nugridpy.ppn¶

Analyze and visualize the output of single-zone ppn simulations

Contains:

class xtime: for analyzing x-time.data time evolutions

class abu_vector: for analyzing iso_massfxxxx.DAT time evolutions

PPN Assumptions¶

The first non white space character in a header line is a ‘#’. Header attributes are separated from their value by white space or by white space surrounding an equals sign.

A Header attribute is separated by the previous Header attribute by white space or a line break.

There are only 6 data columns. The first being the number, second being Z, third being A, fourth being isomere state, fifth being abundance_yps, and sixth the element name.

The first five columns consist purely of numbers, no strings are allowed. Of the values in the final column, the name column, the first two are letters specifying the element name, and the rest are spaces or numbers (in that strict order), except for the element names: Neut and Prot.

All the profile files in the directory have the same cycle attributes. The cycle numbers of the ‘filename’+xxxxx start at 0.

PPN files always end in .DAT and are not allowed any ‘.’.

There can not be any blank lines in the data files.

No cycle numbers are skipped, ie if cycle 0 and 3 are present, 1 and 2 must be here as well.

Classes

`abu_vector`([sldir, filenames, USEEPP, verbose])	Class for reading selem00xxxx.DAT files
`xtime`([sldir, fname])	read and plot x-time.dat output files.

class nugridpy.ppn.abu_vector(sldir='./', filenames='iso_massf', USEEPP='auto', verbose=False)¶

Class for reading selem00xxxx.DAT files

Parameters:	sldir (string, optional) – where fname exists filenames (string, optional) – The default file names of the abundance vectors. The defaults is “iso_massf”. USEEPP (string, optional) – The default is “auto”.
Returns:	A PPN instance.
Return type:	abu_vector

Examples

>>> import ppn
>>> p=ppn.abu_vector('./run')
39 cycle numbers found in ./run
Ranging from 0 to 38

To find the cycle attributes: >>> p.cattrs [‘mod’, ‘dzeit’, ‘agej’, ‘t9’, ‘rho’, ‘densn’, ‘densp’, ‘densa’]

To find the data column attributes

>>> p.dcols
['NUM', 'Z', 'A', 'ISOM', 'ABUNDANCE_MF', 'ISOTP']
>>> p.get('Z',0)
array([1, 2, 2, 4, 5, 3, 6, 6, 7, 7, 6, 7, 8, 8, 8, 9, 9, 9])
>>> p.get('ABUNDANCE_MF',0)
array([  1.43722000e-10,   1.00000000e-99,   9.81499000e-01,
4.08738000e-20,   1.00000000e-99,   2.06944000e-21,
3.42800000e-04,   9.62307000e-05,   1.05081000e-12,
1.25518000e-02,   1.90131000e-08,   1.42230000e-07,
4.98449000e-05,   4.80246000e-07,   4.24345000e-12,
9.85201000e-17,   6.30866000e-16,   9.12726000e-11])

or if the user wants the data from the first 3 cycles:

>>> p.get('ABUNDANCE_MF',[0,1,2])
[array([  1.43722000e-10,   ...,   9.81499000e-01,],
array([  1.43722000e-10,   ...,   9.81499000e-01,],
array([  1.43722000e-10,   ...,   9.81499000e-01,]
>>> p.getElement('C 14',0)
array([  1.50000000e+01,   6.00000000e+00,   1.40000000e+01,
1.90131000e-08])
>>> p.plot('abundance_yps', 'Z',0)

plots data

>>> p.iso_abund(0)

Plots an isotope abundance distribution

>>> p.abu_chart(0)

Plots an isotope abundance chart

One note about the plot functions, if instead of a single cycle the user inputs a list of cycles, the method will then, instead of plotting them, will then save a .png for each cycle. Also if you just want a singular plot saved, the user can input their cycle, in a list like [0]. And that will save their plot.

findFile(fname, numtype)¶

Function that finds the associated file for fname when Fname is time or NDump.

Parameters:	fname (string) – The name of the file we are looking for. numType (string) – Designates how this function acts and how it interprets fname. If numType is ‘file’, this function will get the desired attribute from that file. If numType is ‘cycNum’, this function will get the desired attribute from that file with fname’s model number.

get(attri, fname=None, numtype='cycNum', decayed=False)¶

In this method all data for an entire cycle (basically the content of an iso_massfnnnn.DAT file) or a column of data for the associated attribute is returned.

Parameters:

attri (string or integer) –
If attri is a string, attri is the cycle or name of the attribute we are looking for.

If attri is an integer, attri is the cycle number (cycle arrays are not supported).
fname (string, optional) –
If attri is a string, fname is the name of the file we are getting the data from or the cycle number found in the filename, or a List of either cycles or filenames. If fname is None, the data from all cycles is returned.

If attri is an integer, then fname is not supported.

The default is None.
numtype (string, optional) –
If attri is a string, numtype determines whether fname is the name of a file or, the cycle number. If numtype is ‘file’ it will then interpret fname as a file. If numtype is ‘cycNum’ it will then interpret fname as a cycle number.

If attri is an Integer, then numtype is not supported.

The default is “cycNum”.
decayed (boolean, optional) –
If attri is a string, then decayed is not supported.

If attri is an integer, then get instantaneously decay abundance distribution.

The default is False.

Returns:

If attri is a string, data in the form of a numpy array is returned.

If attri is an integer, Nothing is returned.

Return type:

array

Notes

If attri is an integer, then the following variables will be added to the instance.

a_iso_to_plot: mass number of plotted range of species.

isotope_to_plot: corresponding list of isotopes.

z_iso_to_plot: corresponding charge numbers.

el_iso_to_plot: corresponding element names.

abunds: corresponding abundances.

isom: list of isomers with their abundances.

getColData(attri, fname, numtype='cycNum')¶

In this method a column of data for the associated column attribute is returned.

Parameters:

attri (string) – The name of the attribute we are looking for.
fname (string) – The name of the file we are getting the data from or the cycle number found in the filename.
numtype (string, optional) – Determines whether fname is the name of a file or, the cycle number. If it is ‘file’ it will then interpret it as a file, if it is ‘cycNum’ it will then interpret it as a cycle number. The default is “cycNum”.

getCycleData(attri, fname, numtype='cycNum')¶

In this method a column of data for the associated cycle attribute is returned.

Parameters:

attri (string) – The name of the attribute we are looking for.
fname (string) – The name of the file we are getting the data from or the cycle number found in the filename.
numtype (string, optional) – Determines whether fname is the name of a file or, the cycle number. If it is ‘file’ it will then interpret it as a file, if it is ‘cycNum’ it will then interpret it as a cycle number. The default is “cycNum”.

getElement(attri, fname, numtype='cycNum')¶

In this method instead of getting a particular column of data, the program gets a particular row of data for a particular element name.

attri : string

The name of the attribute we are looking for. A complete list of them can be obtained by calling

>>> get('element_name')

fname : string

The name of the file we are getting the data from or the cycle number found in the filename.

numtype : string, optional

Determines whether fname is the name of a file or, the cycle number. If it is ‘file’ it will then interpret it as a file, if it is ‘cycNum’ it will then interpret it as a cycle number. The default is “cycNum”.

Returns:	A numpy array of the four element attributes, number, Z, A and abundance, in that order.
Return type:	array

Notes

Warning

nugridpy.ppn.beta(a, b, size=None)¶

Draw samples from a Beta distribution.

The Beta distribution is a special case of the Dirichlet distribution, and is related to the Gamma distribution. It has the probability distribution function

\[f(x; a,b) = \frac{1}{B(\alpha, \beta)} x^{\alpha - 1} (1 - x)^{\beta - 1},\]

where the normalisation, B, is the beta function,

\[B(\alpha, \beta) = \int_0^1 t^{\alpha - 1} (1 - t)^{\beta - 1} dt.\]

It is often seen in Bayesian inference and order statistics.

Parameters:	a (float or array_like of floats) – Alpha, non-negative. b (float or array_like of floats) – Beta, non-negative. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `a` and `b` are both scalars. Otherwise, `np.broadcast(a, b).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized beta distribution.
Return type:	ndarray or scalar

nugridpy.ppn.binomial(n, p, size=None)¶

Draw samples from a binomial distribution.

Samples are drawn from a binomial distribution with specified parameters, n trials and p probability of success where n an integer >= 0 and p is in the interval [0,1]. (n may be input as a float, but it is truncated to an integer in use)

Parameters:	n (int or array_like of ints) – Parameter of the distribution, >= 0. Floats are also accepted, but they will be truncated to integers. p (float or array_like of floats) – Parameter of the distribution, >= 0 and <=1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `n` and `p` are both scalars. Otherwise, `np.broadcast(n, p).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized binomial distribution, where each sample is equal to the number of successes over the n trials.
Return type:	ndarray or scalar

See also

scipy.stats.binom(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the binomial distribution is

\[P(N) = \binom{n}{N}p^N(1-p)^{n-N},\]

where $n$ is the number of trials, $p$ is the probability of success, and $N$ is the number of successes.

When estimating the standard error of a proportion in a population by using a random sample, the normal distribution works well unless the product p*n <=5, where p = population proportion estimate, and n = number of samples, in which case the binomial distribution is used instead. For example, a sample of 15 people shows 4 who are left handed, and 11 who are right handed. Then p = 4/15 = 27%. 0.27*15 = 4, so the binomial distribution should be used in this case.

References

[R167]

Dalgaard, Peter, “Introductory Statistics with R”, Springer-Verlag, 2002.

[R267]

Glantz, Stanton A. “Primer of Biostatistics.”, McGraw-Hill, Fifth Edition, 2002.

[R367]

Lentner, Marvin, “Elementary Applied Statistics”, Bogden and Quigley, 1972.

[R467]

Weisstein, Eric W. “Binomial Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/BinomialDistribution.html

[R567]

Wikipedia, “Binomial distribution”, http://en.wikipedia.org/wiki/Binomial_distribution

Examples

Draw samples from the distribution:

>>> n, p = 10, .5  # number of trials, probability of each trial
>>> s = np.random.binomial(n, p, 1000)
# result of flipping a coin 10 times, tested 1000 times.

A real world example. A company drills 9 wild-cat oil exploration wells, each with an estimated probability of success of 0.1. All nine wells fail. What is the probability of that happening?

Let’s do 20,000 trials of the model, and count the number that generate zero positive results.

>>> sum(np.random.binomial(9, 0.1, 20000) == 0)/20000.
# answer = 0.38885, or 38%.

nugridpy.ppn.chisquare(df, size=None)¶

Draw samples from a chi-square distribution.

When df independent random variables, each with standard normal distributions (mean 0, variance 1), are squared and summed, the resulting distribution is chi-square (see Notes). This distribution is often used in hypothesis testing.

