Correlation in R Programming
There are two primary methods to compute the correlation between two variables in R Programming:
Pearson: Parametric correlation Spearman: Non-parametric correlation
In this tutorial, you will learn:
Pearson Correlation Matrix in R Spearman Rank Correlation in R Correlation Matrix in R Visualizing Correlation Matrix in R
Pearson Correlation Matrix in R
The Pearson correlation method is usually used as a primary check for the relationship between two variables. The coefficient of correlation, , is a measure of the strength of the linear relationship between two variables and . It is computed as follow:
with
, i.e. standard deviation of , i.e. standard deviation of
The correlation ranges between -1 and 1.
A value of near or equal to 0 implies little or no linear relationship between and . In contrast, the closer comes to 1 or -1, the stronger the linear relationship.
We can compute the t-test as follow and check the distribution table with a degree of freedom equals to :
Spearman Rank Correlation in R
A rank correlation sorts the observations by rank and computes the level of similarity between the rank. A rank correlation has the advantage of being robust to outliers and is not linked to the distribution of the data. Note that, a rank correlation is suitable for the ordinal variable. Spearman’s rank correlation, , is always between -1 and 1 with a value close to the extremity indicates strong relationship. It is computed as follow:
with stated the covariances between rank and . The denominator calculates the standard deviations. In R, we can use the cor() function. It takes three arguments, , and the method.
cor(x, y, method)
Arguments:
x: First vector y: Second vector method: The formula used to compute the correlation. Three string values:
“pearson” “kendall” “spearman”
An optional argument can be added if the vectors contain missing value: use = “complete.obs” We will use the BudgetUK dataset. This dataset reports the budget allocation of British households between 1980 and 1982. There are 1519 observations with ten features, among them:
wfood: share food share spend wfuel: share fuel spend wcloth: budget share for clothing spend walc: share alcohol spend wtrans: share transport spend wother: share of other goods spend totexp: total household spend in pound income: total net household income age: age of household children: number of children
Example
library(dplyr) PATH <-“https://raw.githubusercontent.com/guru99-edu/R-Programming/master/british_household.csv" data <-read.csv(PATH) filter(income < 500) mutate(log_income = log(income), log_totexp = log(totexp), children_fac = factor(children, order = TRUE, labels = c(“No”, “Yes”))) select(-c(X,X.1, children, totexp, income)) glimpse(data)
Code Explanation
We first import the data and have a look with the glimpse() function from the dplyr library. Three points are above 500K, so we decided to exclude them. It is a common practice to convert a monetary variable in log. It helps to reduce the impact of outliers and decreases the skewness in the dataset.
Output:
Observations: 1,516## Variables: 10
$ wfood 0.4272, 0.3739, 0.1941, 0.4438, 0.3331, 0.3752, 0…
$ wfuel 0.1342, 0.1686, 0.4056, 0.1258, 0.0824, 0.0481, 0…
$ wcloth 0.0000, 0.0091, 0.0012, 0.0539, 0.0399, 0.1170, 0…
$ walc 0.0106, 0.0825, 0.0513, 0.0397, 0.1571, 0.0210, 0…
$ wtrans 0.1458, 0.1215, 0.2063, 0.0652, 0.2403, 0.0955, 0…
$ wother 0.2822, 0.2444, 0.1415, 0.2716, 0.1473, 0.3431, 0…
$ age 25, 39, 47, 33, 31, 24, 46, 25, 30, 41, 48, 24, 2…
$ log_income 4.867534, 5.010635, 5.438079, 4.605170, 4.605170,…
$ log_totexp 3.912023, 4.499810, 5.192957, 4.382027, 4.499810,…
$ children_fac Yes, Yes, Yes, Yes, No, No, No, No, No, No, Yes, …
We can compute the correlation coefficient between income and wfood variables with the “pearson” and “spearman” methods.
cor(data$log_income, data$wfood, method = “pearson”)
Output:
[1] -0.2466986
cor(data$log_income, data$wfood, method = “spearman”)
Output:
[1] -0.2501252
Correlation Matrix in R
The bivariate correlation is a good start, but we can get a broader picture with multivariate analysis. A correlation with many variables is pictured inside a correlation matrix. A correlation matrix is a matrix that represents the pair correlation of all the variables. The cor() function returns a correlation matrix. The only difference with the bivariate correlation is we don’t need to specify which variables. By default, R computes the correlation between all the variables. Note that, a correlation cannot be computed for factor variable. We need to make sure we drop categorical feature before we pass the data frame inside cor(). A correlation matrix is symmetrical which means the values above the diagonal have the same values as the one below. It is more visual to show half of the matrix. We exclude children_fac because it is a factor level variable. cor does not perform correlation on a categorical variable.
