I'm trying to calculate standard deviation for some distribution and keep getting two different results from two paths. It doesn't make much sense to me - could someone explain why is this happening?
scipy.stats.binom(189, 100/189).std()
6.8622115305451707
scipy.stats.tstd([1]*100 + [0]*89)
0.50047821327986164
Why aren't those two numbers equal?
The basic reason is that you're taking the standard deviation of two quite different things there. I think you're misunderstanding what scipy.stats.binom does. From the documentation:
The probability mass function for binom is:
binom.pmf(k) = choose(n,k) * p**k * (1-p)**(n-k)
for k in {0,1,...,n}.
binom takes n and p as shape parameters.
When you do binom(189, 100/189), you are creating a distribution that could take on any value from 0 to 189. This distribution unsurprisingly has a much larger variance than the other sample data you're using, which is restricted to values of either zero or one.
It looks like what you want would be scipy.stats.binom(1, 100/189).std(). However, you still can't expect the exact same value as what you're getting with your sample data, because the binom.std is computing the standard deviation of the overall distribution, whereas the other version (scipy.stats.tstd([1]*100 + [0]*89)) is computing the standard deviation only of a sample. If you increase the size of your sample (e.g., do scipy.stats.tstd([1]*1000 + [0]*890)), the sample standard deviation will approach the value you're getting from binom.std.
You can also get the population (not sample) std by using scipy.std or numpy.std instead of scipy.stats.tstd. scipy.stats.tstd doesn't have a ddof option to let you choose the degrees of freedom, and always computes a sample std.
Related
I was trying one Dataquest exercise and I figured out that the variance I am getting is different for the two packages.
e.g for [1,2,3,4]
from statistics import variance
import numpy as np
print(np.var([1,2,3,4]))
print(variance([1,2,3,4]))
//1.25
//1.6666666666666667
The expected answer of the exercise is calculated with np.var()
Edit
I guess it has to do that the later one is sample variance and not variance. Anyone could explain the difference?
Use this
print(np.var([1,2,3,4],ddof=1))
1.66666666667
Delta Degrees of Freedom: the divisor used in the calculation is N - ddof, where N represents the number of elements. By default, ddof is zero.
The mean is normally calculated as x.sum() / N, where N = len(x). If, however, ddof is specified, the divisor N - ddof is used instead.
In standard statistical practice, ddof=1 provides an unbiased estimator of the variance of a hypothetical infinite population. ddof=0 provides a maximum likelihood estimate of the variance for normally distributed variables.
Statistical libraries like numpy use the variance n for what they call var or variance and the standard deviation
For more information refer this documentation : numpy doc
It is correct that dividing by N-1 gives an unbiased estimate for the mean, which can give the impression that dividing by N-1 is therefore slightly more accurate, albeit a little more complex. What is too often not stated is that dividing by N gives the minimum variance estimate for the mean, which is likely to be closer to the true mean than the unbiased estimate, as well as being somewhat simpler.
I have a question:
Given mean and variance I want to calculate the probability of a sample using a normal distribution as probability basis.
The numbers are:
mean = -0.546369
var = 0.006443
curr_sample = -0.466102
prob = 1/(np.sqrt(2*np.pi*var))*np.exp( -( ((curr_sample - mean)**2)/(2*var) ) )
I get a probability which is larger than 1! I get prob = 3.014558...
What is causing this? The fact that the variance is too small messes something up? It's a totally legal input to the formula and should give something small not greater than 1! Any suggestions?
Ok, what you compute is not a probability, but a probability density (which may be larger than one). In order to get 1 you have to integrate over the normal distribution like so:
import numpy as np
mean = -0.546369
var = 0.006443
curr_sample = np.linspace(-10,10,10000)
prob = np.sum( 1/(np.sqrt(2*np.pi*var))*np.exp( -( ((curr_sample - mean)**2)/(2*var) ) ) * (curr_sample[1]-curr_sample[0]) )
print prob
witch results in
0.99999999999961509
The formula you give is a probability density, not a probability. The density formula is such that when you integrate it between two values of x, you get the probability of being in that interval. However, this means that the probability of getting any particular sample is, in fact, 0 (it's the density times the infinitesimally small dx).
