Metadata-Version: 2.1
Name: sjSDM-py
Version: 0.1.1
Summary: jSDM package
Home-page: https://github.com/TheoreticalEcology/s-jSDM
Author: Maximilian Pichler
Author-email: Maximilian.Pichler@ur.de
License: UNKNOWN
Description: # sjSDM - Fast and Accurate Joint Species distribution Modeling 
        
        Currently we don't provide specifically a API for joint species distribution models. However, it's just a deep multivariate probit model with one layer (example below).
        
        We provide a R package with an API focused on JSDMs which is available [here](https://github.com/TheoreticalEcology/s-jSDM).
        
        References:
        * [Pichler, M., & Hartig, F. (2020). A new method for faster and more accurate inference of species associations from novel community data. arXiv preprint arXiv:2003.05331.](https://arxiv.org/abs/2003.05331)
        
        
        ## Install instructions
        
        Dependencies:
        * PyTorch >= 1.7, see [PyTorch](https://pytorch.org/get-started/locally/) for install instructions.
        
        ```{python}
        pip install sjSDM_py
        ```
        
        ## Example
        
        linear jSDM:
        ```{python}
        import sjSDM_py as sa
        import numpy as np
        Env = np.random.randn(100, 5)
        Occ = np.random.binomial(1, 0.5, [100, 10])
        
        model = sa.Model_base(5) # input_shape == number of environmental predictors
        model.add_layer(sa.layers.Layer_dense(hidden=10)) # number of hidden units in the layer == number of species
        model.build(df=5, optimizer=sa.optimizer_adamax(lr=0.1, weight_decay = 0.01)) # df = degree of freedom 
        model.fit(X = Env, Y = Occ)
        print(model.weights_numpy)
        print(model.get_cov())
        ```
        
        * For species intercept, use 'bias=True' in 'Layer_dense(...)'. 
        * We recommend setting 'df = number of species / 2.'
        
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
