!-- ### Main functionality of `stemflow`
74-
75-
:white_check_mark: Spatiotemporal modeling & prediction<br>
76-
:white_check_mark: Calculate overall feature importances<br>
77-
:white_check_mark: Plot spatiotemporal dynamics<br>
78-
79-
For details see [AdaSTEM Demo](https://chenyangkang.github.io/stemflow/Examples/01.AdaSTEM_demo.html)
80-
81-
---
82-
83-
### Supported data types
84-
85-
:white_check_mark: All spatial indexing (CRS)<br>
86-
:white_check_mark: All temporal indexing<br>
87-
:white_check_mark: Spatial-only modeling<br>
88-
:white_check_mark: Both continuous and categorical features (prefer one-hot encoding)<br>
89-
:white_check_mark: Both static (e.g., yearly mean temperature) and dynamic features (e.g., daily temperature)
90-
91-
For details and tips see [Tips for data types](https://chenyangkang.github.io/stemflow/Tips/Tips_for_data_types.html)
92-
93-
--- -->
94-
95-
<!-- ### Supported tasks
96128

97-
:white_check_mark: Binary classification task<br>
98-
:white_check_mark: Regression task<br>
99-
:white_check_mark: Hurdle task (two step regression – classify then regress the non-zero part)<br>
100-
101-
For details and tips see [Tips for different tasks](https://chenyangkang.github.io/stemflow/Tips/Tips_for_different_tasks.html)
102-
103-
---
104-
105-
### Supported base models
106-
107-
:white_check_mark: sklearn style `BaseEstimator` classes ([you can make your own base model](https://scikit-learn.org/stable/developers/develop.html)), for example [here](https://chenyangkang.github.io/stemflow/Examples/06.Base_model_choices.html)<br>
108-
:white_check_mark: sklearn style Maxent model. [Example here](https://chenyangkang.github.io/stemflow/Examples/03.Binding_with_Maxent.html).
109-
110-
----- -->
111129

112130
## Usage :star:
113131

@@ -175,6 +193,14 @@ model.gridding_plot
175193

176194
Here, each color shows an ensemble generated during model fitting. In each of the 10 ensembles, regions (in terms of space and time) with more training samples were gridded into finer resolution, while the sparse one remained coarse. Prediction results were aggregated across the ensembles (that is, in this example, data were modeled 10 times).
177195

196+
If you use `SphereAdaSTEM` module, the gridding plot is a `plotly` generated interactive object by default:
197+
198+
![Sphere Gridding](https://github.com/chenyangkang/stemflow/raw/main/docs/Sphere_gridding.png)
199+
200+
See ![Interactive spherical gridding plot](https://github.com/chenyangkang/stemflow/raw/main/docs/Sphere_gridding.html).
201+
202+
203+
178204
----
179205
## Example of visualization :world_map:
180206

‎docs/test.json

-1
This file was deleted.

