Probability to z-score and vice versa - python

How do I calculate the z score of a p-value and vice versa?
For example if I have a p-value of 0.95 I should get 1.96 in return.
I saw some functions in scipy but they only run a z-test on an array.
I have access to numpy, statsmodel, pandas, and scipy (I think).

>>> import scipy.stats as st
>>> st.norm.ppf(.95)
1.6448536269514722
>>> st.norm.cdf(1.64)
0.94949741652589625
As other users noted, Python calculates left/lower-tail probabilities by default. If you want to determine the density points where 95% of the distribution is included, you have to take another approach:
>>>st.norm.ppf(.975)
1.959963984540054
>>>st.norm.ppf(.025)
-1.960063984540054

Starting in Python 3.8, the standard library provides the NormalDist object as part of the statistics module.
It can be used to get the zscore for which x% of the area under a normal curve lies (ignoring both tails).
We can obtain one from the other and vice versa using the inv_cdf (inverse cumulative distribution function) and the cdf (cumulative distribution function) on the standard normal distribution:
from statistics import NormalDist
NormalDist().inv_cdf((1 + 0.95) / 2.)
# 1.9599639845400536
NormalDist().cdf(1.9599639845400536) * 2 - 1
# 0.95
An explanation for the '(1 + 0.95) / 2.' formula can be found in this wikipedia section.

If you are interested in T-test, you can do similar:
z-statistics (z-score) is used when the data follows a normal distribution, population standard deviation sigma is known and the sample size is above 30. Z-Score tells you how many standard deviations from the mean your result is. The z-score is calculated using the formula:
z_score = (xbar - mu) / sigma
t-statistics (t-score), also known as Student's T-Distribution, is used when the data follows a normal distribution, population standard deviation (sigma) is NOT known, but the sample standard deviation (s) is known or can be calculated, and the sample size is below 30. T-Score tells you how many standard deviations from the mean your result is. The t-score is calculated using the formula:
t_score = (xbar - mu) / (s/sqrt(n))
Summary: If the sample sizes are larger than 30, the z-distribution and the t-distributions are pretty much the same and either one can be used. If the population standard deviation is available and the sample size is greater than 30, t-distribution can be used with the population standard deviation instead of the sample standard deviation.
teststatistics
lookuptable
lookupvalues
criticalvalue
normaldistribution
populationstandarddeviation (sigma)
samplesize
z-statistics
z-table
z-score
z-critical is z-score at a specific confidence level
yes
known
> 30
t-statistics
t-table
t-score
t-critical is t-score at a specific confidence level
yes
not known
< 30
Python Percent Point Function is used to calculate the critical values at a specific confidence level:
z-critical = stats.norm.ppf(1 - alpha) (use alpha = alpha/2 for two-sided)
t-critical = stats.t.ppf(alpha/numOfTails, ddof)
Codes
import numpy as np
from scipy import stats
# alpha to critical
alpha = 0.05
n_sided = 2 # 2-sided test
z_crit = stats.norm.ppf(1-alpha/n_sided)
print(z_crit) # 1.959963984540054
# critical to alpha
alpha = stats.norm.sf(z_crit) * n_sided
print(alpha) # 0.05

Z-score to probability :
The code snippet below maps the negative of the absolute value of the z-score to cdf of a Std Normal Distribution and multiplies by 2 . This will give the prob of finding the probability of Area1 + Area2 shaded in the picture here :
import numpy as np
from scipy.stats import norm
norm(0, 1).cdf(-np.absolute(zscore)) * 2
Ref: https://mathbitsnotebook.com/Algebra2/Statistics/STzScores.html

