cor(data.frame) infelicities
You can calculate the Kendall rank correlation with such a matrix so you would not want to exclude factors in that case:
cor(iris, method = "kendall")
Sepal.Length Sepal.Width Petal.Length Petal.Width Species Sepal.Length 1.00000000 -0.07699679 0.7185159 0.6553086 0.6704444 Sepal.Width -0.07699679 1.00000000 -0.1859944 -0.1571257 -0.3376144 Petal.Length 0.71851593 -0.18599442 1.0000000 0.8068907 0.8229112 Petal.Width 0.65530856 -0.15712566 0.8068907 1.0000000 0.8396874 Species 0.67044444 -0.33761438 0.8229112 0.8396874 1.0000000
On Dec 3, 2007 9:27 AM, Michael Friendly <friendly at yorku.ca> wrote:
In using cor(data.frame), it is annoying that you have to explicitly filter out non-numeric columns, and when you don't, the error message is misleading:
> cor(iris)
Error in cor(iris) : missing observations in cov/cor In addition: Warning message: In cor(iris) : NAs introduced by coercion It would be nicer if stats:::cor() did the equivalent *itself* of the following for a data.frame:
> cor(iris[,sapply(iris, is.numeric)])
Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1.0000000 -0.1175698 0.8717538 0.8179411 Sepal.Width -0.1175698 1.0000000 -0.4284401 -0.3661259 Petal.Length 0.8717538 -0.4284401 1.0000000 0.9628654 Petal.Width 0.8179411 -0.3661259 0.9628654 1.0000000
>
A change could be implemented here:
if (is.data.frame(x))
x <- as.matrix(x)
Second, the default, use="all" throws an error if there are any
NAs. It would be nicer if the default was use="complete.cases",
which would generate warnings instead. Most other statistical
software is more tolerant of missing data.
> library(corrgram) > data(auto) > cor(auto[,sapply(auto, is.numeric)])
Error in cor(auto[, sapply(auto, is.numeric)]) : missing observations in cov/cor
> cor(auto[,sapply(auto, is.numeric)],use="complete")
# works; output elided -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.