Thanks, I did not realize it was deleting rows! I was afraid to try "pairwise.complete.obs" because it said something about resulting in a matrix which is not "positive semi-definite" (and googling that term just confused me more). But I ran the dataset through JMP and got the same answers so I think that "pairwise.complete.obs" works for what I want to do.
On Sun, Apr 13, 2014 at 7:36 PM, arun <smartpink...@yahoo.com> wrote: > > > > Hi, > > I think in this case, when you use "na.or.complete", all the NA rows are > removed for the full dataset. > cor(swM[-1,1:2]) > # Frtlty Agrclt > #Frtlty 1.0000000 0.3920289 > #Agrclt 0.3920289 1.0000000 > > cor(swM[-1,])[1:2,1:2] > #Frtlty Agrclt > #Frtlty 1.0000000 0.3920289 > #Agrclt 0.3920289 1.0000000 > > May be you can try with "pairwise.complete.obs" > cor(swM, use = "pairwise.complete.obs") > # Frtlty Agrclt Exmntn Eductn Cathlc Infn.M > #Frtlty 1.0000000 0.39202893 -0.6531492 -0.66378886 0.4723129 0.41655603 > #Agrclt 0.3920289 1.00000000 -0.7150561 -0.65221506 0.4152007 -0.03648427 > #Exmntn -0.6531492 -0.71505612 1.0000000 0.69921153 -0.6003402 -0.11433546 > #Eductn -0.6637889 -0.65221506 0.6992115 1.00000000 -0.1791334 -0.09932185 > #Cathlc 0.4723129 0.41520069 -0.6003402 -0.17913339 1.0000000 0.18503786 > #Infn.M 0.4165560 -0.03648427 -0.1143355 -0.09932185 0.1850379 1.00000000 > cor(swM[,1:2],use="pairwise.complete.obs") > # Frtlty Agrclt > #Frtlty 1.0000000 0.3920289 > #Agrclt 0.3920289 1.0000000 > > A.K. > > On Sunday, April 13, 2014 9:11 PM, Paul Tanger <paul.tan...@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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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. ______________________________________________ R-help@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.
