Questions tagged [scipy]

SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.

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14 views

How to calculate chi-square from a contingency table in python? [on hold]

I conducted an online survey where I collected subject interests of women. I created the following contingency table from my survey which shows the frequency of each selected subject. ...
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45 views

Weird sample variance when creating a lognromal sample with pre-defined mean and variance [duplicate]

I have been working with lognormal distributions as a proposal distribution for some MCMC routines which require the proposal distribution to have some pre-defined sample mean and variance, $m$ and $v$...
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21 views

Finding Local Extema in Scipy's Gaussian KDE [on hold]

This is a follow-up to Distribution with 3 Modes, Find the 2 In-Between Minima It was suggested that I use kernel density estimates. Since I'm on Python, I thought of using scipy.stats.gaussian_kde. ...
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1answer
16 views

What is the reasoning behind the default eps value for the 'SLSQP' method in SciPy's minimize function? [closed]

From here: https://docs.scipy.org/doc/scipy/reference/optimize.minimize-slsqp.html#optimize-minimize-slsqp It says that the default value for the eps option is <...
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1answer
23 views

Generating synthetic data based on mean, skewness, standard deviation and autocorrelation

Given that I have the mean, standard deviation, skewness and autocorrelation, How do I generate 1000 years of random data based on the above parameters in python or Matlab? I know for example I can ...
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14 views

linear correlation in N-Dimensional sample

I've an N-dimensional sample linearly correlated to each other in pairs. That is, every event includes N variables, and every variable is a predictor to all the other (or, in other words, putting the ...
2
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1answer
39 views

Kolmogorov-Smirnov (ks_2samp) p-value not as expected - Wrong test or understanding?

Context I am using scipy's ks_samp in order to apply the Kolmogorov-Smirnov-test. The data I use is twofold: I have a dataset ...
1
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1answer
28 views

How do I statistically compare the readings from two different sensors? [duplicate]

I have temperature and humidity readings from two different sensors (located in the same geographical area). The data is logged every hour and I have data for more than a year, logged this way 2/1/...
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1answer
29 views

Comparing sensor data across multiple experiments

I have some questions about doing statistics on a series of sensor measurements. I have 12 series of data of sensor measurements (a force sensor, measuring at 10 Hz for 30 minutes). Each series ...
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14 views

Location and scale estimation for log-logistic in scipy

I have to estimate the location and scale parameters for a log-logistic or fisk distribution using scipy. The shape parameter is already defined and I would like to estimate loc and scale parameter ...
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1answer
65 views

Why does the mean for a beta distribution when input into the scipy beta cdf not return 0.5? [duplicate]

Very likely I am missing some fundamentals here, or my python coding is not up to scratch. When I use the standard formula to calculate the mean for a beta distribution ~ $B(\alpha,\beta)$ $$ \mu = \...
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14 views

What is the name of the significance test scipy.stats.pearsonr is using?

The Notes section in the docs describes it in detail but does not name it. I would like to avoid guessing. They use a beta distribution in this way: ...
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10 views

Is Fisher Kurtosis the same as Excess Kurtosis?

The documentation for scipy.stats.describe() defines the returned kurtosis like so: ...
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0answers
21 views

Fitting data to a distribution that appears lognormal without right-hump

I will like to fit a distribution and extract its moments in Python, given Length of Stay (LOS) data in hospitals. Asking out of curiosity, suppose the plot of the data looks like: The reason why I ...
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1answer
96 views

Fitting Beta Distributions to Data

I am trying to reproduce some beta distribution parameters found in this published paper. I have two data sets, y1 and y2, that ...
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0answers
71 views

Calculating standard errors of non-OLS regressions in python and scipy [closed]

Scipy/statsmodels provides the ability to get a number of metrics from the output of an OLS regression model, a few examples of which (from statsmodels) are the following: ...
1
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1answer
94 views

Weighted Minkowski distance for DBSCAN

I'm trying to make clustering of image's pixels with DBSCAN, using RGB values and pixel's coordinates as features. It works well with just RGB values as features, but I want pixels with the same color,...
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0answers
80 views

Gamma Distribution CDF Intuition; Are My Parameters Correct?

I'm learning about gamma distributions and I want to make sure my reasoning is correct for an example I found here. Suppose you are fishing and you expect to get a fish once every 1/2 hour. ...
1
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1answer
154 views

Goodness of fit measurement in Python

I have a (pretty noisy) 1D array of data in Python that I fit a linear function to -- see plot below. The x-axis is a wavelength scale. I would like to measure the "goodness of fit" of this new line ...
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0answers
20 views

Optimizing a piecewise-linear, convex function [closed]

I want to find the matrix $U$ that minimizes the following loss function: $$ \min_U( \max_{0 \le j \le t} (\operatorname{tr}(W_jU) + b_j) + \operatorname{tr}(U^TU)) $$ The given loss function is ...
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0answers
26 views

Truncate a Hierarchical Clustering tree in order to get the cophenetic coefficient

I've gone ahead and clustered a dataset using a Euclidian Hierarchical Clustering algorithm: ...
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1answer
108 views

Chi Square Analysis Throws Error - The internally computed table of expected frequencies has a zero element at (0,)

I am trying to see the association between two variables. I used Chi-Square analysis in Scipy package in Python. Here is the crosstab result of the two variables: ...
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1answer
46 views

Difference between p-value of chi-squared calculation, and p-value in “critical value” lookup table

