Recently, I began a series on exploratory data analysis; so far, I have written about computing descriptive statistics and creating box plots in R for a univariate data set with missing values. Today, I will continue this series by analyzing the same data set with kernel density estimation, a useful non-parametric technique for visualizing the underlying distribution of a continuous variable. I will show how to construct kernel density estimates and plot them in R. I will also introduce rug plots and show how they can complement kernel density plots. Recall from my previous post that I am using the ozone data from the “airquality” data set that is built into R and simulating a second ozone data set from a fictitious city called Ozonopolis. Just like the post on box plots, this is a long post with many details and useful tips in R, so read it carefully.
Read the rest of this post to learn how to construct these kernel density plots!
What is a Kernel?
- its definite integral over its support set must equal to 1
What is Kernel Density Estimation?
Kernel density estimation is a non-parametric method of estimating the probability density function (PDF) of a continuous random variable. It is non-parametric because it does not assume any underlying distribution for the variable. Essentially, at every datum, a kernel function is created with the datum at its centre – this ensures that the kernel is symmetric about the datum. The PDF is then estimated by adding all of these kernel functions and dividing by the number of data to ensure that it satisfies the 2 properties of a PDF:
- Every possible value of the PDF (i.e. the function, ), is non-negative.
- The definite integral of the PDF over its support set equals to 1.
Intuitively, a kernel density estimate is a sum of “bumps”. A “bump” is assigned to every datum, and the size of the “bump” represents the probability assigned at the neighbourhood of values around that datum; thus, if the data set contains
- 2 data at x = 1.5
- 1 datum at x = 0.5
then the “bump” at x = 1.5 is twice as big as the “bump” at x = 0.5.
Each “bump” is centred at the datum, and it spreads out symmetrically to cover the datum’s neighbouring values. Each kernel has a bandwidth, and it determines the width of the “bump” (the width of the neighbourhood of values to which probability is assigned). A bigger bandwidth results in a shorter and wider “bump” that spreads out farther from the centre and assigns more probability to the neighbouring values.
Constructing a Kernel Density Estimate: Step by Step
1) Choose a kernel; the common ones are normal (Gaussian), uniform (rectangular), and triangular.
2) At each datum, , build the scaled kernel function
where is your chosen kernel function. The parameter is called the bandwidth, the window width, or the smoothing parameter.
3) Add all of the individual scaled kernel functions and divide by ; this places a probability of to each . It also ensures that the kernel density estimate integrates to 1 over its support set.
The density() function in R computes the values of the kernel density estimate. Applying the plot() function to an object created by density() will plot the estimate. Applying the summary() function to the object will reveal useful statistics about the estimate.
Choosing the Bandwidth
It turns out that the choosing the bandwidth is the most difficult step in creating a good kernel density estimate that captures the underlying distribution of the variable (Trosset, Page 166). Choosing the bandwidth is a complicated topic that is better addressed in a more advanced book or paper, but here are some useful guidelines:
- A small results in a small standard deviation, and the kernel places most of the probability on the datum. Use this when the sample size is large and the data are tightly packed.
- A large results in a large standard deviation, and the kernel spreads more of the probability from the datum to its neighbouring values. Use this when the sample size is small and the data are sparse.
There is a tremendous amount of literature on how best to choose the bandwidth, and I will not go into detail about that in this post. There are 2 methods that are common in R: nrd0 and SJ, which refers to the method by Sheather & Jones. These are string arguments for the option ‘bw’ in the density() function. The default in density() is bw = ‘nrd0′.
Here is some R code to generate the following plots of 2 uniform kernel functions; note the use of the dunif() function.
##### Plot 2 Uniform Kernel Functions with Different Bandwidths ##### By Eric Cai - The Chemical Statistician # define support set of X x = seq(-1.5, 1.5, by = 0.01) # obtain uniform kernel function values uniform1 = dunif(x, min = -0.25, max = 0.25) uniform2 = dunif(x, min = -1.00, max = 1.00) # optional printing of PNG image to chosen directory png('INSERT YOUR DIRECTORY PATH HERE/uniform kernels.png') plot(x, uniform1, type = 'l', ylab = 'f(x)', xlab = 'x', main = '2 Uniform Kernels with Different Bandwidths', col = 'red') # add plot of second kernel function lines(x, uniform2, col = 'blue') # add legend; must specify 'lty' option, because these are line plots legend(0.28, 1.5, c('Uniform(-0.25, 0.25)', 'Uniform(-1.00, 1.00)'), lty = c(1,1), col = c('red', 'blue'), box.lwd = 0) dev.off()
Example: Ozone Pollution Data from New York and Ozonopolis
Recall that I used 2 sets of ozone data in my last post about box plots. One came from the “airquality” data set that is built into R. I simulated the other one and named its city of origin “Ozonopolis”. Here are the code and the plot of the kernel density estimates of the 2 ozone pollution data sets. I used the default settings in density() – specifically, I used the normal (Gaussian) kernel and the “nrd0” method of choosing the bandwidth. I encourage you to try the other settings. I have used the set.seed() function so that you can replicate my random numbers.