Parameters:	df (int or array_like of ints) – Number of degrees of freedom. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `df` is a scalar. Otherwise, `np.array(df).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized chi-square distribution.
Return type:	ndarray or scalar
Raises:	`ValueError` – When df <= 0 or when an inappropriate size (e.g. `size=-1`) is given.

Notes

The variable obtained by summing the squares of df independent, standard normally distributed random variables:

\[Q = \sum_{i=0}^{\mathtt{df}} X^2_i\]

is chi-square distributed, denoted

\[Q \sim \chi^2_k.\]

The probability density function of the chi-squared distribution is

\[p(x) = \frac{(1/2)^{k/2}}{\Gamma(k/2)} x^{k/2 - 1} e^{-x/2},\]

where $\Gamma$ is the gamma function,

\[\Gamma(x) = \int_0^{-\infty} t^{x - 1} e^{-t} dt.\]

References

[R672]

NIST “Engineering Statistics Handbook” http://www.itl.nist.gov/div898/handbook/eda/section3/eda3666.htm

Examples

>>> np.random.chisquare(2,4)
array([ 1.89920014,  9.00867716,  3.13710533,  5.62318272])

nugridpy.ppn.choice(a, size=None, replace=True, p=None)¶

Generates a random sample from a given 1-D array

New in version 1.7.0.

Parameters:	a (1-D array-like or int) – If an ndarray, a random sample is generated from its elements. If an int, the random sample is generated as if a were np.arange(a) size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned. replace (boolean, optional) – Whether the sample is with or without replacement p (1-D array-like, optional) – The probabilities associated with each entry in a. If not given the sample assumes a uniform distribution over all entries in a.
Returns:	samples – The generated random samples
Return type:	single item or ndarray
Raises:	`ValueError` – If a is an int and less than zero, if a or p are not 1-dimensional, if a is an array-like of size 0, if p is not a vector of probabilities, if a and p have different lengths, or if replace=False and the sample size is greater than the population size

Examples

Generate a uniform random sample from np.arange(5) of size 3:

>>> np.random.choice(5, 3)
array([0, 3, 4])
>>> #This is equivalent to np.random.randint(0,5,3)

Generate a non-uniform random sample from np.arange(5) of size 3:

>>> np.random.choice(5, 3, p=[0.1, 0, 0.3, 0.6, 0])
array([3, 3, 0])

Generate a uniform random sample from np.arange(5) of size 3 without replacement:

>>> np.random.choice(5, 3, replace=False)
array([3,1,0])
>>> #This is equivalent to np.random.permutation(np.arange(5))[:3]

Generate a non-uniform random sample from np.arange(5) of size 3 without replacement:

>>> np.random.choice(5, 3, replace=False, p=[0.1, 0, 0.3, 0.6, 0])
array([2, 3, 0])

Any of the above can be repeated with an arbitrary array-like instead of just integers. For instance:

>>> aa_milne_arr = ['pooh', 'rabbit', 'piglet', 'Christopher']
>>> np.random.choice(aa_milne_arr, 5, p=[0.5, 0.1, 0.1, 0.3])
array(['pooh', 'pooh', 'pooh', 'Christopher', 'piglet'],
      dtype='|S11')

nugridpy.ppn.dirichlet(alpha, size=None)¶

Draw samples from the Dirichlet distribution.

Draw size samples of dimension k from a Dirichlet distribution. A Dirichlet-distributed random variable can be seen as a multivariate generalization of a Beta distribution. Dirichlet pdf is the conjugate prior of a multinomial in Bayesian inference.

Parameters:	alpha (array) – Parameter of the distribution (k dimension for sample of dimension k). size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	samples – The drawn samples, of shape (size, alpha.ndim).
Return type:	ndarray,

Notes

\[X \approx \prod_{i=1}^{k}{x^{\alpha_i-1}_i}\]

Uses the following property for computation: for each dimension, draw a random sample y_i from a standard gamma generator of shape alpha_i, then $X = \frac{1}{\sum_{i=1}^k{y_i}} (y_1, \ldots, y_n)$ is Dirichlet distributed.

References

[R773]

David McKay, “Information Theory, Inference and Learning Algorithms,” chapter 23, http://www.inference.phy.cam.ac.uk/mackay/

[R873]

Wikipedia, “Dirichlet distribution”, http://en.wikipedia.org/wiki/Dirichlet_distribution

Examples

Taking an example cited in Wikipedia, this distribution can be used if one wanted to cut strings (each of initial length 1.0) into K pieces with different lengths, where each piece had, on average, a designated average length, but allowing some variation in the relative sizes of the pieces.

>>> s = np.random.dirichlet((10, 5, 3), 20).transpose()

>>> plt.barh(range(20), s[0])
>>> plt.barh(range(20), s[1], left=s[0], color='g')
>>> plt.barh(range(20), s[2], left=s[0]+s[1], color='r')
>>> plt.title("Lengths of Strings")

nugridpy.ppn.exponential(scale=1.0, size=None)¶

Draw samples from an exponential distribution.

Its probability density function is

\[f(x; \frac{1}{\beta}) = \frac{1}{\beta} \exp(-\frac{x}{\beta}),\]

for x > 0 and 0 elsewhere. $\beta$ is the scale parameter, which is the inverse of the rate parameter $\lambda = 1/\beta$. The rate parameter is an alternative, widely used parameterization of the exponential distribution [R1175].

The exponential distribution is a continuous analogue of the geometric distribution. It describes many common situations, such as the size of raindrops measured over many rainstorms [R975], or the time between page requests to Wikipedia [R1075].

Parameters:	scale (float or array_like of floats) – The scale parameter, $\beta = 1/\lambda$. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `scale` is a scalar. Otherwise, `np.array(scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized exponential distribution.
Return type:	ndarray or scalar

References

[R975]

Peyton Z. Peebles Jr., “Probability, Random Variables and Random Signal Principles”, 4th ed, 2001, p. 57.

[R1075]

Wikipedia, “Poisson process”, http://en.wikipedia.org/wiki/Poisson_process

[R1175]

Wikipedia, “Exponential distribution”, http://en.wikipedia.org/wiki/Exponential_distribution

nugridpy.ppn.f(dfnum, dfden, size=None)¶

Draw samples from an F distribution.

Samples are drawn from an F distribution with specified parameters, dfnum (degrees of freedom in numerator) and dfden (degrees of freedom in denominator), where both parameters should be greater than zero.

The random variate of the F distribution (also known as the Fisher distribution) is a continuous probability distribution that arises in ANOVA tests, and is the ratio of two chi-square variates.

Parameters:	dfnum (int or array_like of ints) – Degrees of freedom in numerator. Should be greater than zero. dfden (int or array_like of ints) – Degrees of freedom in denominator. Should be greater than zero. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `dfnum` and `dfden` are both scalars. Otherwise, `np.broadcast(dfnum, dfden).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Fisher distribution.
Return type:	ndarray or scalar

See also

scipy.stats.f(): probability density function, distribution or cumulative density function, etc.

Notes

The F statistic is used to compare in-group variances to between-group variances. Calculating the distribution depends on the sampling, and so it is a function of the respective degrees of freedom in the problem. The variable dfnum is the number of samples minus one, the between-groups degrees of freedom, while dfden is the within-groups degrees of freedom, the sum of the number of samples in each group minus the number of groups.

References

[R1278]

Glantz, Stanton A. “Primer of Biostatistics.”, McGraw-Hill, Fifth Edition, 2002.

[R1378]

Wikipedia, “F-distribution”, http://en.wikipedia.org/wiki/F-distribution

Examples

An example from Glantz[1], pp 47-40:

Two groups, children of diabetics (25 people) and children from people without diabetes (25 controls). Fasting blood glucose was measured, case group had a mean value of 86.1, controls had a mean value of 82.2. Standard deviations were 2.09 and 2.49 respectively. Are these data consistent with the null hypothesis that the parents diabetic status does not affect their children’s blood glucose levels? Calculating the F statistic from the data gives a value of 36.01.

Draw samples from the distribution:

>>> dfnum = 1. # between group degrees of freedom
>>> dfden = 48. # within groups degrees of freedom
>>> s = np.random.f(dfnum, dfden, 1000)

The lower bound for the top 1% of the samples is :

>>> sort(s)[-10]
7.61988120985

So there is about a 1% chance that the F statistic will exceed 7.62, the measured value is 36, so the null hypothesis is rejected at the 1% level.

nugridpy.ppn.geometric(p, size=None)¶

Draw samples from the geometric distribution.

Bernoulli trials are experiments with one of two outcomes: success or failure (an example of such an experiment is flipping a coin). The geometric distribution models the number of trials that must be run in order to achieve success. It is therefore supported on the positive integers, k = 1, 2, ....

The probability mass function of the geometric distribution is

\[f(k) = (1 - p)^{k - 1} p\]

where p is the probability of success of an individual trial.

Parameters:	p (float or array_like of floats) – The probability of success of an individual trial. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `p` is a scalar. Otherwise, `np.array(p).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized geometric distribution.
Return type:	ndarray or scalar

Examples

Draw ten thousand values from the geometric distribution, with the probability of an individual success equal to 0.35:

>>> z = np.random.geometric(p=0.35, size=10000)

How many trials succeeded after a single run?

>>> (z == 1).sum() / 10000.
0.34889999999999999 #random

nugridpy.ppn.get_state()¶

Return a tuple representing the internal state of the generator.

For more details, see set_state.

Returns:	out – The returned tuple has the following items: the string ‘MT19937’. a 1-D array of 624 unsigned integer keys. an integer `pos`. an integer `has_gauss`. a float `cached_gaussian`.
Return type:	tuple(str, ndarray of 624 uints, int, int, float)

See also

set_state()

Notes

set_state and get_state are not needed to work with any of the random distributions in NumPy. If the internal state is manually altered, the user should know exactly what he/she is doing.

nugridpy.ppn.gumbel(loc=0.0, scale=1.0, size=None)¶

Draw samples from a Gumbel distribution.

Draw samples from a Gumbel distribution with specified location and scale. For more information on the Gumbel distribution, see Notes and References below.

Parameters:	loc (float or array_like of floats, optional) – The location of the mode of the distribution. Default is 0. scale (float or array_like of floats, optional) – The scale parameter of the distribution. Default is 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `loc` and `scale` are both scalars. Otherwise, `np.broadcast(loc, scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Gumbel distribution.
Return type:	ndarray or scalar

See also

scipy.stats.gumbel_l(), scipy.stats.gumbel_r(), scipy.stats.genextreme(), weibull()

Notes

The Gumbel (or Smallest Extreme Value (SEV) or the Smallest Extreme Value Type I) distribution is one of a class of Generalized Extreme Value (GEV) distributions used in modeling extreme value problems. The Gumbel is a special case of the Extreme Value Type I distribution for maximums from distributions with “exponential-like” tails.

The probability density for the Gumbel distribution is

\[p(x) = \frac{e^{-(x - \mu)/ \beta}}{\beta} e^{ -e^{-(x - \mu)/ \beta}},\]

where $\mu$ is the mode, a location parameter, and $\beta$ is the scale parameter.