I am learning about chi-squared. It has two steps; a) chi-squared calculation b) critical value When I calculate chi-squared, the output includes a) chi-squared statistic (220.5) and b) a p-value (...
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1answer
30 views

least square with equality constraint and singular matrix

I have the following problem to solve: Ax = b where A is singular. To resolve this I introduce a condition Cx = d Even after this, I am not able to solve it using scipy.optimize.minimize as it ...
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0answers
136 views

How to improve Pairwise Euclidean Distance for Similarity Measure

I am trying to identify the most similar stations between two DataFrames like below: ...
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0answers
55 views

Can't understand the Beta distribution as described in this paper

I'm reading through the following paper (1). On page 2, section 2.1, there's a description of the selection of a beta distribution used: Since both the choice of s and the strategy for handling the ...
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1answer
158 views

Fixing the maximum distance within a cluster

I am trying to cluster geographical locations in such a way that all the locations inside each cluster are at max within 25 miles of each other. For this, I am using Agglomerative clustering. I am ...
3
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1answer
378 views

Why is computing ridge regression with a Cholesky decomposition much quicker than using SVD?

By my understanding, for a matrix with n samples and p features: Ridge regression using Cholesky decomposition takes O(p^3) time Ridge regression using SVD takes O(p^3) time Computing SVD when only ...
3
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0answers
54 views

Why is it much quicker to compute ridge regression than regular linear regression?

By my understanding, for a matrix with n samples and p features: Ridge regression using cholesky takes O(p^3) time Ordinary linear regression takes O(p^3) time Singular value decomposition if u, v ...
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0answers
31 views

How to stop fmin_slqsp from converging to local minimum?

I want to run linear regression with inequality constraints and non-negative coefficients. My data looks roughly like this: ...
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0answers
476 views

Proper way to plot confidence interval under normal distribution curve?

I write a small program which calculates a confidence interval for a given norm value. The output is then visualized by plotting the confidence interval and the corresponding hypothetical norm value ...
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0answers
40 views

Numerical approximation of sandwich estimator

I have found the MLE of a model using scipy.optimize.minimize with the BFGS algorithm. As is commonly done, I intend to estimate the variance from $$ Var(\theta_0) ...
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1answer
26 views
1
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1answer
80 views

How to estimate the leafsize of the kd-tree?

The kd-tree implementation proposed by the scipy python libray asks for the value of the leafsize parameter that is to say the maximum number of points a node can hold. It is by default set to 10. ...
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0answers
13 views

Constructing an appropriate null hypothesis?

I have a collection of 20 2D surfaces embedded in 3D. The mean curvature of each surface has been sampled. The number of samples per surface varies from ~700,000 to ~20,000,000. The choice of ...
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0answers
380 views

Calculating P-value for multivariate normal distributions?

I'm given a set of 500 ($\sigma_i, \mu_i$) that define a 500-dimensional multivariate normal distribution, where each dimension is effectively independent from all the others. Given a 500-...
2
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1answer
376 views

How does scipy calculate the binomial CDF so fast?

I ran scipy.stats.binom.cdf(500006, 1000000, 0.5) and it took less than a milisecond. This is crazy as binomial CDF involves summing up a bunch of binomial coefficients. What approximation algorithm ...
0
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1answer
180 views

How to perform batch training using L-BFGS?

I want to train a neural network for regression. The neural network is actually composed of 4 separate child neural networks, each child neural network has a layer structure of ...
1
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3answers
561 views

How to calculate the p-value of a test, that checked for a binary property?

16081 subjects were randomly assigned into two groups: test group: 7916 subjects control group: 8165 subjects Only the test group was exposed to something. During the test period 10 subjects of ...
0
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1answer
212 views

Normal distribution test ( D'Agostino and Pearson's) in Scipy - results don't make sense

I want to test if an array of numbers is approximately normally distributed. ...
1
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0answers
21 views

3 Layer neural network (feedforward and backpropagation) - Desired error not necessarily achieved due to precision loss

I am trying to implement a 3 layer neural network with feedforward and backpropagation. I have tested my cost function and it is working fine. My gradient function also seems ok. but when I try to ...
0
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1answer
30 views

Remove individual points and find slope

I am trying to delete one pair of x and y coordinates from a set of 10 data points and get the slope for the other 9 points. How do I go about this issue? Attached herewith is an image of what I am ...
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0answers
250 views

Update R2 and slope by removing outliers-python [closed]

I am using the following code to find out Linregress parameters: ...
0
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1answer
649 views

Statsmodels' Negative Binomial: after .fit_regularized(), how to turn PMF into PPF to get the discrete values?

I used the package statsmodels to fit a Negative Binomial to my data. This data contains ~1500 samples with 21 covariates. Since I have overdispersion in my data ...
0
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1answer
17 views

Can findings based on low values be considered valid?

Lets say i do have a TimeSeries with N > 300 but values like [0, 1, 2, 1, 2, 0, 2, ...] representing the visitors count of a website per day. Since there are only few visitors and each of them can be ...
1
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1answer
606 views

How to know if a parameter is statistically significant in a “curve_fit” estimation? [closed]

I use curve_fit from scipy to estimate parameter values from a specific function. ...
0
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1answer
148 views

nmf in scipy returns components with all zero weights

I'm trying to understand whether this behavior is a bug or a feature. Essentially, I have a dataset of ten thousand short pieces of text. I have used the CountVectorizer function to turn this into a ...
1
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0answers
25 views

Mode of function kstest in module scipy.stats.stats

In the function kstest in module scipy.stats.stats, there are two options for the mode, described in the help file: ...
2
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1answer
392 views

Gaussian Mixture Model

with the following code I fit a Gaussian Mixture Model to arbitrarily created data. The code is working. The only thing I encounter is that during the calculation of the multivariate_normal I ...