##### Kernel Density Estimation ##### By Eric Cai - The Chemical Statistician # extract "Ozone" data vector for New York ozone = airquality$Ozone # calculate the number of non-missing values in "ozone" n = sum(!is.na(ozone)) # calculate mean, variance and standard deviation of "ozone" by excluding missing values mean.ozone = mean(ozone, na.rm = T) var.ozone = var(ozone, na.rm = T) sd.ozone = sd(ozone, na.rm = T) # simulate ozone pollution data for ozonopolis # set seed for you to replicate my random numbers for comparison set.seed(1) ozone2 = rgamma(n, shape = mean.ozone^2/var.ozone+3, scale = var.ozone/mean.ozone+3) # obtain values of the kernel density estimates density.ozone = density(ozone, na.rm = T) density.ozone2 = density(ozone2, na.rm = T) # number of points used in density plot n.density1 = density.ozone$n n.density2 = density.ozone2$n # bandwidth in density plot bw.density1 = density.ozone$bw bw.density2 = density.ozone2$bw png('INSERT YOUR DIRECTORY PATH HERE/kernel density plot ozone.png') plot(density.ozone2, main = 'Kernel Density Estimates of Ozone \n in New York and Ozonopolis', xlab = 'Ozone (ppb)', ylab = 'Density', ylim = c(0, max(density.ozone$y, na.rm = T)), lty = 1) # add second density plot lines(density.ozone, lty = 3) # add legends to state sample sizes and bandwidths; notice use of paste() legend(100, 0.015, paste('New York: N = ', n.density1, ', Bandwidth = ', round(bw.density1, 1), sep = ''), bty = 'n') legend(100, 0.013, paste('Ozonopolis: N = ', n.density2, ', Bandwidth = ', round(bw.density2, 1), sep = ''), bty = 'n') # add legend to label plots legend(115, 0.011, c('New York', 'Ozonopolis'), lty = c(3,1), bty = 'n') dev.off()
It is clear that Ozonopolis has more ozone pollution than New York. The right-skewed shapes of both curves also suggest that the normal distribution may not be suitable. (If you read my blog post carefully, you will already see evidence of a different distribution!) In a later post, I will use quantile-quantile plots to illustrate this. Stay tuned!
To give you a better sense of why the density plots have higher “bumps” at certain places, take a look at the following plot of the ozone pollution just in New York. Below the density plot, you will find a rug plot – a plot of tick marks along the horizontal axis indicating where the data are located. Clearly, there are more data in the neighbourhood between 0 and 50, where the highest “bump” is located. Use the rug() function to get the rug plot in R.
##### Kernel Density Plot with Rug Plot ##### By Eric Cai - The Chemical Statistician png('INSERT YOUR DIRECTORY PATH HERE/kernel density plot with rug plot ozone New York.png') plot(density.ozone, main = 'Kernel Density Plot and Rug Plot of Ozone \n in New York', xlab = 'Ozone (ppb)', ylab = 'Density') rug(ozone) dev.off()
Trosset, Michael W. An introduction to statistical inference and its applications with R. Chapman and Hall/CRC, 2011.
Everitt, Brian S., and Torsten Hothorn. A handbook of statistical analyses using R. Chapman and Hall/CRC, 2006.
Filed under: Applied Statistics, Descriptive Statistics, Plots, R programming Tagged: applied statistics, density plot, density(), dunif(), Gaussian distribution, kernel, kernel density estimate, kernel density estimation, kernel density plot, kernel function, legend(), lines(), New York, normal distribution, ozone, Ozonopolis, pdf, plot, plots, plotting, probability density function, R, R programming, rug plot, rug(), set.seed(), statistics, summary(), triangular kernel, uniform distribution, uniform kernel