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How to avoid the warning “Cannot compute exact p-value with ties” while perform correlation test for Spearman’s correlation in R?
When the variables are not continuous but could be ranked then we do not use pearson correlation coefficient to find the linear relationship, in this case spearman correlation coefficient comes into the scene. Since the spearman correlation coefficient considers the rank of values, the correlation test ignores the same ranks to find the p-values as a result we get the warning “Cannot compute exact p-value with ties”. This can be avoided by using exact = FALSE inside the cor.test function.
Example
Consider the below vectors and perform spearman correlation test to check the relationship between them −
x1<-rpois(20,2) y1<-rpois(20,5) cor.test(x1,y1,method="spearman")
Output
Spearman's rank correlation rho data: x1 and y1 S = 1401.7, p-value = 0.8214 alternative hypothesis: true rho is not equal to 0 sample estimates: rho -0.05390585 Warning message: In cor.test.default(x1, y1, method = "spearman") : Cannot compute exact p-value with ties
Here, we have the warning for ties, this can be avoided by using exact=FALSE as shown below −
Example
cor.test(x1,y1,method="spearman",exact=FALSE)
Output
Spearman's rank correlation rho data: x1 and y1 S = 1401.7, p-value = 0.8214 alternative hypothesis: true rho is not equal to 0 sample estimates: rho -0.05390585
Let’s have a look at some more examples −
Example
x2<-sample(1:100,500,replace=TRUE) y2<-sample(1:50,500,replace=TRUE) cor.test(x2,y2,method="spearman")
Output
Spearman's rank correlation rho data: x2 and y2 S = 20110148, p-value = 0.4387 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.03470902 Warning message: In cor.test.default(x2, y2, method = "spearman") : Cannot compute exact p-value with ties
Example
cor.test(x2,y2,method="spearman",exact=FALSE)
Output
Spearman's rank correlation rho data: x2 and y2 S = 20110148, p-value = 0.4387 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.03470902
Example
x3<-sample(101:110,5000,replace=TRUE) y3<-sample(501:510,5000,replace=TRUE) cor.test(x3,y3,method="spearman")
Output
Spearman's rank correlation rho data: x3 and y3 S = 2.0642e+10, p-value = 0.5155 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.009199129 Warning message: In cor.test.default(x3, y3, method = "spearman") : Cannot compute exact p-value with ties
Example
cor.test(x3,y3,method="spearman",exact=FALSE)
Output
Spearman's rank correlation rho data: x3 and y3 S = 2.0642e+10, p-value = 0.5155 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.009199129
Updated on: 08-Sep-2020
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