Did you try taking out P7, which is text? Moreover, if you get a message saying ' the standard deviation is zero', it means that the entire column is constant. By definition, the covariance of a constant with a random variable is 0, but your data consists of values, so cor() understandably throws a warning that one or more of your columns are constant. Applying the following to your data (which I named expd instead), we get
sapply(expd[, -12], var) P1 P2 P3 P4 P5 P6 5.433333e-01 1.083333e+00 5.766667e-01 1.083333e+00 6.433333e-01 5.566667e-01 P8 P9 P10 P11 P12 SITE 5.733333e-01 3.193333e+00 5.066667e-01 2.500000e-01 5.500000e+00 2.493333e+00 Errors warnings Manual Total H_tot HP1.1 9.072840e+03 2.081334e+04 7.433333e-01 3.823500e+04 3.880250e+03 2.676667e+00 HP1.2 HP1.3 HP1.4 HP_tot HO1.1 HO1.2 0.000000e+00 2.008440e+03 3.057067e+02 3.827250e+03 8.400000e-01 0.000000e+00 HO1.3 HO1.4 HO_tot HU1.1 HU1.2 HU1.3 0.000000e+00 0.000000e+00 8.400000e-01 0.000000e+00 2.100000e-01 2.266667e-01 HU_tot HR L_tot LP1.1 LP1.2 LP1.3 6.233333e-01 7.433333e-01 3.754610e+03 3.209333e+01 0.000000e+00 2.065010e+03 LP1.4 LP_tot LO1.1 LO1.2 LO1.3 LO1.4 2.246233e+02 3.590040e+03 3.684000e+01 0.000000e+00 0.000000e+00 2.840000e+00 LO_tot LU1.1 LU1.2 LU1.3 LU_tot LR_tot 6.000000e+01 0.000000e+00 1.440000e+00 3.626667e+00 8.373333e+00 4.943333e+00 SP_tot SP1.1 SP1.2 SP1.3 SP1.4 SP_tot.1 6.911067e+02 4.225000e+01 0.000000e+00 1.009600e+02 4.161600e+02 3.071600e+02 SO1.1 SO1.2 SO1.3 SO1.4 SO_tot SU1.1 4.543333e+00 2.500000e-01 0.000000e+00 2.100000e-01 5.250000e+00 0.000000e+00 SU1.2 SU1.3 SU_tot SR 1.556667e+00 4.225000e+01 3.504000e+01 4.225000e+01 Which columns are constant? which(sapply(expd[, -12], var) < .Machine$double.eps) HP1.2 HO1.2 HO1.3 HO1.4 HU1.1 LP1.2 LO1.2 LO1.3 LU1.1 SP1.2 SO1.3 SU1.1 19 24 25 26 28 35 40 41 44 51 57 60 I suspect that in your real data set, there aren't so many constant columns, but this is one way to check. HTH, Dennis On Wed, Sep 8, 2010 at 12:35 PM, Stephane Vaucher <vauch...@iro.umontreal.ca > wrote: > Hi everyone, > > I'm observing what I believe is weird behaviour when attempting to do > something very simple. I want a correlation matrix, but my matrix seems to > contain correlation values that are not found when executed on pairs: > > test2$P2 >> > [1] 2 2 4 4 1 3 2 4 3 3 2 3 4 1 2 2 4 3 4 1 2 3 2 1 3 > >> test2$HP_tot >> > [1] 10 10 10 10 10 10 10 10 136 136 136 136 136 136 136 136 136 > 136 15 > [20] 15 15 15 15 15 15 c=cor(test2$P3,test2$HP_tot,method='spearman') > >> c >> > [1] -0.2182876 > >> c=cor(test2,method='spearman') >> > Warning message: > In cor(test2, method = "spearman") : the standard deviation is zero > >> write(c,file='out.csv') >> > > from my spreadsheet > -0.25028783918741 > > Most cells are correct, but not that one. > > If this is expected behaviour, I apologise for bothering you, I read the > documentation, but I do not know if the calculation of matrices and pairs is > done using the same function (eg, with respect to equal value observations). > > If this is not a desired behaviour, I noticed that it only occurs with a > relatively large matrix (I couldn't reproduce on a simple 2 column data > set). There might be a naming error. > > names(test2) >> > [1] "ID" "NOMBRE" "MAIL" > [4] "Age" "SEXO" "Studies" > [7] "Hours_Internet" "Vision.Disabilities" "Other.disabilities" > [10] "Technology_Knowledge" "Start_Time" "End_Time" > [13] "Duration" "P1" "P1Book" > [16] "P1DVD" "P2" "P3" > [19] "P4" "P5" "P6" > [22] "P8" "P9" "P10" > [25] "P11" "P12" "P7" > [28] "SITE" "Errors" "warnings" > [31] "Manual" "Total" "H_tot" > [34] "HP1.1" "HP1.2" "HP1.3" > [37] "HP1.4" "HP_tot" "HO1.1" > [40] "HO1.2" "HO1.3" "HO1.4" > [43] "HO_tot" "HU1.1" "HU1.2" > [46] "HU1.3" "HU_tot" "HR" > [49] "L_tot" "LP1.1" "LP1.2" > [52] "LP1.3" "LP1.4" "LP_tot" > [55] "LO1.1" "LO1.2" "LO1.3" > [58] "LO1.4" "LO_tot" "LU1.1" > [61] "LU1.2" "LU1.3" "LU_tot" > [64] "LR_tot" "SP_tot" "SP1.1" > [67] "SP1.2" "SP1.3" "SP1.4" > [70] "SP_tot.1" "SO1.1" "SO1.2" > [73] "SO1.3" "SO1.4" "SO_tot" > [76] "SU1.1" "SU1.2" "SU1.3" > [79] "SU_tot" "SR" > > Thank you in advance, > Stephane Vaucher > > ______________________________________________ > 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. > [[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.