the last column of data is a factor level. We don’t include it in the code
mat_1 <-as.dist(round(cor(data[,1:9]),2)) mat_1
Code Explanation
cor(data): Display the correlation matrix round(data, 2): Round the correlation matrix with two decimals as.dist(): Shows the second half only
Output:
wfood wfuel wcloth walc wtrans wother age log_income
wfuel 0.11
wcloth -0.33 -0.25
walc -0.12 -0.13 -0.09
wtrans -0.34 -0.16 -0.19 -0.22
wother -0.35 -0.14 -0.22 -0.12 -0.29
age 0.02 -0.05 0.04 -0.14 0.03 0.02
log_income -0.25 -0.12 0.10 0.04 0.06 0.13 0.23
log_totexp -0.50 -0.36 0.34 0.12 0.15 0.15 0.21 0.49
Significance level
The significance level is useful in some situations when we use the pearson or spearman method. The function rcorr() from the library Hmisc computes for us the p-value. We can download the library from conda and copy the code to paste it in the terminal:
conda install -c r r-hmisc
The rcorr() requires a data frame to be stored as a matrix. We can convert our data into a matrix before to compute the correlation matrix with the p-value.
library(“Hmisc”) data_rcorr <-as.matrix(data[, 1: 9])
mat_2 <-rcorr(data_rcorr)
mat_2 <-rcorr(as.matrix(data)) returns the same output
The list object mat_2 contains three elements:
r: Output of the correlation matrix n: Number of observation P: p-value
We are interested in the third element, the p-value. It is common to show the correlation matrix with the p-value instead of the coefficient of correlation.
p_value <-round(mat_2[[“P”]], 3) p_value
Code Explanation
mat_2[[“P”]]: The p-values are stored in the element called P round(mat_2[[“P”]], 3): Round the elements with three digits
Output:
wfood wfuel wcloth walc wtrans wother age log_income log_totexp
wfood NA 0.000 0.000 0.000 0.000 0.000 0.365 0.000 0 wfuel 0.000 NA 0.000 0.000 0.000 0.000 0.076 0.000 0 wcloth 0.000 0.000 NA 0.001 0.000 0.000 0.160 0.000 0 walc 0.000 0.000 0.001 NA 0.000 0.000 0.000 0.105 0 wtrans 0.000 0.000 0.000 0.000 NA 0.000 0.259 0.020 0 wother 0.000 0.000 0.000 0.000 0.000 NA 0.355 0.000 0 age 0.365 0.076 0.160 0.000 0.259 0.355 NA 0.000 0 log_income 0.000 0.000 0.000 0.105 0.020 0.000 0.000 NA 0 log_totexp 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 NA
Visualizing Correlation Matrix in R
A heat map is another way to show a correlation matrix. The GGally library is an extension of ggplot2. Currently, it is not available in the conda library. We can install directly in the console.
install.packages(“GGally”)
The library includes different functions to show the summary statistics such as the correlation and distribution of all the variables in a matrix. The ggcorr() function has lots of arguments. We will introduce only the arguments we will use in the tutorial:
The ggcorr Function
ggcorr(df, method = c(“pairwise”, “pearson”), nbreaks = NULL, digits = 2, low = “#3B9AB2”, mid = “#EEEEEE”, high = “#F21A00”, geom = “tile”, label = FALSE, label_alpha = FALSE)
Arguments:
df: Dataset used
method: Formula to compute the correlation. By default, pairwise and Pearson are computed
nbreaks: Return a categorical range for the coloration of the coefficients. By default, no break and the color gradient is continuous
digits: Round the correlation coefficient. By default, set to 2
low: Control the lower level of the coloration
mid: Control the middle level of the coloration
high: Control the high level of the coloration
geom: Control the shape of the geometric argument. By default, “tile”
label: Boolean value. Display or not the label. By default, set to FALSE
Basic heat map
The most basic plot of the package is a heat map. The legend of the graph shows a gradient color from – 1 to 1, with hot color indicating strong positive correlation and cold color, a negative correlation.
library(GGally) ggcorr(data)
Code Explanation
ggcorr(data): Only one argument is needed, which is the data frame name. Factor level variables are not included in the plot.