The Gumbel (named for German mathematician Emil Julius Gumbel) was used very early in the hydrology literature, for modeling the occurrence of flood events. It is also used for modeling maximum wind speed and rainfall rates. It is a “fat-tailed” distribution - the probability of an event in the tail of the distribution is larger than if one used a Gaussian, hence the surprisingly frequent occurrence of 100-year floods. Floods were initially modeled as a Gaussian process, which underestimated the frequency of extreme events.

It is one of a class of extreme value distributions, the Generalized Extreme Value (GEV) distributions, which also includes the Weibull and Frechet.

The function has a mean of $\mu + 0.57721\beta$ and a variance of $\frac{\pi^2}{6}\beta^2$.

References

[R1480]

Gumbel, E. J., “Statistics of Extremes,” New York: Columbia University Press, 1958.

[R1580]

Reiss, R.-D. and Thomas, M., “Statistical Analysis of Extreme Values from Insurance, Finance, Hydrology and Other Fields,” Basel: Birkhauser Verlag, 2001.

Examples

Draw samples from the distribution:

>>> mu, beta = 0, 0.1 # location and scale
>>> s = np.random.gumbel(mu, beta, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 30, normed=True)
>>> plt.plot(bins, (1/beta)*np.exp(-(bins - mu)/beta)
...          * np.exp( -np.exp( -(bins - mu) /beta) ),
...          linewidth=2, color='r')
>>> plt.show()

Show how an extreme value distribution can arise from a Gaussian process and compare to a Gaussian:

>>> means = []
>>> maxima = []
>>> for i in range(0,1000) :
...    a = np.random.normal(mu, beta, 1000)
...    means.append(a.mean())
...    maxima.append(a.max())
>>> count, bins, ignored = plt.hist(maxima, 30, normed=True)
>>> beta = np.std(maxima) * np.sqrt(6) / np.pi
>>> mu = np.mean(maxima) - 0.57721*beta
>>> plt.plot(bins, (1/beta)*np.exp(-(bins - mu)/beta)
...          * np.exp(-np.exp(-(bins - mu)/beta)),
...          linewidth=2, color='r')
>>> plt.plot(bins, 1/(beta * np.sqrt(2 * np.pi))
...          * np.exp(-(bins - mu)**2 / (2 * beta**2)),
...          linewidth=2, color='g')
>>> plt.show()

nugridpy.ppn.hypergeometric(ngood, nbad, nsample, size=None)¶

Draw samples from a Hypergeometric distribution.

Samples are drawn from a hypergeometric distribution with specified parameters, ngood (ways to make a good selection), nbad (ways to make a bad selection), and nsample = number of items sampled, which is less than or equal to the sum ngood + nbad.

Parameters:	ngood (int or array_like of ints) – Number of ways to make a good selection. Must be nonnegative. nbad (int or array_like of ints) – Number of ways to make a bad selection. Must be nonnegative. nsample (int or array_like of ints) – Number of items sampled. Must be at least 1 and at most `ngood + nbad`. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `ngood`, `nbad`, and `nsample` are all scalars. Otherwise, `np.broadcast(ngood, nbad, nsample).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized hypergeometric distribution.
Return type:	ndarray or scalar

See also

scipy.stats.hypergeom(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Hypergeometric distribution is

\[P(x) = \frac{\binom{m}{n}\binom{N-m}{n-x}}{\binom{N}{n}},\]

where $0 \le x \le m$ and $n+m-N \le x \le n$

for P(x) the probability of x successes, n = ngood, m = nbad, and N = number of samples.

Consider an urn with black and white marbles in it, ngood of them black and nbad are white. If you draw nsample balls without replacement, then the hypergeometric distribution describes the distribution of black balls in the drawn sample.

Note that this distribution is very similar to the binomial distribution, except that in this case, samples are drawn without replacement, whereas in the Binomial case samples are drawn with replacement (or the sample space is infinite). As the sample space becomes large, this distribution approaches the binomial.

References

[R1682]

Lentner, Marvin, “Elementary Applied Statistics”, Bogden and Quigley, 1972.

[R1782]

Weisstein, Eric W. “Hypergeometric Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/HypergeometricDistribution.html

[R1882]

Wikipedia, “Hypergeometric distribution”, http://en.wikipedia.org/wiki/Hypergeometric_distribution

Examples

Draw samples from the distribution:

>>> ngood, nbad, nsamp = 100, 2, 10
# number of good, number of bad, and number of samples
>>> s = np.random.hypergeometric(ngood, nbad, nsamp, 1000)
>>> hist(s)
#   note that it is very unlikely to grab both bad items

Suppose you have an urn with 15 white and 15 black marbles. If you pull 15 marbles at random, how likely is it that 12 or more of them are one color?

>>> s = np.random.hypergeometric(15, 15, 15, 100000)
>>> sum(s>=12)/100000. + sum(s<=3)/100000.
#   answer = 0.003 ... pretty unlikely!

nugridpy.ppn.laplace(loc=0.0, scale=1.0, size=None)¶

Draw samples from the Laplace or double exponential distribution with specified location (or mean) and scale (decay).

The Laplace distribution is similar to the Gaussian/normal distribution, but is sharper at the peak and has fatter tails. It represents the difference between two independent, identically distributed exponential random variables.

Parameters:	loc (float or array_like of floats, optional) – The position, $\mu$, of the distribution peak. Default is 0. scale (float or array_like of floats, optional) – $\lambda$, the exponential decay. Default is 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `loc` and `scale` are both scalars. Otherwise, `np.broadcast(loc, scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Laplace distribution.
Return type:	ndarray or scalar

Notes

It has the probability density function

\[f(x; \mu, \lambda) = \frac{1}{2\lambda} \exp\left(-\frac{|x - \mu|}{\lambda}\right).\]

The first law of Laplace, from 1774, states that the frequency of an error can be expressed as an exponential function of the absolute magnitude of the error, which leads to the Laplace distribution. For many problems in economics and health sciences, this distribution seems to model the data better than the standard Gaussian distribution.

References

[R1985]

Abramowitz, M. and Stegun, I. A. (Eds.). “Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables, 9th printing,” New York: Dover, 1972.

[R2085]

Kotz, Samuel, et. al. “The Laplace Distribution and Generalizations, ” Birkhauser, 2001.

[R2185]

Weisstein, Eric W. “Laplace Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/LaplaceDistribution.html

[R2285]

Wikipedia, “Laplace distribution”, http://en.wikipedia.org/wiki/Laplace_distribution

Examples

Draw samples from the distribution

>>> loc, scale = 0., 1.
>>> s = np.random.laplace(loc, scale, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 30, normed=True)
>>> x = np.arange(-8., 8., .01)
>>> pdf = np.exp(-abs(x-loc)/scale)/(2.*scale)
>>> plt.plot(x, pdf)

Plot Gaussian for comparison:

>>> g = (1/(scale * np.sqrt(2 * np.pi)) *
...      np.exp(-(x - loc)**2 / (2 * scale**2)))
>>> plt.plot(x,g)

nugridpy.ppn.logistic(loc=0.0, scale=1.0, size=None)¶

Draw samples from a logistic distribution.

Samples are drawn from a logistic distribution with specified parameters, loc (location or mean, also median), and scale (>0).

Parameters:	loc (float or array_like of floats, optional) – Parameter of the distribution. Default is 0. scale (float or array_like of floats, optional) – Parameter of the distribution. Should be greater than zero. Default is 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `loc` and `scale` are both scalars. Otherwise, `np.broadcast(loc, scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized logistic distribution.
Return type:	ndarray or scalar

See also

scipy.stats.logistic(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Logistic distribution is

\[P(x) = P(x) = \frac{e^{-(x-\mu)/s}}{s(1+e^{-(x-\mu)/s})^2},\]

where $\mu$ = location and $s$ = scale.

The Logistic distribution is used in Extreme Value problems where it can act as a mixture of Gumbel distributions, in Epidemiology, and by the World Chess Federation (FIDE) where it is used in the Elo ranking system, assuming the performance of each player is a logistically distributed random variable.

References

[R2389]

Reiss, R.-D. and Thomas M. (2001), “Statistical Analysis of Extreme Values, from Insurance, Finance, Hydrology and Other Fields,” Birkhauser Verlag, Basel, pp 132-133.

[R2489]

Weisstein, Eric W. “Logistic Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/LogisticDistribution.html

[R2589]

Wikipedia, “Logistic-distribution”, http://en.wikipedia.org/wiki/Logistic_distribution

Examples

Draw samples from the distribution:

>>> loc, scale = 10, 1
>>> s = np.random.logistic(loc, scale, 10000)
>>> count, bins, ignored = plt.hist(s, bins=50)

# plot against distribution

>>> def logist(x, loc, scale):
...     return exp((loc-x)/scale)/(scale*(1+exp((loc-x)/scale))**2)
>>> plt.plot(bins, logist(bins, loc, scale)*count.max()/\
... logist(bins, loc, scale).max())
>>> plt.show()

nugridpy.ppn.lognormal(mean=0.0, sigma=1.0, size=None)¶

Draw samples from a log-normal distribution.

Draw samples from a log-normal distribution with specified mean, standard deviation, and array shape. Note that the mean and standard deviation are not the values for the distribution itself, but of the underlying normal distribution it is derived from.

Parameters:	mean (float or array_like of floats, optional) – Mean value of the underlying normal distribution. Default is 0. sigma (float or array_like of floats, optional) – Standard deviation of the underlying normal distribution. Should be greater than zero. Default is 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `mean` and `sigma` are both scalars. Otherwise, `np.broadcast(mean, sigma).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized log-normal distribution.
Return type:	ndarray or scalar

See also

scipy.stats.lognorm(): probability density function, distribution, cumulative density function, etc.

Notes

A variable x has a log-normal distribution if log(x) is normally distributed. The probability density function for the log-normal distribution is:

\[p(x) = \frac{1}{\sigma x \sqrt{2\pi}} e^{(-\frac{(ln(x)-\mu)^2}{2\sigma^2})}\]

where $\mu$ is the mean and $\sigma$ is the standard deviation of the normally distributed logarithm of the variable. A log-normal distribution results if a random variable is the product of a large number of independent, identically-distributed variables in the same way that a normal distribution results if the variable is the sum of a large number of independent, identically-distributed variables.

References

[R2692]

Limpert, E., Stahel, W. A., and Abbt, M., “Log-normal Distributions across the Sciences: Keys and Clues,” BioScience, Vol. 51, No. 5, May, 2001. http://stat.ethz.ch/~stahel/lognormal/bioscience.pdf

[R2792]

Reiss, R.D. and Thomas, M., “Statistical Analysis of Extreme Values,” Basel: Birkhauser Verlag, 2001, pp. 31-32.

Examples

Draw samples from the distribution:

>>> mu, sigma = 3., 1. # mean and standard deviation
>>> s = np.random.lognormal(mu, sigma, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 100, normed=True, align='mid')

>>> x = np.linspace(min(bins), max(bins), 10000)
>>> pdf = (np.exp(-(np.log(x) - mu)**2 / (2 * sigma**2))
...        / (x * sigma * np.sqrt(2 * np.pi)))

>>> plt.plot(x, pdf, linewidth=2, color='r')
>>> plt.axis('tight')
>>> plt.show()

Demonstrate that taking the products of random samples from a uniform distribution can be fit well by a log-normal probability density function.

>>> # Generate a thousand samples: each is the product of 100 random
>>> # values, drawn from a normal distribution.
>>> b = []
>>> for i in range(1000):
...    a = 10. + np.random.random(100)
...    b.append(np.product(a))

>>> b = np.array(b) / np.min(b) # scale values to be positive
>>> count, bins, ignored = plt.hist(b, 100, normed=True, align='mid')
>>> sigma = np.std(np.log(b))
>>> mu = np.mean(np.log(b))

>>> x = np.linspace(min(bins), max(bins), 10000)
>>> pdf = (np.exp(-(np.log(x) - mu)**2 / (2 * sigma**2))
...        / (x * sigma * np.sqrt(2 * np.pi)))

>>> plt.plot(x, pdf, color='r', linewidth=2)
>>> plt.show()

nugridpy.ppn.logseries(p, size=None)¶

Draw samples from a logarithmic series distribution.

Samples are drawn from a log series distribution with specified shape parameter, 0 < p < 1.

Parameters:	p (float or array_like of floats) – Shape parameter for the distribution. Must be in the range (0, 1). size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `p` is a scalar. Otherwise, `np.array(p).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized logarithmic series distribution.
Return type:	ndarray or scalar

See also

scipy.stats.logser(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Log Series distribution is

\[P(k) = \frac{-p^k}{k \ln(1-p)},\]

where p = probability.

The log series distribution is frequently used to represent species richness and occurrence, first proposed by Fisher, Corbet, and Williams in 1943 [2]. It may also be used to model the numbers of occupants seen in cars [3].

References

[R2894]

Buzas, Martin A.; Culver, Stephen J., Understanding regional species diversity through the log series distribution of occurrences: BIODIVERSITY RESEARCH Diversity & Distributions, Volume 5, Number 5, September 1999 , pp. 187-195(9).

[R2994]

Fisher, R.A,, A.S. Corbet, and C.B. Williams. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology, 12:42-58.

[R3094]

D. J. Hand, F. Daly, D. Lunn, E. Ostrowski, A Handbook of Small Data Sets, CRC Press, 1994.

[R3194]

Wikipedia, “Logarithmic distribution”, http://en.wikipedia.org/wiki/Logarithmic_distribution

Examples

Draw samples from the distribution:

>>> a = .6
>>> s = np.random.logseries(a, 10000)
>>> count, bins, ignored = plt.hist(s)

# plot against distribution

>>> def logseries(k, p):
...     return -p**k/(k*log(1-p))
>>> plt.plot(bins, logseries(bins, a)*count.max()/
             logseries(bins, a).max(), 'r')
>>> plt.show()

nugridpy.ppn.multinomial(n, pvals, size=None)¶

Draw samples from a multinomial distribution.

The multinomial distribution is a multivariate generalisation of the binomial distribution. Take an experiment with one of p possible outcomes. An example of such an experiment is throwing a dice, where the outcome can be 1 through 6. Each sample drawn from the distribution represents n such experiments. Its values, X_i = [X_0, X_1, ..., X_p], represent the number of times the outcome was i.

Parameters:

n (int) – Number of experiments.
pvals (sequence of floats, length p) – Probabilities of each of the p different outcomes. These should sum to 1 (however, the last element is always assumed to account for the remaining probability, as long as sum(pvals[:-1]) <= 1).
size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., (m, n, k), then m * n * k samples are drawn. Default is None, in which case a single value is returned.

Returns:

out – The drawn samples, of shape size, if that was provided. If not, the shape is (N,).

In other words, each entry out[i,j,...,:] is an N-dimensional value drawn from the distribution.

Return type:

ndarray

Examples

Throw a dice 20 times:

>>> np.random.multinomial(20, [1/6.]*6, size=1)
array([[4, 1, 7, 5, 2, 1]])

It landed 4 times on 1, once on 2, etc.

Now, throw the dice 20 times, and 20 times again:

>>> np.random.multinomial(20, [1/6.]*6, size=2)
array([[3, 4, 3, 3, 4, 3],
       [2, 4, 3, 4, 0, 7]])

For the first run, we threw 3 times 1, 4 times 2, etc. For the second, we threw 2 times 1, 4 times 2, etc.

A loaded die is more likely to land on number 6:

>>> np.random.multinomial(100, [1/7.]*5 + [2/7.])
array([11, 16, 14, 17, 16, 26])

The probability inputs should be normalized. As an implementation detail, the value of the last entry is ignored and assumed to take up any leftover probability mass, but this should not be relied on. A biased coin which has twice as much weight on one side as on the other should be sampled like so:

>>> np.random.multinomial(100, [1.0 / 3, 2.0 / 3])  # RIGHT
array([38, 62])

not like:

>>> np.random.multinomial(100, [1.0, 2.0])  # WRONG
array([100,   0])

nugridpy.ppn.multivariate_normal(mean, cov[, size, check_valid, tol])¶

Draw random samples from a multivariate normal distribution.

The multivariate normal, multinormal or Gaussian distribution is a generalization of the one-dimensional normal distribution to higher dimensions. Such a distribution is specified by its mean and covariance matrix. These parameters are analogous to the mean (average or “center”) and variance (standard deviation, or “width,” squared) of the one-dimensional normal distribution.

Parameters:

mean (1-D array_like, of length N) – Mean of the N-dimensional distribution.
cov (2-D array_like, of shape (N, N)) – Covariance matrix of the distribution. It must be symmetric and positive-semidefinite for proper sampling.
size (int or tuple of ints, optional) – Given a shape of, for example, (m,n,k), m*n*k samples are generated, and packed in an m-by-n-by-k arrangement. Because each sample is N-dimensional, the output shape is (m,n,k,N). If no shape is specified, a single (N-D) sample is returned.
check_valid ({ 'warn', 'raise', 'ignore' }, optional) – Behavior when the covariance matrix is not positive semidefinite.
tol (float, optional) – Tolerance when checking the singular values in covariance matrix.

Returns:

out – The drawn samples, of shape size, if that was provided. If not, the shape is (N,).

In other words, each entry out[i,j,...,:] is an N-dimensional value drawn from the distribution.

Return type:

ndarray

Notes

The mean is a coordinate in N-dimensional space, which represents the location where samples are most likely to be generated. This is analogous to the peak of the bell curve for the one-dimensional or univariate normal distribution.

Covariance indicates the level to which two variables vary together. From the multivariate normal distribution, we draw N-dimensional samples, $X = [x_1, x_2, ... x_N]$. The covariance matrix element $C_{ij}$ is the covariance of $x_i$ and $x_j$. The element $C_{ii}$ is the variance of $x_i$ (i.e. its “spread”).

Instead of specifying the full covariance matrix, popular approximations include:

Spherical covariance (cov is a multiple of the identity matrix)

Diagonal covariance (cov has non-negative elements, and only on the diagonal)

This geometrical property can be seen in two dimensions by plotting generated data-points:

>>> mean = [0, 0]
>>> cov = [[1, 0], [0, 100]]  # diagonal covariance

Diagonal covariance means that points are oriented along x or y-axis:

>>> import matplotlib.pyplot as plt
>>> x, y = np.random.multivariate_normal(mean, cov, 5000).T
>>> plt.plot(x, y, 'x')
>>> plt.axis('equal')
>>> plt.show()

Note that the covariance matrix must be positive semidefinite (a.k.a. nonnegative-definite). Otherwise, the behavior of this method is undefined and backwards compatibility is not guaranteed.

References

[R3298]

Papoulis, A., “Probability, Random Variables, and Stochastic Processes,” 3rd ed., New York: McGraw-Hill, 1991.

[R3398]

Duda, R. O., Hart, P. E., and Stork, D. G., “Pattern Classification,” 2nd ed., New York: Wiley, 2001.

Examples

>>> mean = (1, 2)
>>> cov = [[1, 0], [0, 1]]
>>> x = np.random.multivariate_normal(mean, cov, (3, 3))
>>> x.shape
(3, 3, 2)

The following is probably true, given that 0.6 is roughly twice the standard deviation:

>>> list((x[0,0,:] - mean) < 0.6)
[True, True]

nugridpy.ppn.negative_binomial(n, p, size=None)¶

Draw samples from a negative binomial distribution.

Samples are drawn from a negative binomial distribution with specified parameters, n trials and p probability of success where n is an integer > 0 and p is in the interval [0, 1].

Parameters:	n (int or array_like of ints) – Parameter of the distribution, > 0. Floats are also accepted, but they will be truncated to integers. p (float or array_like of floats) – Parameter of the distribution, >= 0 and <=1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `n` and `p` are both scalars. Otherwise, `np.broadcast(n, p).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized negative binomial distribution, where each sample is equal to N, the number of trials it took to achieve n - 1 successes, N - (n - 1) failures, and a success on the, (N + n)th trial.
Return type:	ndarray or scalar

Notes

The probability density for the negative binomial distribution is

\[P(N;n,p) = \binom{N+n-1}{n-1}p^{n}(1-p)^{N},\]

where $n-1$ is the number of successes, $p$ is the probability of success, and $N+n-1$ is the number of trials. The negative binomial distribution gives the probability of n-1 successes and N failures in N+n-1 trials, and success on the (N+n)th trial.

If one throws a die repeatedly until the third time a “1” appears, then the probability distribution of the number of non-“1”s that appear before the third “1” is a negative binomial distribution.

References

[R34100]

Weisstein, Eric W. “Negative Binomial Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/NegativeBinomialDistribution.html

[R35100]

Wikipedia, “Negative binomial distribution”, http://en.wikipedia.org/wiki/Negative_binomial_distribution

Examples

Draw samples from the distribution:

A real world example. A company drills wild-cat oil exploration wells, each with an estimated probability of success of 0.1. What is the probability of having one success for each successive well, that is what is the probability of a single success after drilling 5 wells, after 6 wells, etc.?

>>> s = np.random.negative_binomial(1, 0.1, 100000)
>>> for i in range(1, 11):
...    probability = sum(s<i) / 100000.
...    print i, "wells drilled, probability of one success =", probability

nugridpy.ppn.noncentral_chisquare(df, nonc, size=None)¶

Draw samples from a noncentral chi-square distribution.

The noncentral $\chi^2$ distribution is a generalisation of the $\chi^2$ distribution.

