[R] correlation with missing values.. different answers

[Jeff Newmiller]

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Read ?cor, particularly the part about "complete.cases". Your two cases have different effective input rows.
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Sent from my phone. Please excuse my brevity.

On April 13, 2014 6:08:51 PM PDT, Paul Tanger <paul.tanger at colostate.edu> wrote:
>Hi,
>I can't seem to figure out why this gives me different answers. 
>Probably
>something obvious, but I thought they would be the same.
>This is an minimal example from the help page of cor() :
>
>> ## swM := "swiss" with  3 "missing"s :
>> swM <- swiss
>> colnames(swM) <- abbreviate(colnames(swiss), min=6)
>> swM[1,2] <- swM[7,3] <- swM[25,5] <- NA # create 3 "missing"
>> cor(swM, use = "na.or.complete")
>       Frtlty      Agrclt     Exmntn      Eductn     Cathlc      Infn.M
>Frtlty  1.0000000  0.37821953 -0.6548306 -0.67421581  0.4772298 
>0.38781500
>Agrclt  0.3782195  1.00000000 -0.7127078 -0.64337782  0.4014837
>-0.07168223
>Exmntn -0.6548306 -0.71270778  1.0000000  0.69776906 -0.6079436
>-0.10710047
>Eductn -0.6742158 -0.64337782  0.6977691  1.00000000 -0.1701445
>-0.08343279
>Cathlc  0.4772298  0.40148365 -0.6079436 -0.17014449  1.0000000 
>0.17221594
>Infn.M  0.3878150 -0.07168223 -0.1071005 -0.08343279  0.1722159 
>1.00000000
>> # why isn't this the same?
>> cor(swM[,c(1:2)], use = "na.or.complete")
>          Frtlty    Agrclt
>Frtlty 1.0000000 0.3920289
>Agrclt 0.3920289 1.0000000
>
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>
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