spotpy

A Statistical Parameter Optimization Framework for Python

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Purpose

SPOTPY is a Python tool that enables the use of Computational optimization techniques for calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model. The package is puplished in the open source journal PLoS One:

Houska, T., Kraft, P., Chamorro-Chavez, A. and Breuer, L.: SPOTting Model Parameters Using a Ready-Made Python Package, PLoS ONE, 10(12), e0145180, doi:10.1371/journal.pone.0145180, 2015

The simplicity and flexibility enables the use and test of different algorithms of almost any model, without the need of complex codes::

sampler = spotpy.algorithms.sceua(model_setup())     # Initialize your model with a setup file
sampler.sample(10000)                                # Run the model
results = sampler.getdata()                          # Load the results
spotpy.analyser.plot_parametertrace(results)         # Show the results

Features

Complex algorithms bring complex tasks to link them with a model. We want to make this task as easy as possible. Some features you can use with the SPOTPY package are:

• Fitting models to evaluation data with different algorithms. Available algorithms are:

  • Monte Carlo (MC)
  • Markov-Chain Monte-Carlo (MCMC)
  • Maximum Likelihood Estimation (MLE)
  • Latin-Hypercube Sampling (LHS)
  • Simulated Annealing (SA)
  • Shuffled Complex Evolution Algorithm (SCE-UA)
  • Differential Evolution Adaptive Metropolis Algorithm (DE-MCz)
  • RObust Parameter Estimation (ROPE).
  • Fourier Amplitude Sensitivity Test (FAST)
  • Artificial Bee Colony (ABC)
  • Fitness Scaled Chaotic Artificial Bee Colony (FSCABC)

• Wide range of objective functions (also known as loss function, fitness function or energy function) to validate the sampled results. Available functions are

  • Bias
  • PBias
  • Nash-Sutcliff (NSE)
  • logarithmic Nash-Sutcliff (logNSE)
  • logarithmic probability (logp)
  • Correlation Coefficient (r)
  • Coefficient of Determination (r^2)
  • Mean Squared Error (MSE)
  • Root Mean Squared Error (RMSE)
  • Mean Absolute Error (MAE)
  • Relative Root Mean Squared Error (RRMSE)
  • Agreement Index (AI)
  • Covariance, Decomposed MSE (dMSE)
  • Kling-Gupta Efficiency (KGE).

• Prebuild parameter distribution functions:

  • Uniform
  • Normal
  • logNormal
  • Chisquare
  • Exponential
  • Gamma
  • Wald
  • Weilbull

• Wide range to adapt algorithms to perform uncertainty-, sensitivity analysis or calibration of a model.

• Multi-objective support

• MPI support for fast parallel computing

• A progress bar monitoring the sampling loops. Enables you to plan your coffee brakes.

• Use of NumPy functions as often as possible. This makes your coffee brakes short.

• Different databases solutions: ram storage for fast sampling a simple , csv tables the save solution for long duration samplings.

• Automatic best run selecting and plotting

• Parameter trace plotting

• Parameter interaction plot including the Gaussian-kde function

• Regression analysis between simulation and evaluation data

• Posterior distribution plot

• Convergence diagnostics with Gelman-Rubin and the Geweke plot

Install

Installing SPOTPY is easy. Just use:

pip install spotpy

Or, after downloading the source code and making sure python is in your OS path:

python setup.py install

Support

• Documentation: http://www.uni-giessen.de/cms/faculties/f09/institutes/ilr/hydro/download/spotpy

• Feel free to contact the authors of this tool for any support questions.

• Please contact the authors in case of any bug.

• If you use this package for a scientific research paper, please cite SPOTPY. It is peer-reviewed.

• Patches/enhancements and any other contributions to this package are very welcome!

Getting started

Have a look at https://github.com/thouska/spotpy/tree/master/spotpy/examples and http://fb09-pasig.umwelt.uni-giessen.de/spotpy/Tutorial/2-Rosenbrock/