Parameters:	df (int or array_like of ints) – Degrees of freedom, should be > 0 as of NumPy 1.10.0, should be > 1 for earlier versions. nonc (float or array_like of floats) – Non-centrality, should be non-negative. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `df` and `nonc` are both scalars. Otherwise, `np.broadcast(df, nonc).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized noncentral chi-square distribution.
Return type:	ndarray or scalar

Notes

The probability density function for the noncentral Chi-square distribution is

\[P(x;df,nonc) = \sum^{\infty}_{i=0} \frac{e^{-nonc/2}(nonc/2)^{i}}{i!} \P_{Y_{df+2i}}(x),\]

where $Y_{q}$ is the Chi-square with q degrees of freedom.

In Delhi (2007), it is noted that the noncentral chi-square is useful in bombing and coverage problems, the probability of killing the point target given by the noncentral chi-squared distribution.

References

[R36102]

Delhi, M.S. Holla, “On a noncentral chi-square distribution in the analysis of weapon systems effectiveness”, Metrika, Volume 15, Number 1 / December, 1970.

[R37102]

Wikipedia, “Noncentral chi-square distribution” http://en.wikipedia.org/wiki/Noncentral_chi-square_distribution

Examples

Draw values from the distribution and plot the histogram

>>> import matplotlib.pyplot as plt
>>> values = plt.hist(np.random.noncentral_chisquare(3, 20, 100000),
...                   bins=200, normed=True)
>>> plt.show()

Draw values from a noncentral chisquare with very small noncentrality, and compare to a chisquare.

>>> plt.figure()
>>> values = plt.hist(np.random.noncentral_chisquare(3, .0000001, 100000),
...                   bins=np.arange(0., 25, .1), normed=True)
>>> values2 = plt.hist(np.random.chisquare(3, 100000),
...                    bins=np.arange(0., 25, .1), normed=True)
>>> plt.plot(values[1][0:-1], values[0]-values2[0], 'ob')
>>> plt.show()

Demonstrate how large values of non-centrality lead to a more symmetric distribution.

>>> plt.figure()
>>> values = plt.hist(np.random.noncentral_chisquare(3, 20, 100000),
...                   bins=200, normed=True)
>>> plt.show()

nugridpy.ppn.noncentral_f(dfnum, dfden, nonc, size=None)¶

Draw samples from the noncentral F distribution.

Samples are drawn from an F distribution with specified parameters, dfnum (degrees of freedom in numerator) and dfden (degrees of freedom in denominator), where both parameters > 1. nonc is the non-centrality parameter.

Parameters:	dfnum (int or array_like of ints) – Parameter, should be > 1. dfden (int or array_like of ints) – Parameter, should be > 1. nonc (float or array_like of floats) – Parameter, should be >= 0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `dfnum`, `dfden`, and `nonc` are all scalars. Otherwise, `np.broadcast(dfnum, dfden, nonc).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized noncentral Fisher distribution.
Return type:	ndarray or scalar

Notes

When calculating the power of an experiment (power = probability of rejecting the null hypothesis when a specific alternative is true) the non-central F statistic becomes important. When the null hypothesis is true, the F statistic follows a central F distribution. When the null hypothesis is not true, then it follows a non-central F statistic.

References

[R38104]

Weisstein, Eric W. “Noncentral F-Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/NoncentralF-Distribution.html

[R39104]

Wikipedia, “Noncentral F-distribution”, http://en.wikipedia.org/wiki/Noncentral_F-distribution

Examples

In a study, testing for a specific alternative to the null hypothesis requires use of the Noncentral F distribution. We need to calculate the area in the tail of the distribution that exceeds the value of the F distribution for the null hypothesis. We’ll plot the two probability distributions for comparison.

>>> dfnum = 3 # between group deg of freedom
>>> dfden = 20 # within groups degrees of freedom
>>> nonc = 3.0
>>> nc_vals = np.random.noncentral_f(dfnum, dfden, nonc, 1000000)
>>> NF = np.histogram(nc_vals, bins=50, normed=True)
>>> c_vals = np.random.f(dfnum, dfden, 1000000)
>>> F = np.histogram(c_vals, bins=50, normed=True)
>>> plt.plot(F[1][1:], F[0])
>>> plt.plot(NF[1][1:], NF[0])
>>> plt.show()

nugridpy.ppn.normal(loc=0.0, scale=1.0, size=None)¶

Draw random samples from a normal (Gaussian) distribution.

The probability density function of the normal distribution, first derived by De Moivre and 200 years later by both Gauss and Laplace independently [R41106], is often called the bell curve because of its characteristic shape (see the example below).

The normal distributions occurs often in nature. For example, it describes the commonly occurring distribution of samples influenced by a large number of tiny, random disturbances, each with its own unique distribution [R41106].

Parameters:	loc (float or array_like of floats) – Mean (“centre”) of the distribution. scale (float or array_like of floats) – Standard deviation (spread or “width”) of the distribution. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `loc` and `scale` are both scalars. Otherwise, `np.broadcast(loc, scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized normal distribution.
Return type:	ndarray or scalar

See also

scipy.stats.norm(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Gaussian distribution is

\[p(x) = \frac{1}{\sqrt{ 2 \pi \sigma^2 }} e^{ - \frac{ (x - \mu)^2 } {2 \sigma^2} },\]

where $\mu$ is the mean and $\sigma$ the standard deviation. The square of the standard deviation, $\sigma^2$, is called the variance.

The function has its peak at the mean, and its “spread” increases with the standard deviation (the function reaches 0.607 times its maximum at $x + \sigma$ and $x - \sigma$ [R41106]). This implies that numpy.random.normal is more likely to return samples lying close to the mean, rather than those far away.

References

[R40106]

Wikipedia, “Normal distribution”, http://en.wikipedia.org/wiki/Normal_distribution

[R41106]

(1, 2, 3) P. R. Peebles Jr., “Central Limit Theorem” in “Probability, Random Variables and Random Signal Principles”, 4th ed., 2001, pp. 51, 51, 125.

Examples

Draw samples from the distribution:

>>> mu, sigma = 0, 0.1 # mean and standard deviation
>>> s = np.random.normal(mu, sigma, 1000)

Verify the mean and the variance:

>>> abs(mu - np.mean(s)) < 0.01
True

>>> abs(sigma - np.std(s, ddof=1)) < 0.01
True

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 30, normed=True)
>>> plt.plot(bins, 1/(sigma * np.sqrt(2 * np.pi)) *
...                np.exp( - (bins - mu)**2 / (2 * sigma**2) ),
...          linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn.pareto(a, size=None)¶

Draw samples from a Pareto II or Lomax distribution with specified shape.

The Lomax or Pareto II distribution is a shifted Pareto distribution. The classical Pareto distribution can be obtained from the Lomax distribution by adding 1 and multiplying by the scale parameter m (see Notes). The smallest value of the Lomax distribution is zero while for the classical Pareto distribution it is mu, where the standard Pareto distribution has location mu = 1. Lomax can also be considered as a simplified version of the Generalized Pareto distribution (available in SciPy), with the scale set to one and the location set to zero.

The Pareto distribution must be greater than zero, and is unbounded above. It is also known as the “80-20 rule”. In this distribution, 80 percent of the weights are in the lowest 20 percent of the range, while the other 20 percent fill the remaining 80 percent of the range.

Parameters:	a (float or array_like of floats) – Shape of the distribution. Should be greater than zero. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `a` is a scalar. Otherwise, `np.array(a).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Pareto distribution.
Return type:	ndarray or scalar

See also

scipy.stats.lomax(): probability density function, distribution or cumulative density function, etc.
scipy.stats.genpareto(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Pareto distribution is

\[p(x) = \frac{am^a}{x^{a+1}}\]

where $a$ is the shape and $m$ the scale.

The Pareto distribution, named after the Italian economist Vilfredo Pareto, is a power law probability distribution useful in many real world problems. Outside the field of economics it is generally referred to as the Bradford distribution. Pareto developed the distribution to describe the distribution of wealth in an economy. It has also found use in insurance, web page access statistics, oil field sizes, and many other problems, including the download frequency for projects in Sourceforge [R42108]. It is one of the so-called “fat-tailed” distributions.

References

[R42108]

Francis Hunt and Paul Johnson, On the Pareto Distribution of Sourceforge projects.

[R43108]

Pareto, V. (1896). Course of Political Economy. Lausanne.

[R44108]

Reiss, R.D., Thomas, M.(2001), Statistical Analysis of Extreme Values, Birkhauser Verlag, Basel, pp 23-30.

[R45108]

Wikipedia, “Pareto distribution”, http://en.wikipedia.org/wiki/Pareto_distribution

Examples

Draw samples from the distribution:

>>> a, m = 3., 2.  # shape and mode
>>> s = (np.random.pareto(a, 1000) + 1) * m

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, _ = plt.hist(s, 100, normed=True)
>>> fit = a*m**a / bins**(a+1)
>>> plt.plot(bins, max(count)*fit/max(fit), linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn.permutation(x)¶

Randomly permute a sequence, or return a permuted range.

If x is a multi-dimensional array, it is only shuffled along its first index.

Parameters:	x (int or array_like) – If x is an integer, randomly permute `np.arange(x)`. If x is an array, make a copy and shuffle the elements randomly.
Returns:	out – Permuted sequence or array range.
Return type:	ndarray

Examples

>>> np.random.permutation(10)
array([1, 7, 4, 3, 0, 9, 2, 5, 8, 6])

>>> np.random.permutation([1, 4, 9, 12, 15])
array([15,  1,  9,  4, 12])

>>> arr = np.arange(9).reshape((3, 3))
>>> np.random.permutation(arr)
array([[6, 7, 8],
       [0, 1, 2],
       [3, 4, 5]])

nugridpy.ppn.poisson(lam=1.0, size=None)¶

Draw samples from a Poisson distribution.

The Poisson distribution is the limit of the binomial distribution for large N.

Parameters:	lam (float or array_like of floats) – Expectation of interval, should be >= 0. A sequence of expectation intervals must be broadcastable over the requested size. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `lam` is a scalar. Otherwise, `np.array(lam).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Poisson distribution.
Return type:	ndarray or scalar

Notes

The Poisson distribution

\[f(k; \lambda)=\frac{\lambda^k e^{-\lambda}}{k!}\]

For events with an expected separation $\lambda$ the Poisson distribution $f(k; \lambda)$ describes the probability of $k$ events occurring within the observed interval $\lambda$.

Because the output is limited to the range of the C long type, a ValueError is raised when lam is within 10 sigma of the maximum representable value.