‎mkdocs.yml

+25-12
Original file line numberDiff line numberDiff line change
@@ -86,22 +86,35 @@ nav:
8686
- 'Tips for different tasks': Tips/Tips_for_different_tasks.md
8787
- API Documentation:
8888
- stemflow.model:
89-
- 'AdaSTEM': API_Documentation/stemflow.model.AdaSTEM.md
90-
- 'STEM': API_Documentation/stemflow.model.STEM.md
91-
- 'static_func_AdaSTEM': API_Documentation/stemflow.model.static_func_AdaSTEM.md
92-
- 'Hurdle': API_Documentation/stemflow.model.Hurdle.md
93-
- 'dummy_model': API_Documentation/stemflow.model.dummy_model.md
94-
- 'special_hurdle': API_Documentation/stemflow.model.special_hurdle.md
89+
- 'AdaSTEM': API_Documentation/model/stemflow.model.AdaSTEM.md
90+
- 'SphereAdaSTEM': API_Documentation/model/stemflow.model.SphereAdaSTEM.md
91+
- 'STEM': API_Documentation/model/stemflow.model.STEM.md
92+
- 'static_func_AdaSTEM': API_Documentation/model/stemflow.model.static_func_AdaSTEM.md
93+
- 'Hurdle': API_Documentation/model/stemflow.model.Hurdle.md
94+
- 'dummy_model': API_Documentation/model/stemflow.model.dummy_model.md
95+
- 'special_hurdle': API_Documentation/model/stemflow.model.special_hurdle.md
9596
- stemflow.gridding:
96-
- 'Q_blocks': API_Documentation/stemflow.gridding.Q_blocks.md
97-
- 'QTree': API_Documentation/stemflow.gridding.QTree.md
98-
- 'QuadGrid': API_Documentation/stemflow.gridding.QuadGrid.md
97+
- 'Q_blocks': API_Documentation/gridding/stemflow.gridding.Q_blocks.md
98+
- 'QTree': API_Documentation/gridding/stemflow.gridding.QTree.md
99+
- 'Sphere_QTree': API_Documentation/gridding/stemflow.gridding.Sphere_QTree.md
100+
- 'QuadGrid': API_Documentation/gridding/stemflow.gridding.QuadGrid.md
99101
- stemflow.utils:
100-
- 'quadtree': API_Documentation/stemflow.utils.quadtree.md
101-
- 'plot_gif': API_Documentation/stemflow.utils.plot_gif.md
102-
- 'generate_soft_colors': API_Documentation/stemflow.utils.generate_soft_colors.md
102+
- 'jitterrotation':
103+
- 'jitterrotator': API_Documentation/utils/jitterrotation/stemflow.utils.jitterrotation.jitterrotator.md
104+
- 'sphere':
105+
- 'coordinate_transform': API_Documentation/utils/sphere/stemflow.utils.sphere.coordinate_transform.md
106+
- 'discriminant_formula': API_Documentation/utils/sphere/stemflow.utils.sphere.discriminant_formula.md
107+
- 'distance': API_Documentation/utils/sphere/stemflow.utils.sphere.distance.md
108+
- 'Icosahedron': API_Documentation/utils/sphere/stemflow.utils.sphere.Icosahedron.md
109+
- 'quadtree': API_Documentation/utils/stemflow.utils.quadtree.md
110+
- 'sphere_quadtree': API_Documentation/utils/stemflow.utils.sphere_quadtree.md
111+
- 'plot_gif': API_Documentation/utils/stemflow.utils.plot_gif.md
112+
- 'generate_soft_colors': API_Documentation/utils/stemflow.utils.generate_soft_colors.md
113+
- 'validation': API_Documentation/utils/stemflow.utils.validation.md
114+
- 'wrapper': API_Documentation/utils/stemflow.utils.wrapper.md
103115
- stemflow.model_selection: API_Documentation/stemflow.model_selection.md
104116
- stemflow.manually_testing: API_Documentation/stemflow.manually_testing.md
117+
105118
- Fun Visualization:
106119
- 'Global Bird Diversity': Fun_Visualization/Global_Bird_Shannon_H_Index.md
107120
- 'Ruby-crowned_Kinglet': Fun_Visualization/Ruby-crowned_Kinglet_2020.md

‎stemflow/.DS_Store

0 Bytes
Binary file not shown.

‎stemflow/model/STEM.py

+1
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@ class STEM(AdaSTEM):
1515
1616
Children:
1717
stemflow.model.STEM.STEMClassifier
18+
1819
stemflow.model.STEM.STEMRegressor
1920
2021
"""

‎stemflow/model/SphereAdaSTEM.py

+1
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,7 @@ class SphereAdaSTEM(AdaSTEM):
4343
4444
Children:
4545
stemflow.model.SphereAdaSTEM.SphereAdaSTEMClassifier
46+
4647
stemflow.model.SphereAdaSTEM.SphereAdaSTEMRegressor
4748
4849
"""

‎stemflow/utils/jitterrotation/__init__.py

Whitespace-only changes.

‎stemflow/utils/sphere/__init__.py

Whitespace-only changes.

0 commit comments

Comments
 (0)