# [R] cor inside/outside a function has different output

Bernzweig, Bruce (Consultant) bbernzwe at bear.com
Tue Jul 24 17:24:28 CEST 2007

I'm calculating correlations between two matrices

mat1 <- matrix(sample(1:500,25), ncol = 5,

dimnames=list(paste("mat1row", 1:5, sep=""),

paste("mat1col", 1:5, sep="")))

mat2 <- matrix(sample(501:1000,25), ncol = 5,

dimnames=list(paste("mat2row", 1:5, sep=""),

paste("mat2col", 1:5, sep="")))

using what would seem to be two similar methods:

Method 1:

> f <- function(x,y) cor(x,y)

> apply(mat1, 1, f, y=mat2)

Method 2:

> cor(mat1, mat2)

However, the results (see blow) are different:

> apply(mat1, 1, f, y=mat2)

mat1row1   mat1row2    mat1row3    mat1row4    mat1row5

[1,] -0.27601028 -0.1352143  0.03538690 -0.03084075 -0.60171704

[2,] -0.01595532 -0.3881197 -0.43663982  0.49081806  0.33291995

[3,]  0.35969624 -0.0582948  0.57462169  0.09926796 -0.02948423

[4,] -0.41435920 -0.7164638 -0.21213496 -0.55183934 -0.25341790

[5,]  0.33802803  0.5371508  0.05219095  0.83533575  0.17850291

> cor(mat1, mat2)

mat2col1    mat2col2   mat2col3   mat2col4   mat2col5

mat1col1 -0.84077496 -0.01538414 -0.6078933 -0.2263840 -0.1421335

mat1col2  0.23074421  0.54606286 -0.2354733  0.5214255 -0.2129077

mat1col3 -0.80000528  0.19550100 -0.5920509 -0.8694040  0.6853990

mat1col4  0.08050976 -0.55449840  0.6225666  0.6187971 -0.8971584

mat1col5 -0.10199564 -0.43854767 -0.5803077 -0.5100285  0.2848351

Also, for method 2, the calculations are done on a column x column
basis.  Is there any way to do this on a row by row basis.  Looking at
the help page for cor, I don't see any parameters that could be used to
do this.

Thanks,

- Bruce

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