References

[R46112]

Weisstein, Eric W. “Poisson Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/PoissonDistribution.html

[R47112]

Wikipedia, “Poisson distribution”, http://en.wikipedia.org/wiki/Poisson_distribution

Examples

Draw samples from the distribution:

>>> import numpy as np
>>> s = np.random.poisson(5, 10000)

Display histogram of the sample:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 14, normed=True)
>>> plt.show()

Draw each 100 values for lambda 100 and 500:

>>> s = np.random.poisson(lam=(100., 500.), size=(100, 2))

nugridpy.ppn.rand(d0, d1, ..., dn)¶

Random values in a given shape.

Create an array of the given shape and populate it with random samples from a uniform distribution over [0, 1).

Parameters:	d1, .., dn (d0,) – The dimensions of the returned array, should all be positive. If no argument is given a single Python float is returned.
Returns:	out – Random values.
Return type:	ndarray, shape `(d0, d1, ..., dn)`

See also

random()

Notes

This is a convenience function. If you want an interface that takes a shape-tuple as the first argument, refer to np.random.random_sample .

Examples

>>> np.random.rand(3,2)
array([[ 0.14022471,  0.96360618],  #random
       [ 0.37601032,  0.25528411],  #random
       [ 0.49313049,  0.94909878]]) #random

nugridpy.ppn.randint(low, high=None, size=None, dtype='l')¶

Return random integers from low (inclusive) to high (exclusive).

Return random integers from the “discrete uniform” distribution of the specified dtype in the “half-open” interval [low, high). If high is None (the default), then results are from [0, low).

Parameters:	low (int) – Lowest (signed) integer to be drawn from the distribution (unless `high=None`, in which case this parameter is one above the highest such integer). high (int, optional) – If provided, one above the largest (signed) integer to be drawn from the distribution (see above for behavior if `high=None`). size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned. dtype (dtype, optional) – Desired dtype of the result. All dtypes are determined by their name, i.e., ‘int64’, ‘int’, etc, so byteorder is not available and a specific precision may have different C types depending on the platform. The default value is ‘np.int’. New in version 1.11.0.
Returns:	out – size-shaped array of random integers from the appropriate distribution, or a single such random int if size not provided.
Return type:	int or ndarray of ints

See also

random.random_integers(): similar to randint, only for the closed interval [low, high], and 1 is the lowest value if high is omitted. In particular, this other one is the one to use to generate uniformly distributed discrete non-integers.

Examples

>>> np.random.randint(2, size=10)
array([1, 0, 0, 0, 1, 1, 0, 0, 1, 0])
>>> np.random.randint(1, size=10)
array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0])

Generate a 2 x 4 array of ints between 0 and 4, inclusive:

>>> np.random.randint(5, size=(2, 4))
array([[4, 0, 2, 1],
       [3, 2, 2, 0]])

nugridpy.ppn.randn(d0, d1, ..., dn)¶

Return a sample (or samples) from the “standard normal” distribution.

If positive, int_like or int-convertible arguments are provided, randn generates an array of shape (d0, d1, ..., dn), filled with random floats sampled from a univariate “normal” (Gaussian) distribution of mean 0 and variance 1 (if any of the $d_i$ are floats, they are first converted to integers by truncation). A single float randomly sampled from the distribution is returned if no argument is provided.

This is a convenience function. If you want an interface that takes a tuple as the first argument, use numpy.random.standard_normal instead.

Parameters:	d1, .., dn (d0,) – The dimensions of the returned array, should be all positive. If no argument is given a single Python float is returned.
Returns:	Z – A `(d0, d1, ..., dn)`-shaped array of floating-point samples from the standard normal distribution, or a single such float if no parameters were supplied.
Return type:	ndarray or float

See also

random.standard_normal(): Similar, but takes a tuple as its argument.

Notes

For random samples from $N(\mu, \sigma^2)$, use:

sigma * np.random.randn(...) + mu

Examples

>>> np.random.randn()
2.1923875335537315 #random

Two-by-four array of samples from N(3, 6.25):

>>> 2.5 * np.random.randn(2, 4) + 3
array([[-4.49401501,  4.00950034, -1.81814867,  7.29718677],  #random
       [ 0.39924804,  4.68456316,  4.99394529,  4.84057254]]) #random

nugridpy.ppn.random_integers(low, high=None, size=None)¶

Random integers of type np.int between low and high, inclusive.

Return random integers of type np.int from the “discrete uniform” distribution in the closed interval [low, high]. If high is None (the default), then results are from [1, low]. The np.int type translates to the C long type used by Python 2 for “short” integers and its precision is platform dependent.

This function has been deprecated. Use randint instead.

Deprecated since version 1.11.0.

Parameters:	low (int) – Lowest (signed) integer to be drawn from the distribution (unless `high=None`, in which case this parameter is the highest such integer). high (int, optional) – If provided, the largest (signed) integer to be drawn from the distribution (see above for behavior if `high=None`). size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – size-shaped array of random integers from the appropriate distribution, or a single such random int if size not provided.
Return type:	int or ndarray of ints

See also

random.randint(): Similar to random_integers, only for the half-open interval [low, high), and 0 is the lowest value if high is omitted.

Notes

To sample from N evenly spaced floating-point numbers between a and b, use:

a + (b - a) * (np.random.random_integers(N) - 1) / (N - 1.)

Examples

>>> np.random.random_integers(5)
4
>>> type(np.random.random_integers(5))
<type 'int'>
>>> np.random.random_integers(5, size=(3,2))
array([[5, 4],
       [3, 3],
       [4, 5]])

Choose five random numbers from the set of five evenly-spaced numbers between 0 and 2.5, inclusive (i.e., from the set ${0, 5/8, 10/8, 15/8, 20/8}$):

>>> 2.5 * (np.random.random_integers(5, size=(5,)) - 1) / 4.
array([ 0.625,  1.25 ,  0.625,  0.625,  2.5  ])

Roll two six sided dice 1000 times and sum the results:

>>> d1 = np.random.random_integers(1, 6, 1000)
>>> d2 = np.random.random_integers(1, 6, 1000)
>>> dsums = d1 + d2

Display results as a histogram:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(dsums, 11, normed=True)
>>> plt.show()

nugridpy.ppn.random_sample(size=None)¶

Return random floats in the half-open interval [0.0, 1.0).

Results are from the “continuous uniform” distribution over the stated interval. To sample $Unif[a, b), b > a$ multiply the output of random_sample by (b-a) and add a:

(b - a) * random_sample() + a

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – Array of random floats of shape size (unless `size=None`, in which case a single float is returned).
Return type:	float or ndarray of floats

Examples

>>> np.random.random_sample()
0.47108547995356098
>>> type(np.random.random_sample())
<type 'float'>
>>> np.random.random_sample((5,))
array([ 0.30220482,  0.86820401,  0.1654503 ,  0.11659149,  0.54323428])

Three-by-two array of random numbers from [-5, 0):

>>> 5 * np.random.random_sample((3, 2)) - 5
array([[-3.99149989, -0.52338984],
       [-2.99091858, -0.79479508],
       [-1.23204345, -1.75224494]])

nugridpy.ppn.ranf(size=None)¶

Return random floats in the half-open interval [0.0, 1.0).

Results are from the “continuous uniform” distribution over the stated interval. To sample $Unif[a, b), b > a$ multiply the output of random_sample by (b-a) and add a:

(b - a) * random_sample() + a

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – Array of random floats of shape size (unless `size=None`, in which case a single float is returned).
Return type:	float or ndarray of floats

Examples

>>> np.random.random_sample()
0.47108547995356098
>>> type(np.random.random_sample())
<type 'float'>
>>> np.random.random_sample((5,))
array([ 0.30220482,  0.86820401,  0.1654503 ,  0.11659149,  0.54323428])

Three-by-two array of random numbers from [-5, 0):

>>> 5 * np.random.random_sample((3, 2)) - 5
array([[-3.99149989, -0.52338984],
       [-2.99091858, -0.79479508],
       [-1.23204345, -1.75224494]])

nugridpy.ppn.rayleigh(scale=1.0, size=None)¶

Draw samples from a Rayleigh distribution.

The $\chi$ and Weibull distributions are generalizations of the Rayleigh.

Parameters:	scale (float or array_like of floats, optional) – Scale, also equals the mode. Should be >= 0. Default is 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `scale` is a scalar. Otherwise, `np.array(scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Rayleigh distribution.
Return type:	ndarray or scalar

Notes

The probability density function for the Rayleigh distribution is

\[P(x;scale) = \frac{x}{scale^2}e^{\frac{-x^2}{2 \cdotp scale^2}}\]

The Rayleigh distribution would arise, for example, if the East and North components of the wind velocity had identical zero-mean Gaussian distributions. Then the wind speed would have a Rayleigh distribution.

References

[R48114]

Brighton Webs Ltd., “Rayleigh Distribution,” http://www.brighton-webs.co.uk/distributions/rayleigh.asp

[R49114]

Wikipedia, “Rayleigh distribution” http://en.wikipedia.org/wiki/Rayleigh_distribution

Examples

Draw values from the distribution and plot the histogram

>>> values = hist(np.random.rayleigh(3, 100000), bins=200, normed=True)

Wave heights tend to follow a Rayleigh distribution. If the mean wave height is 1 meter, what fraction of waves are likely to be larger than 3 meters?

>>> meanvalue = 1
>>> modevalue = np.sqrt(2 / np.pi) * meanvalue
>>> s = np.random.rayleigh(modevalue, 1000000)

The percentage of waves larger than 3 meters is:

>>> 100.*sum(s>3)/1000000.
0.087300000000000003

nugridpy.ppn.sample(size=None)¶

Return random floats in the half-open interval [0.0, 1.0).

Results are from the “continuous uniform” distribution over the stated interval. To sample $Unif[a, b), b > a$ multiply the output of random_sample by (b-a) and add a:

(b - a) * random_sample() + a

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – Array of random floats of shape size (unless `size=None`, in which case a single float is returned).
Return type:	float or ndarray of floats

Examples

>>> np.random.random_sample()
0.47108547995356098
>>> type(np.random.random_sample())
<type 'float'>
>>> np.random.random_sample((5,))
array([ 0.30220482,  0.86820401,  0.1654503 ,  0.11659149,  0.54323428])

Three-by-two array of random numbers from [-5, 0):

>>> 5 * np.random.random_sample((3, 2)) - 5
array([[-3.99149989, -0.52338984],
       [-2.99091858, -0.79479508],
       [-1.23204345, -1.75224494]])

nugridpy.ppn.seed(seed=None)¶

Seed the generator.

This method is called when RandomState is initialized. It can be called again to re-seed the generator. For details, see RandomState.

Parameters:	seed (int or array_like, optional) – Seed for RandomState. Must be convertible to 32 bit unsigned integers.

See also

RandomState()

nugridpy.ppn.set_state(state)¶

Set the internal state of the generator from a tuple.

For use if one has reason to manually (re-)set the internal state of the “Mersenne Twister”[R50116] pseudo-random number generating algorithm.