So what are you actually trying to calculate? You probably want something like the probability of getting your value or larger, the so-called tail probability, which is often used in statistics (it so happens that this is given by the error function when you're talking about a normal distribution, although you need to be careful of exactly how it's defined).
When considering the bell-shaped probability distribution function (PDF) of given mean and variance, the peak value of the curve (height of mode) is 1/sqrt(2*pi*var). It is 1 for standard normal distribution (mean 0 and var 1). Hence when trying to calculate a specific value of a general normal distribution pdf, values larger than 1 are possible.
I try to convert matlab code to numpy and figured out that numpy has a different result with the std function.
in matlab
std([1,3,4,6])
ans = 2.0817
in numpy
np.std([1,3,4,6])
1.8027756377319946
Is this normal? And how should I handle this?
The NumPy function np.std takes an optional parameter ddof: "Delta Degrees of Freedom". By default, this is 0. Set it to 1 to get the MATLAB result:
>>> np.std([1,3,4,6], ddof=1)
2.0816659994661326
To add a little more context, in the calculation of the variance (of which the standard deviation is the square root) we typically divide by the number of values we have.
But if we select a random sample of N elements from a larger distribution and calculate the variance, division by N can lead to an underestimate of the actual variance. To fix this, we can lower the number we divide by (the degrees of freedom) to a number less than N (usually N-1). The ddof parameter allows us change the divisor by the amount we specify.
Unless told otherwise, NumPy will calculate the biased estimator for the variance (ddof=0, dividing by N). This is what you want if you are working with the entire distribution (and not a subset of values which have been randomly picked from a larger distribution). If the ddof parameter is given, NumPy divides by N - ddof instead.
The default behaviour of MATLAB's std is to correct the bias for sample variance by dividing by N-1. This gets rid of some of (but probably not all of) of the bias in the standard deviation. This is likely to be what you want if you're using the function on a random sample of a larger distribution.
The nice answer by #hbaderts gives further mathematical details.
The standard deviation is the square root of the variance. The variance of a random variable X is defined as
An estimator for the variance would therefore be
where denotes the sample mean. For randomly selected , it can be shown that this estimator does not converge to the real variance, but to
If you randomly select samples and estimate the sample mean and variance, you will have to use a corrected (unbiased) estimator
which will converge to . The correction term is also called Bessel's correction.
Now by default, MATLABs std calculates the unbiased estimator with the correction term n-1. NumPy however (as #ajcr explained) calculates the biased estimator with no correction term by default. The parameter ddof allows to set any correction term n-ddof. By setting it to 1 you get the same result as in MATLAB.
Similarly, MATLAB allows to add a second parameter w, which specifies the "weighing scheme". The default, w=0, results in the correction term n-1 (unbiased estimator), while for w=1, only n is used as correction term (biased estimator).
For people who aren't great with statistics, a simplistic guide is:
Include ddof=1 if you're calculating np.std() for a sample taken from your full dataset.
Ensure ddof=0 if you're calculating np.std() for the full population
The DDOF is included for samples in order to counterbalance bias that can occur in the numbers.
from random import *
def main():
t = 0
for i in range(1000): # thousand
t += random()
print(t/1000)
main()
I was looking at the source code for a sample program my professor gave me and I came across this RNG. can anyone explain how this RNG works?
If you plotted the points, you would see that this actually produces a Gaussian ("normal") distribution about the mean of the random function.
Generate random numbers following a normal distribution in C/C++ talks about random number generation; it's a pretty common technique to do this if all you have is a uniform number generator like in standard C.
What I've given you here is a histogram of 100,000 values drawn from your function (of course, returned not printed, if you aren't familiar with python). The y axis is the frequency that the value appears, the x axis is the bin of the value. As you can see, the average value is 1/2, and by 3 standard deviations (99.7 percent of the data) we have almost no values in the range. That should be intuitive; we "usually" get 1/2, and very rarely get .99999
Have a look at the documentation. Its quite well written:
https://docs.python.org/2/library/random.html
The idea is that that program generates a random number 1000 times which is sufficiently enough to get mean as 0.5
The program is using the Central Limit Theorem - sums of independent and identically distributed random variables X with finite variance asymptotically converge to a normal (a.k.a. Gaussian) distribution whose mean is the sum of the means, and variance is the sum of the variances. Scaling this by N, the number of X's summed, gives the sample mean (a.k.a. average). If the expected value of X is μ and the variance of X is σ2, the expected value of the sample mean is also μ and it has variance σ2 / N.
Since a Uniform(0,1) has mean 0.5 and variance 1/12, your algorithm will generate results that are pretty close to normally distributed with a mean of 0.5 and a variance of 1/12000. Consequently 99.7% of the outcomes should fall within +/-3 standard deviations of the mean, i.e., in the range 0.5+/-0.0274.
This is a ridiculously inefficient way to generate normals. Better alternatives include the Box-Muller method, Polar method, or ziggurat method.
The thing making this random is the random() function being called. random() will generate 1 (for most practical purposes) random float between 0 and 1.
>>>random()
0.1759916412898097
>>>random()
0.5489228122596088
etc.
The rest of it is just adding each random to a total and then dividing by the number of randoms, essentially finding the average of all 1000 randoms, which as Cyber pointed out is actually not a random number at all.
This is a simple test
import numpy as np
data = np.array([-1,0,1])
print data.std()
>> 0.816496580928
I don't understand how this result been generated? Obviously:
( (1^0.5 + 1^0.5 + 0^0.5)/(3-1) )^0.5 = 1
and in matlab it gives me std([-1,0,1]) = 1. Could you help me get understand how numpy.std() works?
The crux of this problem is that you need to divide by N (3), not N-1 (2). As Iarsmans pointed out, numpy will use the population variance, not the sample variance.
So the real answer is sqrt(2/3) which is exactly that: 0.8164965...
If you happen to be trying to deliberately use a different value (than the default of 0) for the degrees of freedom, use the keyword argument ddofwith a positive value other than 0:
np.std(data, ddof=1)
... but doing so here would reintroduce your original problem as numpy will divide by N - ddof.
It is worth reading the help page for the function/method before suggesting it is incorrect. The method does exactly what the doc-string says it should be doing, divides by 3, because By default ddofis zero.:
In [3]: numpy.std?
String form: <function std at 0x104222398>
File: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/fromnumeric.py
Definition: numpy.std(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False)
Docstring:
Compute the standard deviation along the specified axis.
...
ddof : int, optional
Means Delta Degrees of Freedom. The divisor used in calculations
is ``N - ddof``, where ``N`` represents the number of elements.
By default `ddof` is zero.
When getting into NumPy from Matlab, you'll probably want to keep the docs for both handy. They're similar but often differ in small but important details. Basically, they calculate the standard deviation differently. I would strongly recommend checking the documentation for anything you use that calculates standard deviation, whether a pocket calculator or a programming language, since the default is not (sorry!) standardized.
Numpy STD: http://docs.scipy.org/doc/numpy/reference/generated/numpy.std.html
Matlab STD: http://www.mathworks.com/help/matlab/ref/std.html
The Numpy docs for std are a bit opaque, IMHO, especially considering that NumPy docs are generally fairly clear. If you read far enough: The average squared deviation is normally calculated as x.sum() / N, where N = len(x). If, however, ddof is specified, the divisor N - ddof is used instead. In standard statistical practice, ddof=1 provides an unbiased estimator of the variance of the infinite population. (In english, default is pop std dev, set ddof=1 for sample std dev).
OTOH, the Matlab docs make clear the difference that's tripping you up:
There are two common textbook definitions for the standard deviation s of a data vector X. [equations omitted] n is the number of elements in the sample. The two forms of the equation differ only in n – 1 versus n in the divisor.
So, by default, Matlab calculates the sample standard deviation (N-1 in the divisor, so bigger to compensate for the fact this is a sample) and Numpy calculates the population standard deviation (N in the divisor). You use the ddof parameter to switch to the sample standard, or any other denominator you want (which goes beyond my statistics knowledge).
Lastly, it doesn't help on this problem, but you'll probably find this helpful at some point. Link