Related

Generating random numbers with upper and lower standard deviation of the scatter

I have to produce randomly generated, normally distributed numbers, based on an astronomical table containing a most probable value and a standard deviation. The peculiar thing is that the standard deviation is not given by one, but two numbers - an upper standard deviation of the error and a lower, something like this:
mass_object, error_up, error_down
7.33, 0.12, 0.07
9.40, 0.04, 0.02
6.01, 0.11, 0.09
...
For example, this means for the first object that if a random mass m gets generated with m<7.33, then probably it will be further away from 7.33 than in the case that m>7.33. So I am looking now for a way to randomly generate the numbers and this way has to include the 2 possible standard deviations. If I was dealing with just one standard deviation per object, I would create the random number (mass) of the first object like that:
mass_random = np.random.normal(loc=7.33, scale=0.12)
Do you have ideas how to create these random numbers with upper and lower standard deviation of the scatter? Tnx
As we discussed in the comments, a normal distribution has the same standard deviation in each direction (it's symmetric around the mean). So we know our distribution won't be normal. We can try a lognormal approach, since this allows us to introduce the idea of skewness. To do this in Python, you'll need Scipy. Here's a crude approach, assuming that 68% of data is on the mean, 16% is at the high point, and 16% is at the low point. We fit the distribution to that crude dataset, then we can calculate new points from the distribution:
import scipy.stats
# Choose one of the rows
mean, high, low = 7.33, 0.12, 0.07
# Create a dummy dataset to fit the distribution
values = [mean] * 68 + [mean + high] * 16 + [mean - low ] * 16
# Print the fit distribution
fit_dist = scipy.stats.lognorm.fit(values)
print(fit_dist)
# Calculate 10 new random values based on the fit
scipy.stats.lognorm.rvs(*fit_dist, size=10)
array([7.25541865, 7.34873107, 7.33831589, 7.36387121, 7.26912469,
7.33084677, 7.35626689, 7.33907124, 7.32522422, 7.31688687])
The immediate solution would be a two step sampling:
for a given row i, one samples from a uniform distribution over the interval error_down and error_up obtaining \sigma_i, and then one samples the final value from a normal distribution with mean m_i and standard deviation \sigma_i.
In practice, one imports numpy, defines a custom function sampling and, then, applies it at the whole table:
import numpy as np
def sampling (row) :
sigma = np.random.uniform(row[1], row[2])
m = row[0]
return (np.random.normal(m, sigma))
sampled_values = map(sampling, table)

Obtaining the percentile from a distribution

How can I obtain the percentiles (for example the mean, or the 10% and 90% percentile) of a distribution received from some program or experiments? In the sample below I generate a normal distribution just for illustration.
from scipy.stats import norm
x = np.linspace(1,10,1001)
count = norm.pdf(x,5,1)
This will be a gaussian curve (for this particular illustration case) if plotted as plt.plot(x,count). Note that this is not the data points but the distribution (which you can obtain with, e.g., x,count = plt.hist(data)), so I can't use p10 = np.percentile(count,10)
but I would want something similar, such as
p10 = module.percentile(x,dist,10)
Does any of you know of such a module, or do you know of some other means of obtaining the percentile?
I am not sure if this is what you are looking for, but scipy.stats distributions have ppf method that computes their percentiles. For example, to get the 30th percentile of the normal distribution with mean 5 and standard deviation 1 you can use:
from scipy.stats import norm
norm.ppf(0.3, loc=5, scale=1)
This gives:
4.475599487291959
Then, you can select elements of an array x which are in this percentile:
x[x < norm.ppf(0.3, loc=5, scale=1)]

How to use norm.ppf()?