Parameters:

state (tuple(str, ndarray of 624 uints, int, int, float)) –

The state tuple has the following items:

the string ‘MT19937’, specifying the Mersenne Twister algorithm.
a 1-D array of 624 unsigned integers keys.
an integer pos.
an integer has_gauss.
a float cached_gaussian.

Returns: out – Returns ‘None’ on success.

Return type: None

See also

get_state()

Notes

set_state and get_state are not needed to work with any of the random distributions in NumPy. If the internal state is manually altered, the user should know exactly what he/she is doing.

For backwards compatibility, the form (str, array of 624 uints, int) is also accepted although it is missing some information about the cached Gaussian value: state = ('MT19937', keys, pos).

References

[R50116]

M. Matsumoto and T. Nishimura, “Mersenne Twister: A 623-dimensionally equidistributed uniform pseudorandom number generator,” ACM Trans. on Modeling and Computer Simulation, Vol. 8, No. 1, pp. 3-30, Jan. 1998.

nugridpy.ppn.shuffle(x)¶

Modify a sequence in-place by shuffling its contents.

This function only shuffles the array along the first axis of a multi-dimensional array. The order of sub-arrays is changed but their contents remains the same.

Parameters:	x (array_like) – The array or list to be shuffled.
Returns:
Return type:	None

Examples

>>> arr = np.arange(10)
>>> np.random.shuffle(arr)
>>> arr
[1 7 5 2 9 4 3 6 0 8]

Multi-dimensional arrays are only shuffled along the first axis:

>>> arr = np.arange(9).reshape((3, 3))
>>> np.random.shuffle(arr)
>>> arr
array([[3, 4, 5],
       [6, 7, 8],
       [0, 1, 2]])

nugridpy.ppn.standard_cauchy(size=None)¶

Draw samples from a standard Cauchy distribution with mode = 0.

Also known as the Lorentz distribution.

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	samples – The drawn samples.
Return type:	ndarray or scalar

Notes

The probability density function for the full Cauchy distribution is

\[P(x; x_0, \gamma) = \frac{1}{\pi \gamma \bigl[ 1+ (\frac{x-x_0}{\gamma})^2 \bigr] }\]

and the Standard Cauchy distribution just sets $x_0=0$ and $\gamma=1$

The Cauchy distribution arises in the solution to the driven harmonic oscillator problem, and also describes spectral line broadening. It also describes the distribution of values at which a line tilted at a random angle will cut the x axis.

When studying hypothesis tests that assume normality, seeing how the tests perform on data from a Cauchy distribution is a good indicator of their sensitivity to a heavy-tailed distribution, since the Cauchy looks very much like a Gaussian distribution, but with heavier tails.

References

[R51117]

NIST/SEMATECH e-Handbook of Statistical Methods, “Cauchy Distribution”, http://www.itl.nist.gov/div898/handbook/eda/section3/eda3663.htm

[R52117]

Weisstein, Eric W. “Cauchy Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/CauchyDistribution.html

[R53117]

Wikipedia, “Cauchy distribution” http://en.wikipedia.org/wiki/Cauchy_distribution

Examples

Draw samples and plot the distribution:

>>> s = np.random.standard_cauchy(1000000)
>>> s = s[(s>-25) & (s<25)]  # truncate distribution so it plots well
>>> plt.hist(s, bins=100)
>>> plt.show()

nugridpy.ppn.standard_exponential(size=None)¶

Draw samples from the standard exponential distribution.

standard_exponential is identical to the exponential distribution with a scale parameter of 1.

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – Drawn samples.
Return type:	float or ndarray

Examples

Output a 3x8000 array:

>>> n = np.random.standard_exponential((3, 8000))

nugridpy.ppn.standard_gamma(shape, size=None)¶

Draw samples from a standard Gamma distribution.

Samples are drawn from a Gamma distribution with specified parameters, shape (sometimes designated “k”) and scale=1.

Parameters:	shape (float or array_like of floats) – Parameter, should be > 0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `shape` is a scalar. Otherwise, `np.array(shape).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized standard gamma distribution.
Return type:	ndarray or scalar

See also

scipy.stats.gamma(): probability density function, distribution or cumulative density function, etc.

Notes

The probability density for the Gamma distribution is

\[p(x) = x^{k-1}\frac{e^{-x/\theta}}{\theta^k\Gamma(k)},\]

where $k$ is the shape and $\theta$ the scale, and $\Gamma$ is the Gamma function.

The Gamma distribution is often used to model the times to failure of electronic components, and arises naturally in processes for which the waiting times between Poisson distributed events are relevant.

References

[R54120]

Weisstein, Eric W. “Gamma Distribution.” From MathWorld–A Wolfram Web Resource. http://mathworld.wolfram.com/GammaDistribution.html

[R55120]

Wikipedia, “Gamma distribution”, http://en.wikipedia.org/wiki/Gamma_distribution

Examples

Draw samples from the distribution:

>>> shape, scale = 2., 1. # mean and width
>>> s = np.random.standard_gamma(shape, 1000000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> import scipy.special as sps
>>> count, bins, ignored = plt.hist(s, 50, normed=True)
>>> y = bins**(shape-1) * ((np.exp(-bins/scale))/ \
...                       (sps.gamma(shape) * scale**shape))
>>> plt.plot(bins, y, linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn.standard_normal(size=None)¶

Draw samples from a standard Normal distribution (mean=0, stdev=1).

Parameters:	size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. Default is None, in which case a single value is returned.
Returns:	out – Drawn samples.
Return type:	float or ndarray

Examples

>>> s = np.random.standard_normal(8000)
>>> s
array([ 0.6888893 ,  0.78096262, -0.89086505, ...,  0.49876311, #random
       -0.38672696, -0.4685006 ])                               #random
>>> s.shape
(8000,)
>>> s = np.random.standard_normal(size=(3, 4, 2))
>>> s.shape
(3, 4, 2)

nugridpy.ppn.standard_t(df, size=None)¶

Draw samples from a standard Student’s t distribution with df degrees of freedom.

A special case of the hyperbolic distribution. As df gets large, the result resembles that of the standard normal distribution (standard_normal).

Parameters:	df (int or array_like of ints) – Degrees of freedom, should be > 0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `df` is a scalar. Otherwise, `np.array(df).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized standard Student’s t distribution.
Return type:	ndarray or scalar

Notes

The probability density function for the t distribution is

\[P(x, df) = \frac{\Gamma(\frac{df+1}{2})}{\sqrt{\pi df} \Gamma(\frac{df}{2})}\Bigl( 1+\frac{x^2}{df} \Bigr)^{-(df+1)/2}\]

The t test is based on an assumption that the data come from a Normal distribution. The t test provides a way to test whether the sample mean (that is the mean calculated from the data) is a good estimate of the true mean.

The derivation of the t-distribution was first published in 1908 by William Gosset while working for the Guinness Brewery in Dublin. Due to proprietary issues, he had to publish under a pseudonym, and so he used the name Student.

References

[R56122]

Dalgaard, Peter, “Introductory Statistics With R”, Springer, 2002.

[R57122]

Wikipedia, “Student’s t-distribution” http://en.wikipedia.org/wiki/Student’s_t-distribution

Examples

From Dalgaard page 83 [R56122], suppose the daily energy intake for 11 women in Kj is:

>>> intake = np.array([5260., 5470, 5640, 6180, 6390, 6515, 6805, 7515, \
...                    7515, 8230, 8770])

Does their energy intake deviate systematically from the recommended value of 7725 kJ?

We have 10 degrees of freedom, so is the sample mean within 95% of the recommended value?

>>> s = np.random.standard_t(10, size=100000)
>>> np.mean(intake)
6753.636363636364
>>> intake.std(ddof=1)
1142.1232221373727

Calculate the t statistic, setting the ddof parameter to the unbiased value so the divisor in the standard deviation will be degrees of freedom, N-1.

>>> t = (np.mean(intake)-7725)/(intake.std(ddof=1)/np.sqrt(len(intake)))
>>> import matplotlib.pyplot as plt
>>> h = plt.hist(s, bins=100, normed=True)

For a one-sided t-test, how far out in the distribution does the t statistic appear?

>>> np.sum(s<t) / float(len(s))
0.0090699999999999999  #random

So the p-value is about 0.009, which says the null hypothesis has a probability of about 99% of being true.

nugridpy.ppn.triangular(left, mode, right, size=None)¶

Draw samples from the triangular distribution over the interval [left, right].

The triangular distribution is a continuous probability distribution with lower limit left, peak at mode, and upper limit right. Unlike the other distributions, these parameters directly define the shape of the pdf.

Parameters:	left (float or array_like of floats) – Lower limit. mode (float or array_like of floats) – The value where the peak of the distribution occurs. The value should fulfill the condition `left <= mode <= right`. right (float or array_like of floats) – Upper limit, should be larger than left. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `left`, `mode`, and `right` are all scalars. Otherwise, `np.broadcast(left, mode, right).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized triangular distribution.
Return type:	ndarray or scalar

Notes

The probability density function for the triangular distribution is

\[\begin{split}P(x;l, m, r) = \begin{cases} \frac{2(x-l)}{(r-l)(m-l)}& \text{for $l \leq x \leq m$},\\ \frac{2(r-x)}{(r-l)(r-m)}& \text{for $m \leq x \leq r$},\\ 0& \text{otherwise}. \end{cases}\end{split}\]

The triangular distribution is often used in ill-defined problems where the underlying distribution is not known, but some knowledge of the limits and mode exists. Often it is used in simulations.

References

[R58124]

Wikipedia, “Triangular distribution” http://en.wikipedia.org/wiki/Triangular_distribution

Examples

Draw values from the distribution and plot the histogram:

>>> import matplotlib.pyplot as plt
>>> h = plt.hist(np.random.triangular(-3, 0, 8, 100000), bins=200,
...              normed=True)
>>> plt.show()

nugridpy.ppn.uniform(low=0.0, high=1.0, size=None)¶

Draw samples from a uniform distribution.

Samples are uniformly distributed over the half-open interval [low, high) (includes low, but excludes high). In other words, any value within the given interval is equally likely to be drawn by uniform.

Parameters:	low (float or array_like of floats, optional) – Lower boundary of the output interval. All values generated will be greater than or equal to low. The default value is 0. high (float or array_like of floats) – Upper boundary of the output interval. All values generated will be less than high. The default value is 1.0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `low` and `high` are both scalars. Otherwise, `np.broadcast(low, high).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized uniform distribution.
Return type:	ndarray or scalar

See also

randint(): Discrete uniform distribution, yielding integers.
random_integers(): Discrete uniform distribution over the closed interval [low, high].
random_sample(): Floats uniformly distributed over [0, 1).
random(): Alias for random_sample.
rand(): Convenience function that accepts dimensions as input, e.g., rand(2,2) would generate a 2-by-2 array of floats, uniformly distributed over [0, 1).

Notes

The probability density function of the uniform distribution is

\[p(x) = \frac{1}{b - a}\]

anywhere within the interval [a, b), and zero elsewhere.

