There is an equation of exponential truncated power law in the article below:
Gonzalez, M. C., Hidalgo, C. A., & Barabasi, A. L. (2008). Understanding individual human mobility patterns. Nature, 453(7196), 779-782.
like this:
It is an exponential truncated power law. There are three parameters to be estimated: rg0, beta and K. Now we have got several users' radius of gyration(rg), and uploaded it onto Github: radius of gyrations.txt
The following codes can be used to read data and calculate P(rg):
import numpy as np
# read radius of gyration from file
rg = []
with open('/path-to-the-data/radius of gyrations.txt', 'r') as f:
for i in f:
rg.append(float(i.strip('\n')))
# calculate P(rg)
rg = sorted(rg, reverse=True)
rg = np.array(rg)
prg = np.arange(len(sorted_data)) / float(len(sorted_data)-1)
or you can directly get rg and prg data as the following:
rg = np.array([ 20.7863444 , 9.40547933, 8.70934714, 8.62690145,
7.16978087, 7.02575052, 6.45280959, 6.44755478,
5.16630287, 5.16092884, 5.15618737, 5.05610068,
4.87023561, 4.66753197, 4.41807645, 4.2635671 ,
3.54454372, 2.7087178 , 2.39016885, 1.9483156 ,
1.78393238, 1.75432688, 1.12789787, 1.02098332,
0.92653501, 0.32586582, 0.1514813 , 0.09722761,
0. , 0. ])
prg = np.array([ 0. , 0.03448276, 0.06896552, 0.10344828, 0.13793103,
0.17241379, 0.20689655, 0.24137931, 0.27586207, 0.31034483,
0.34482759, 0.37931034, 0.4137931 , 0.44827586, 0.48275862,
0.51724138, 0.55172414, 0.5862069 , 0.62068966, 0.65517241,
0.68965517, 0.72413793, 0.75862069, 0.79310345, 0.82758621,
0.86206897, 0.89655172, 0.93103448, 0.96551724, 1. ])
I can plot the P(r_g) and r_g using the following python script:
import matplotlib.pyplot as plt
%matplotlib inline
plt.plot(rg, prg, 'bs', alpha = 0.3)
# roughly estimated params:
# rg0=1.8, beta=0.15, K=5
plt.plot(rg, (rg+1.8)**-.15*np.exp(-rg/5))
plt.yscale('log')
plt.xscale('log')
plt.xlabel('$r_g$', fontsize = 20)
plt.ylabel('$P(r_g)$', fontsize = 20)
plt.show()
How can I use these data of rgs to estimate the three parameters above? I hope to solve it using python.
According to @Michael 's suggestion, we can solve the problem using scipy.optimize.curve_fit
def func(rg, rg0, beta, K):
return (rg + rg0) ** (-beta) * np.exp(-rg / K)
from scipy import optimize
popt, pcov = optimize.curve_fit(func, rg, prg, p0=[1.8, 0.15, 5])
print popt
print pcov
The results are given below:
[ 1.04303608e+03 3.02058550e-03 4.85784945e+00]
[[ 1.38243336e+18 -6.14278286e+11 -1.14784675e+11]
[ -6.14278286e+11 2.72951900e+05 5.10040746e+04]
[ -1.14784675e+11 5.10040746e+04 9.53072925e+03]]
Then we can inspect the results by plotting the fitted curve.
%matplotlib inline
import matplotlib.pyplot as plt
plt.plot(rg, prg, 'bs', alpha = 0.3)
plt.plot(rg, (rg+popt[0])**-(popt[1])*np.exp(-rg/popt[2]) )
plt.yscale('log')
plt.xscale('log')
plt.xlabel('$r_g$', fontsize = 20)
plt.ylabel('$P(r_g)$', fontsize = 20)
plt.show()