Metadata-Version: 2.1
Name: sjSDM-py
Version: 0.0.3
Summary: jSDM package
Home-page: https://github.com/TheoreticalEcology/s-jSDM
Author: Maximilian Pichler
Author-email: Maximilian.Pichler@ur.de
License: UNKNOWN
Description: # s-jSDM - Fast and accurate Joint Species Distribution Modeling
        
        ## About the method
        
        The method is described in the preprint Pichler & Hartig (2020) A new method for faster and more accurate inference of species associations from novel community data, https://arxiv.org/abs/2003.05331. The code for producing the results in this paper is available under the subfolder publications in this repo.
        
        The method itself is wrapped into an R package, available under subfolder sjSDM. You can also use it stand-alone under Python (see instructions below). Note: for both the R and the python package, python >= 3.6 and pytorch must be installed (more details below).
        ## Install instructions
        
        Dependencies:
        * PyTorch >= 1.4, see [PyTorch](https://pytorch.org/get-started/locally/) for install instructions.
        
        ```{python}
        pip install sjSDM_py
        ```
        
        ## Example
        
        
        ```python
        import sjSDM_py as fa
        import numpy as np
        import torch
        Env = np.random.randn(100, 5)
        Occ = np.random.binomial(1, 0.5, [100, 10])
        
        model = fa.Model_sjSDM(device=torch.device("cpu"), dtype=torch.float32)
        model.add_env(5, 10)
        model.build(5, optimizer=fa.optimizer_adamax(0.001),scheduler=False)
        model.fit(Env, Occ, batch_size = 20, epochs = 100)
        # print(model.weights)
        # print(model.covariance)
        ```
        
        
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