When high == low, values of low will be returned. If high < low, the results are officially undefined and may eventually raise an error, i.e. do not rely on this function to behave when passed arguments satisfying that inequality condition.

Examples

Draw samples from the distribution:

>>> s = np.random.uniform(-1,0,1000)

All values are within the given interval:

>>> np.all(s >= -1)
True
>>> np.all(s < 0)
True

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> count, bins, ignored = plt.hist(s, 15, normed=True)
>>> plt.plot(bins, np.ones_like(bins), linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn.vonmises(mu, kappa, size=None)¶

Draw samples from a von Mises distribution.

Samples are drawn from a von Mises distribution with specified mode (mu) and dispersion (kappa), on the interval [-pi, pi].

The von Mises distribution (also known as the circular normal distribution) is a continuous probability distribution on the unit circle. It may be thought of as the circular analogue of the normal distribution.

Parameters:	mu (float or array_like of floats) – Mode (“center”) of the distribution. kappa (float or array_like of floats) – Dispersion of the distribution, has to be >=0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `mu` and `kappa` are both scalars. Otherwise, `np.broadcast(mu, kappa).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized von Mises distribution.
Return type:	ndarray or scalar

See also

scipy.stats.vonmises(): probability density function, distribution, or cumulative density function, etc.

Notes

The probability density for the von Mises distribution is

\[p(x) = \frac{e^{\kappa cos(x-\mu)}}{2\pi I_0(\kappa)},\]

where $\mu$ is the mode and $\kappa$ the dispersion, and $I_0(\kappa)$ is the modified Bessel function of order 0.

The von Mises is named for Richard Edler von Mises, who was born in Austria-Hungary, in what is now the Ukraine. He fled to the United States in 1939 and became a professor at Harvard. He worked in probability theory, aerodynamics, fluid mechanics, and philosophy of science.

References

[R59125]

Abramowitz, M. and Stegun, I. A. (Eds.). “Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables, 9th printing,” New York: Dover, 1972.

[R60125]

von Mises, R., “Mathematical Theory of Probability and Statistics”, New York: Academic Press, 1964.

Examples

Draw samples from the distribution:

>>> mu, kappa = 0.0, 4.0 # mean and dispersion
>>> s = np.random.vonmises(mu, kappa, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> from scipy.special import i0
>>> plt.hist(s, 50, normed=True)
>>> x = np.linspace(-np.pi, np.pi, num=51)
>>> y = np.exp(kappa*np.cos(x-mu))/(2*np.pi*i0(kappa))
>>> plt.plot(x, y, linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn.wald(mean, scale, size=None)¶

Draw samples from a Wald, or inverse Gaussian, distribution.

As the scale approaches infinity, the distribution becomes more like a Gaussian. Some references claim that the Wald is an inverse Gaussian with mean equal to 1, but this is by no means universal.

The inverse Gaussian distribution was first studied in relationship to Brownian motion. In 1956 M.C.K. Tweedie used the name inverse Gaussian because there is an inverse relationship between the time to cover a unit distance and distance covered in unit time.

Parameters:	mean (float or array_like of floats) – Distribution mean, should be > 0. scale (float or array_like of floats) – Scale parameter, should be >= 0. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `mean` and `scale` are both scalars. Otherwise, `np.broadcast(mean, scale).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Wald distribution.
Return type:	ndarray or scalar

Notes

The probability density function for the Wald distribution is

\[P(x;mean,scale) = \sqrt{\frac{scale}{2\pi x^3}}e^ \frac{-scale(x-mean)^2}{2\cdotp mean^2x}\]

As noted above the inverse Gaussian distribution first arise from attempts to model Brownian motion. It is also a competitor to the Weibull for use in reliability modeling and modeling stock returns and interest rate processes.

References

[R61127]

Brighton Webs Ltd., Wald Distribution, http://www.brighton-webs.co.uk/distributions/wald.asp

[R62127]

Chhikara, Raj S., and Folks, J. Leroy, “The Inverse Gaussian Distribution: Theory : Methodology, and Applications”, CRC Press, 1988.

[R63127]

Wikipedia, “Wald distribution” http://en.wikipedia.org/wiki/Wald_distribution

Examples

Draw values from the distribution and plot the histogram:

>>> import matplotlib.pyplot as plt
>>> h = plt.hist(np.random.wald(3, 2, 100000), bins=200, normed=True)
>>> plt.show()

nugridpy.ppn.weibull(a, size=None)¶

Draw samples from a Weibull distribution.

Draw samples from a 1-parameter Weibull distribution with the given shape parameter a.

\[X = (-ln(U))^{1/a}\]

Here, U is drawn from the uniform distribution over (0,1].

The more common 2-parameter Weibull, including a scale parameter $\lambda$ is just $X = \lambda(-ln(U))^{1/a}$.

Parameters:	a (float or array_like of floats) – Shape of the distribution. Should be greater than zero. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `a` is a scalar. Otherwise, `np.array(a).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Weibull distribution.
Return type:	ndarray or scalar

See also

scipy.stats.weibull_max(), scipy.stats.weibull_min(), scipy.stats.genextreme(), gumbel()

Notes

The Weibull (or Type III asymptotic extreme value distribution for smallest values, SEV Type III, or Rosin-Rammler distribution) is one of a class of Generalized Extreme Value (GEV) distributions used in modeling extreme value problems. This class includes the Gumbel and Frechet distributions.

The probability density for the Weibull distribution is

\[p(x) = \frac{a} {\lambda}(\frac{x}{\lambda})^{a-1}e^{-(x/\lambda)^a},\]

where $a$ is the shape and $\lambda$ the scale.

The function has its peak (the mode) at $\lambda(\frac{a-1}{a})^{1/a}$.

When a = 1, the Weibull distribution reduces to the exponential distribution.

References

[R64130]

Waloddi Weibull, Royal Technical University, Stockholm, 1939 “A Statistical Theory Of The Strength Of Materials”, Ingeniorsvetenskapsakademiens Handlingar Nr 151, 1939, Generalstabens Litografiska Anstalts Forlag, Stockholm.

[R65130]

Waloddi Weibull, “A Statistical Distribution Function of Wide Applicability”, Journal Of Applied Mechanics ASME Paper 1951.

[R66130]

Wikipedia, “Weibull distribution”, http://en.wikipedia.org/wiki/Weibull_distribution

Examples

Draw samples from the distribution:

>>> a = 5. # shape
>>> s = np.random.weibull(a, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> x = np.arange(1,100.)/50.
>>> def weib(x,n,a):
...     return (a / n) * (x / n)**(a - 1) * np.exp(-(x / n)**a)

>>> count, bins, ignored = plt.hist(np.random.weibull(5.,1000))
>>> x = np.arange(1,100.)/50.
>>> scale = count.max()/weib(x, 1., 5.).max()
>>> plt.plot(x, weib(x, 1., 5.)*scale)
>>> plt.show()

class nugridpy.ppn.xtime(sldir='./', fname='x-time.dat')¶

read and plot x-time.dat output files.

Parameters:	sldir (string, optional) – The directory of the specified filename. The default is ‘./’. fname (string, optional) – Specify alternative filename of file of type x-time.dat. The default is ‘x-time.dat’.
Returns:	A xtime instance.
Return type:	xtime

Examples

>>> import ppn
>>> f=ppn.xtime()
There are 1099 species found.
There are 19 time steps found.

>>> f.col
f.col_num  f.col_tot  f.cols

>>> f.cols[0:10]
['age',
't9',
'rho',
'sum_yps',
'NEUT',
'PROT',
'H   2',
'HE  3',
'HE  4',
'BE  7']

>>> f.plot('HE  4')
age HE  4

>>> f.plot('C  12')
age C  12

>>> f.plot('PROT')

get(col_str)¶

get one data column with the data

Parameters:	col_str (string) – One of the column strings in self.cols.

plot_xtime(y, x='t_y', label='default', labelx=None, labely=None, title=None, shape='.', logx=False, logy=True, base=10)¶

make a simple plot of two columns against each other.

An example would be instance.plot_xtime(‘PB206’, label=’PB206 vs t_y’ Recomend using the plot function DataPlot.plot() it has more functionality.

Parameters:

Y (string) – Column on Y-axis.
X (string, optional) – Column on X-axis. The default is “t_y”.
label (string, optional) – Legend label. The default is “default”.
labelX (string, optional) – The label on the X axis. The default is None.
labelY (string, optional) – The label on the Y axis. The default is None.
title (string, optional) – The Title of the Graph. The default is None.
shape (string, optional) – What shape and colour the user would like their plot in. The default is ‘.’.
logX (boolean, optional) – A boolean of weather the user wants the x axis logarithmically. The default is False.
logY (boolean, optional) – A boolean of weather the user wants the Y axis logarithmically. The default is True.
base (integer, optional) – The base of the logarithm. The default is 10.

Notes

For all possable choices visit, <http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.plot>

nugridpy.ppn.zipf(a, size=None)¶

Draw samples from a Zipf distribution.

Samples are drawn from a Zipf distribution with specified parameter a > 1.

The Zipf distribution (also known as the zeta distribution) is a continuous probability distribution that satisfies Zipf’s law: the frequency of an item is inversely proportional to its rank in a frequency table.

Parameters:	a (float or array_like of floats) – Distribution parameter. Should be greater than 1. size (int or tuple of ints, optional) – Output shape. If the given shape is, e.g., `(m, n, k)`, then `m * n * k` samples are drawn. If size is `None` (default), a single value is returned if `a` is a scalar. Otherwise, `np.array(a).size` samples are drawn.
Returns:	out – Drawn samples from the parameterized Zipf distribution.
Return type:	ndarray or scalar

See also

scipy.stats.zipf(): probability density function, distribution, or cumulative density function, etc.

Notes

The probability density for the Zipf distribution is

\[p(x) = \frac{x^{-a}}{\zeta(a)},\]

where $\zeta$ is the Riemann Zeta function.

It is named for the American linguist George Kingsley Zipf, who noted that the frequency of any word in a sample of a language is inversely proportional to its rank in the frequency table.

References

[R67133]

Zipf, G. K., “Selected Studies of the Principle of Relative Frequency in Language,” Cambridge, MA: Harvard Univ. Press, 1932.

Examples

Draw samples from the distribution:

>>> a = 2. # parameter
>>> s = np.random.zipf(a, 1000)

Display the histogram of the samples, along with the probability density function:

>>> import matplotlib.pyplot as plt
>>> from scipy import special

Truncate s values at 50 so plot is interesting:

>>> count, bins, ignored = plt.hist(s[s<50], 50, normed=True)
>>> x = np.arange(1., 50.)
>>> y = x**(-a) / special.zetac(a)
>>> plt.plot(x, y/max(y), linewidth=2, color='r')
>>> plt.show()

nugridpy.ppn¶

PPN Assumptions¶

NuGridPy

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