fonnesbeck's Gists

Last active 2014-04-08

Sao Paulo SIR model in PyMC 2

      
            from pymc import *
 
# Deterministic duration of infection (2 weeks)
delta = 14.
gamma = 1./delta
 
def sir():
    
    # Early case-detection probability
    theta = Beta('theta', 1, 1, value=[0.5, 0.9])

fonnesbeck / kernel_regression.py

Last active 2014-04-03

Kernel regression using Theano

View kernel_regression.py

      
            """ 
Implementation of kernel regression: 
""" 
 
from pylearn.old_dataset.learner import OfflineLearningAlgorithm 
from theano import tensor as T 
from theano.tensor.nnet import prepend_1_to_each_row 
from theano.scalar import as_scalar 
from common.autoname import AutoName 
import theano

fonnesbeck / Bimodal-bilateral Analysis.ipynb

Created 2014-04-03

View Bimodal-bilateral Analysis.ipynb

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fonnesbeck / 0_reuse_code.js

Created 2014-04-02 — forked from jookyboi/0_reuse_code.js

Here are some things you can do with Gists in GistBox.

View 0_reuse_code.js

      
            // Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

fonnesbeck / ELSO Survival.ipynb

Last active 2014-04-01

View ELSO Survival.ipynb

      
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fonnesbeck / test_pymc.ipynb

Created 2014-03-24

View test_pymc.ipynb

      
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fonnesbeck / Sau Paulo Measles.ipynb

Last active 2014-03-21

View Sau Paulo Measles.ipynb

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fonnesbeck / Epidemiology.ipynb

Created 2014-03-18

Epidemiology paper summaries

View Epidemiology.ipynb

      
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fonnesbeck / sir.py

Created 2014-03-05

Hierarchical disease dynamics model

View sir.py

      
            # =======================================
# = Hierarchical disease dynamics model =
# =======================================
 
# Methods taken from: Zipkin, E.F., Jennelle, C.S. and Cooch, E.G. 2010. A primer on the
# application of Markov chains to the study of wildlife disease dynamics. Methods in Ecology
# and Evolution. 1: 192-198
 
from numpy import *
from pymc import *

fonnesbeck / ELSO Database.ipynb

Created 2014-03-04

ELSO Database Summary

View ELSO Database.ipynb

      
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Chris Fonnesbeck fonnesbeck