In [5]:

    

%pylab inline


    

    




Populating the interactive namespace from numpy and matplotlib






    




WARNING: pylab import has clobbered these variables: ['gamma', 'histogram']
`%matplotlib` prevents importing * from pylab and numpy

In [6]:

    

from pyndamics import Simulation
from pyndamics.emcee import *


    

In [7]:

    

t=array([7,14,21,28,35,42,49,56,63,70,77,84],float)
h=array([17.93,36.36,67.76,98.10,131,169.5,205.5,228.3,247.1,250.5,253.8,254.5])

sim=Simulation()
sim.add("h'=a*h*(1-h/K)",1,plot=True)
sim.add_data(t=t,h=h,plot=True)
sim.params(a=1,K=500)
sim.run(0,90)

# fig=sim.figures[0]
# fig.savefig('sunflower_logistic1.pdf')
# fig.savefig('sunflower_logistic1.png')


    

    













    






<matplotlib.figure.Figure at 0x112e723d0>

In [8]:

    

model=MCMCModel(sim,
                a=Uniform(.001,5),
                K=Uniform(100,500),
                initial_h=Uniform(0,100),
                )


    

In [11]:

    

model.run_mcmc(500)
model.set_initial_values('samples')  # reset using the 16-84 percentile values from the samples
model.run_mcmc(500)


    

    




Running MCMC...
Done.
23.89 s
Running MCMC...
Done.
26.14 s

In [12]:

    

model.triangle_plot()


    

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