I couldn't understand how to properly use this function, could someone please explain it to me?
Let's say I have:
a mean of 172.7815
a standard deviation of 4.1532
N = 50 (50 samples)
When I'm asked to calculate the (95%) margin of error using norm.ppf() will the code look like below?
norm.ppf(0.95, loc=172.78, scale=4.15)
or will it look like this?
norm.ppf(0.95, loc=0, scale=1)
Because I know it's calculating the area of the curve to the right of the confidence interval (95%, 97.5% etc...see image below), but when I have a mean and a standard deviation, I get really confused as to how to use the function.
The method norm.ppf() takes a percentage and returns a standard deviation multiplier for what value that percentage occurs at.
It is equivalent to a, 'One-tail test' on the density plot.
From scipy.stats.norm:
ppf(q, loc=0, scale=1) Percent point function (inverse of cdf — percentiles).
Standard Normal Distribution
The code:
norm.ppf(0.95, loc=0, scale=1)
Returns a 95% significance interval for a one-tail test on a standard normal distribution (i.e. a special case of the normal distribution where the mean is 0 and the standard deviation is 1).
Our Example
To calculate the value for OP-provided example at which our 95% significance interval lies (For a one-tail test) we would use:
norm.ppf(0.95, loc=172.7815, scale=4.1532)
This will return a value (that functions as a 'standard-deviation multiplier') marking where 95% of data points would be contained if our data is a normal distribution.
To get the exact number, we take the norm.ppf() output and multiply it by our standard deviation for the distribution in question.
A Two-Tailed Test
If we need to calculate a 'Two-tail test' (i.e. We're concerned with values both greater and less than our mean) then we need to split the significance (i.e. our alpha value) because we're still using a calculation method for one-tail. The split in half symbolizes the significance level being appropriated to both tails. A 95% significance level has a 5% alpha; splitting the 5% alpha across both tails returns 2.5%. Taking 2.5% from 100% returns 97.5% as an input for the significance level.
Therefore, if we were concerned with values on both sides of our mean, our code would input .975 to represent a 95% significance level across two-tails:
norm.ppf(0.975, loc=172.7815, scale=4.1532)
Margin of Error
Margin of error is a significance level used when estimating a population parameter with a sample statistic. We want to generate our 95% confidence interval using the two-tailed input to norm.ppf() since we're concerned with values both greater and less than our mean:
ppf = norm.ppf(0.975, loc=172.7815, scale=4.1532)
Next, we'd take the ppf and multiply it by our standard deviation to return the interval value:
interval_value = std * ppf
Finally, we'd mark the confidence intervals by adding & subtracting the interval value from the mean:
lower_95 = mean - interval_value
upper_95 = mean + interval_value
Plot with a vertical line:
_ = plt.axvline(lower_95, color='r', linestyle=':')
_ = plt.axvline(upper_95, color='r', linestyle=':')
James' statement that norm.ppf returns a "standard deviation multiplier" is wrong. This feels pertinent as his post is the top google result when one searches for norm.ppf.
'norm.ppf' is the inverse of 'norm.cdf'. In the example, it simply returns the value at the 95% percentile. There is no "standard deviation multiplier" involved.
A better answer exists here:
How to calculate the inverse of the normal cumulative distribution function in python?
You can figure out the confidence interval with norm.ppf directly, without calculating margin of error
upper_of_interval = norm.ppf(0.975, loc=172.7815, scale=4.1532/np.sqrt(50))
lower_of_interval = norm.ppf(0.025, loc=172.7815, scale=4.1532/np.sqrt(50))
4.1532 is sample standard deviation, not the standard deviation of the sampling distribution of the sample mean. So, scale in norm.ppf will be specified as scale = 4.1532 / np.sqrt(50), which is the estimator of standard deviation of the sampling distribution.
(The value of standard deviation of the sampling distribution is equal to population standard deviation / np.sqrt(sample size). Here, we did not know the population standard deviation and the sample size is more than 30, so sample standard deviation / np.sqrt(sample size) can be used as a good estimator).
Margin of error can be calculated with (upper_of_interval - lower_of_interval) / 2.
calculate the amount for the 95% percentile and draw a vertical line and an annotation with the amount
mean=172.7815
std=4.1532
N = 50
results=norm.rvs(mean,std, size=N)
pct_5 = norm.ppf(.95,mean,std)
plt.hist(results,bins=10)
plt.axvline(pct_5)
plt.annotate(pct_5,xy=(pct_5,6))
plt.show()
As other answers pointed out, norm.ppf(1-alpha) returns the value on the (1-alpha)x100-th percentile of a normal distribution specified by the parameters passed to the it. For example in the OP, it returns the 95th percentile of a normal distribution with mean 172.78 and standard deviation 4.15.
If you're looking for a function that returns the same value (N-th percentile on the normal distribution) as a function of alpha instead, there's the inverse survival function, norm.isf(alpha), which tells you the number at which (1-alpha) is above it.
from scipy.stats import norm
alpha = 0.05
v1 = norm.isf(alpha)
v2 = norm.ppf(1-alpha)
np.isclose(v1, v2) # True