Output:
Adding Control to the Heat Map
We can add more controls to the graph:
ggcorr(data, nbreaks = 6, low = “steelblue”, mid = “white”, high = “darkred”, geom = “circle”)
Code Explanation
nbreaks=6: break the legend with 6 ranks. low = “steelblue”: Use lighter colors for negative correlation mid = “white”: Use white colors for middle ranges correlation high = “darkred”: Use dark colors for positive correlation geom = “circle”: Use circle as the shape of the windows in the heat map. The size of the circle is proportional to the absolute value of the correlation.
Output:
Adding Label to the Heat Map
GGally allows us to add a label inside the windows:
ggcorr(data, nbreaks = 6, label = TRUE, label_size = 3, color = “grey50”)
Code Explanation
label = TRUE: Add the values of the coefficients of correlation inside the heat map. color = “grey50”: Choose the color, i.e. grey label_size = 3: Set the size of the label equals to 3
Output:
The ggpairs Function
Finally, we introduce another function from the GGaly library. Ggpair. It produces a graph in a matrix format. We can display three kinds of computation within one graph. The matrix is a dimension, with equals the number of observations. The upper/lower part displays windows and in the diagonal. We can control what information we want to show in each part of the matrix. The formula for ggpair is:
ggpair(df, columns = 1: ncol(df), title = NULL, upper = list(continuous = “cor”), lower = list(continuous = “smooth”), mapping = NULL)
Arguments:
df: Dataset used columns: Select the columns to draw the plot title: Include a title upper: Control the boxes above the diagonal of the plot. Need to supply the type of computations or graph to return. If continuous = “cor”, we ask R to compute the correlation. Note that, the argument needs to be a list. Other arguments can be used, see the vignette for more information. Lower: Control the boxes below the diagonal. Mapping: Indicates the aesthetic of the graph. For instance, we can compute the graph for different groups.
Bivariate analysis with ggpair with grouping
The next graph plots three information:
The correlation matrix between log_totexp, log_income, age and wtrans variable grouped by whether the household has a kid or not. Plot the distribution of each variable by group Display the scatter plot with the trend by group
library(ggplot2) ggpairs(data, columns = c(“log_totexp”, “log_income”, “age”, “wtrans”), title = “Bivariate analysis of revenue expenditure by the British household”, upper = list(continuous = wrap(“cor”, size = 3)), lower = list(continuous = wrap(“smooth”, alpha = 0.3, size = 0.1)), mapping = aes(color = children_fac))
Code Explanation
columns = c(“log_totexp”, “log_income”, “age”, “wtrans”): Choose the variables to show in the graph title = “Bivariate analysis of revenue expenditure by the British household”: Add a title upper = list(): Control the upper part of the graph. I.e. Above the diagonal continuous = wrap(“cor”, size = 3)): Compute the coefficient of correlation. We wrap the argument continuous inside the wrap() function to control for the aesthetic of the graph ( i.e. size = 3) -lower = list(): Control the lower part of the graph. I.e. Below the diagonal. continuous = wrap(“smooth”,alpha = 0.3,size=0.1): Add a scatter plot with a linear trend. We wrap the argument continuous inside the wrap() function to control for the aesthetic of the graph ( i.e. size=0.1, alpha=0.3) mapping = aes(color = children_fac): We want each part of the graph to be stacked by the variable children_fac, which is a categorical variable taking the value of 1 if the household does not have kids and 2 otherwise
Output:
Bivariate analysis with ggpair with partial grouping
The graph below is a little bit different. We change the position of the mapping inside the upper argument.
ggpairs(data, columns = c(“log_totexp”, “log_income”, “age”, “wtrans”), title = “Bivariate analysis of revenue expenditure by the British household”, upper = list(continuous = wrap(“cor”, size = 3), mapping = aes(color = children_fac)), lower = list( continuous = wrap(“smooth”, alpha = 0.3, size = 0.1)) )
Code Explanation
Exact same code as previous example except for: mapping = aes(color = children_fac): Move the list in upper = list(). We only want the computation stacked by group in the upper part of the graph.
Output:
Summary
A Bivariate relationship describes a relationship -or correlation- between two variables in R. There are two primary methods to compute the correlation between two variables in R Programming: Pearson & Spearman. The Pearson correlation method is usually used as a primary check for the relationship between two variables. A rank correlation sorts the observations by rank and computes the level of similarity between the rank. Spearman’s rank correlation, , is always between -1 and 1 with a value close to the extremity indicates strong relationship. A correlation matrix is a matrix that represents the pair correlation of all the variables. The significance level is useful in some situations when we use the pearson or spearman method.
We can summarize all the Correlation functions in R in the table below:
