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Questions tagged [kernel-density]

kernel density estimation is a non-parametric way to estimate the probability density function of a random variable.

Kernel density estimation is a fundamental data smoothing problem where inferences about the population are made, based on a finite data sample. Kernel density estimates are closely related to histograms, but can be endowed with properties such as smoothness or continuity by using a suitable kernel

http://en.wikipedia.org/wiki/Kernel_density_estimation

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Height values for each point in a plot

I have a data of protein-protein interactions in a data frame entitled: s1m. Each DB and AD pair make an interaction and I can plot it as well: > head(s1m) DB_num AD_num [1,] 2 8153 [2,] 7 3553 [3,] 8 4812 [4,] 13 …
Kerpal Jenkiens
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kde2d density comparison

I have a question about the kde2d (Kernel density estimator). I am computing two different kde2d for two different sets of data in the same space of variables. When I compare both with a filled.contour2 or contours I see that the set with lower…
Andre
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Density plots with multiple groups

I am trying to produce something similar to densityplot() from the lattice package, using ggplot2 after using multiple imputation with the mice package. Here is a reproducible example: require(mice) dt <- nhanes impute <- mice(dt, seed =…
Joe King
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Seaborn error with kde plot: The following variable cannot be assigned with wide-form data `hue`

I have a pandas dataframe df with two columns (type and IR) as this one: type IR 0 a 0.1 1 b 0.3 2 b 0.2 3 c 0.8 4 c 0.5 ... I want to plot three distributions (one for each type) with the values of…
Palinuro
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Python--calculate normalized probability of a value given a list of samples

So, as the title says, I'm trying to calculate the probability of a value given a list of samples, preferably normalized so the probability is 0
Tessa
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How to calculate percent overlap in distributions in r?

I have a dummy dataframe below where I'd like to calculate the pairwise percent overlap between site distributions. Basically, what percent of site1 and site2 are overlapping, site2 vs site3 and site1 vs site3? structure(list(site = c("site1",…
T1802173
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Why does stat_density2d not always depict densities correctly?

I am currently working on a project, and so far I have extracted data. Im in the works of visualising some of it. Thats where the issue starts. I have an issue with ggmap density-plotting, especially in areas with smaller amounts of points. I can…
R. Alexander
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What is the Python equivalent (i.e. same output) for the R function density()?

In R, there is a function called density(). The syntax for the function is - density(x, bw = "nrd0", adjust = 1, kernel = c("gaussian", "epanechnikov", "rectangular", "triangular", "biweight","cosine", "optcosine"), weights = NULL,…
Ral'akkai
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Kernel density estimation for periodic data

Is it possible to obtain a KDE for periodic data in sklearn or a different Python package? Here is a simplified example: I am creating a mockup dataset from two normal distributions and map it to the interval from 0 to 20. import numpy as np import…
fuenfundachtzig
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Kernel density estimation in Python for over 4d data

I am trying to use SciPy's gaussian_kde function to estimate the density of multivariate data. In my code below, if the number of dimensions is over 4d, the following error may occur(about 50%). If the number is under 3d, the error does not occur in…
hiro_fff
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integrating the square of probability density?

Suppose I have set.seed(2020) # make the results reproducible a <- rnorm(100, 0, 1) My probability density is estimated through kernel density estimator (gaussian) in R using the R built in function density. The question is how to integrate the…
Z B
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Estimating density from interval [start, stop] data in R

Description The motivation for this question is from clinical/epidemiological research, wherein studies often enroll patients and then follow them for variable lengths of time. The distribution of age at study entry is often of interest and is…
user1231088
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Kernel Density Estimation in Computer Graphics

Evidently there is this high quality KDE algorithm that is used in the computer graphics industry, but everyone I've asked refuse to tell me what it is. I've implemented http://en.wikipedia.org/wiki/Kernel_density_estimation , but noise is still a…
Arlen
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Gaussian KDE of n-dimensional data : leading minor of the array is not positive definite

I have two subsets of n-dimensional data A and B, and I would like to know, for each sample in B the density of samples from A around it. Example datasets with 5 samples in 3 dimensions A = np.array([[-2.44528668, -0.09326276, -1.06527892], …
usernumber
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Density Estimation on Single Point

I am trying to plot the densities by using non-parametric kernel estimation method. For this purpose 'm using asymmetrical kernels like Weibull, Gamma, Inverse Gaussian, etc. i have successfully plotted the densities as given in their articles. My…
Angel
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