Confidence Interval for Inverse Gauss distribution with scipy.stats

I am attempting to fit an inverse gauss distribution to data using the scipy.stats toolbox. The data fits well using the following code:
import scipy.stats
dist = stats.invgauss
# fit a distribution to the data
dist_fit = dist.fit(data);
dist_model = dist(*dist_fit);
# find the distribution mean
dist_mu = dist_model.mean();
# find the distribution standard deviation
dist_std = dist_model.std();
Which produces a fit to the distribution that looks like this: inverse_gaussian_fit.
I am trying to determine the confidence interval for the mean of this distribution. From my understanding, the confidence interval of the mean is equal to the standard error of the mean (which is equal to the standard deviation divided by the square root of the number of tests) multiplied by the percent point function (which is equal to the inverse of the cumulative distribution function) at the confidence level desired. I can do this using the following code:
# find the inverse gaussian standard error/confidence interval
dist_se = dist_std / np.sqrt(n);
dist_ci_l = dist_se * dist_model.ppf(0.05);
dist_ci_h = dist_se * dist_model.ppf(0.95);
Unfortunately, this produces unrealistic results like this:
inverse_gaussian_running_averages.
How can I generate the asymmetric confidence interval for an inverse gauss function? I have seen many applications where one assumes the confidence interval from a normal distribution, but that creates symmetric confidence intervals.

Correct way to obtain confidence interval with scipy

I have a 1-dimensional array of data:
a = np.array([1,2,3,4,4,4,5,5,5,5,4,4,4,6,7,8])
for which I want to obtain the 68% confidence interval (ie: the 1 sigma).
The first comment in this answer states that this can be achieved using scipy.stats.norm.interval from the scipy.stats.norm function, via:
from scipy import stats
import numpy as np
mean, sigma = np.mean(a), np.std(a)
conf_int = stats.norm.interval(0.68, loc=mean,
scale=sigma)
But a comment in this post states that the actual correct way of obtaining the confidence interval is:
conf_int = stats.norm.interval(0.68, loc=mean,
scale=sigma / np.sqrt(len(a)))
that is, sigma is divided by the square-root of the sample size: np.sqrt(len(a)).
The question is: which version is the correct one?
The 68% confidence interval for a single draw from a normal distribution with
mean mu and std deviation sigma is
stats.norm.interval(0.68, loc=mu, scale=sigma)
The 68% confidence interval for the mean of N draws from a normal distribution
with mean mu and std deviation sigma is
stats.norm.interval(0.68, loc=mu, scale=sigma/sqrt(N))
Intuitively, these formulas make sense, since if you hold up a jar of jelly beans and ask a large number of people to guess the number of jelly beans, each individual may be off by a lot -- the same std deviation sigma -- but the average of the guesses will do a remarkably fine job of estimating the actual number and this is reflected by the standard deviation of the mean shrinking by a factor of 1/sqrt(N).
If a single draw has variance sigma**2, then by the Bienaymé formula, the sum of N uncorrelated draws has variance N*sigma**2.
The mean is equal to the sum divided by N. When you multiply a random variable (like the sum) by a constant, the variance is multiplied by the constant squared. That is
Var(cX) = c**2 * Var(X)
So the variance of the mean equals
(variance of the sum)/N**2 = N * sigma**2 / N**2 = sigma**2 / N
and so the standard deviation of the mean (which is the square root of the variance) equals
sigma/sqrt(N).
This is the origin of the sqrt(N) in the denominator.
Here is some example code, based on Tom's code, which demonstrates the claims made above:
import numpy as np
from scipy import stats
N = 10000
a = np.random.normal(0, 1, N)
mean, sigma = a.mean(), a.std(ddof=1)
conf_int_a = stats.norm.interval(0.68, loc=mean, scale=sigma)
print('{:0.2%} of the single draws are in conf_int_a'
.format(((a >= conf_int_a[0]) & (a < conf_int_a[1])).sum() / float(N)))
M = 1000
b = np.random.normal(0, 1, (N, M)).mean(axis=1)
conf_int_b = stats.norm.interval(0.68, loc=0, scale=1 / np.sqrt(M))
print('{:0.2%} of the means are in conf_int_b'
.format(((b >= conf_int_b[0]) & (b < conf_int_b[1])).sum() / float(N)))
prints
68.03% of the single draws are in conf_int_a
67.78% of the means are in conf_int_b
Beware that if you define conf_int_b with the estimates for mean and sigma
based on the sample a, the mean may not fall in conf_int_b with the desired
frequency.
If you take a sample from a distribution and compute the
sample mean and std deviation,
mean, sigma = a.mean(), a.std()
be careful to note that there is no guarantee that these will
equal the population mean and standard deviation and that we are assuming
the population is normally distributed -- those are not automatic givens!
If you take a sample and want to estimate the population mean and standard
deviation, you should use
mean, sigma = a.mean(), a.std(ddof=1)
since this value for sigma is the unbiased estimator for the population standard deviation.
I just checked how R and GraphPad calculate confidence intervals, and they increase the interval in case of small sample size (n). E.g., more than 6-fold for n=2 compared to a large n. This code (based on shasan's answer) matches their confidence intervals:
import numpy as np, scipy.stats as st
# returns confidence interval of mean
def confIntMean(a, conf=0.95):
mean, sem, m = np.mean(a), st.sem(a), st.t.ppf((1+conf)/2., len(a)-1)
return mean - m*sem, mean + m*sem
For R, I checked against t.test(a). GraphPad's confidence interval of a mean page has "user level" info on the sample size dependency.
Here the output for Gabriel's example:
In [2]: a = np.array([1,2,3,4,4,4,5,5,5,5,4,4,4,6,7,8])
In [3]: confIntMean(a, 0.68)
Out[3]: (3.9974214366806184, 4.877578563319382)
In [4]: st.norm.interval(0.68, loc=np.mean(a), scale=st.sem(a))
Out[4]: (4.0120010966037407, 4.8629989033962593)
Note that the difference between the confIntMean() and st.norm.interval() intervals is relatively small here; len(a) == 16 is not too small.
I tested out your methods using an array with a known confidence interval. numpy.random.normal(mu,std,size) returns an array centered on mu with a standard deviation of std (in the docs, this is defined as Standard deviation (spread or “width”) of the distribution.).
from scipy import stats
import numpy as np
from numpy import random
a = random.normal(0,1,10000)
mean, sigma = np.mean(a), np.std(a)
conf_int_a = stats.norm.interval(0.68, loc=mean, scale=sigma)
conf_int_b = stats.norm.interval(0.68, loc=mean, scale=sigma / np.sqrt(len(a)))
conf_int_a
(-1.0011149125527312, 1.0059797764202412)
conf_int_b
(-0.0076030415111100983, 0.012467905378619625)
As the sigma value should be -1 to 1, the / np.sqrt(len(a)) method appears to be incorrect.
Edit
Since I don't have the reputation to comment above I'll clarify how this answer ties into unutbu's thorough answer. If you populate a random array with a normal distribution, 68% of the total will fall within 1-σ of the mean. In the case above, if you check that you see
b = a[np.where((a>-1)&(a <1))]
len(a)
> 6781
or 68% of the population falls within 1σ. Well, about 68%. As you use a larger and larger array, you will approach 68% (In a trial of 10, 9 were between -1 and 1). That's because the 1-σ is the inherent distribution of the data, and the more data you have the better you can resolve it.
Basically, my interpretation of your question was If I have a sample of data I want to use to describe the distribution they were drawn from, what is the method to find the standard deviation of that data? whereas unutbu's interpretation appears to be more What is the interval to which I can place the mean with 68% confidence?. Which would mean, for jelly beans, I answered How are they guessing and unutbu answered What do their guesses tell us about the jelly beans.

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