Thanks Gavin, Jari,
Trying to get the message across more clear, this are the commands I used to calculate the distance matrix for fso function. It seems there is a problem with the dissimilarity matrix attachment; maybe it is not in the right form... Any suggestion appreciated. Dragos George http://webs.uvigo.es/zdragos/ library(fso) #metals > MET Al Li Ti Mn Cu As Pb 1 20895 76.0 37.50000 543.29 20.11 15.61 26.42 2 22148 84.0 33.33333 591.40 25.08 16.99 28.90 3 27574 93.0 38.11881 628.63 23.48 18.15 29.30 4 25135 87.0 24.77477 853.39 23.57 22.19 30.60 5 23015 83.0 23.50000 706.67 19.74 20.02 28.08 6 22965 91.0 24.24242 637.84 21.44 21.35 29.66 7 24895 87.5 27.00000 646.62 23.01 21.51 31.04 8 21784 87.0 25.00000 618.32 21.37 19.99 29.01 9 17827 80.0 27.40385 581.50 20.11 18.27 28.43 10 17889 83.0 34.34343 651.70 21.96 17.39 30.78 11 16005 72.0 42.66055 554.42 15.94 13.40 22.53 12 17694 80.0 42.85714 629.78 21.52 17.82 29.87 13 21342 78.0 42.57426 708.46 22.73 17.47 32.51 14 18380 76.0 34.00000 692.82 17.90 15.45 26.09 15 13439 62.0 14.95327 544.17 13.07 12.50 20.45 16 15240 64.5 17.50000 590.62 14.72 13.56 23.00 17 16562 72.0 19.02655 605.47 15.81 12.42 21.79 18 19750 86.5 20.50000 559.13 20.89 16.54 29.26 19 21710 88.0 23.00000 666.26 21.41 17.86 29.79 20 17904 78.0 17.50000 791.57 16.77 15.37 27.36 21 15000 72.0 23.52941 552.09 15.54 11.93 22.55 22 17000 75.0 19.04762 531.31 14.51 12.37 24.65 23 18657 85.0 13.72549 548.93 13.68 12.56 20.14 24 15765 86.5 17.50000 571.96 14.66 12.30 22.12 25 15517 72.0 15.21739 495.06 14.44 11.64 22.38 26 16625 72.5 16.50000 460.57 14.50 11.64 21.93 27 17228 72.0 18.81188 483.02 12.43 11.94 19.93 28 20380 77.0 21.63462 561.09 14.72 12.03 21.76 29 19204 74.0 21.84466 596.23 17.29 11.51 29.30 30 15717 64.0 16.66667 563.92 16.05 12.10 22.87 31 19014 71.0 11.21495 528.77 15.47 12.50 21.35 32 18826 83.0 11.60714 498.92 16.72 11.29 25.53 33 17580 64.5 13.00000 499.45 14.07 11.12 19.13 #environmental variables > CC SpringFreezLevel PrecipitDays SnowDays 1 2124.354 95 18 2 2488.462 117 24 3 2391.031 108 17 4 2447.431 91 25 5 2408.462 89 9 6 2444.354 65 26 7 2326.415 77 23 8 2757.185 97 13 9 2326.415 111 17 10 2424.877 90 17 11 2406.415 97 18 12 2359.738 99 14 13 2333.585 103 16 14 2241.277 99 12 15 2416.154 104 15 16 2436.662 100 16 17 2318.723 107 15 18 2457.185 120 22 19 2267.431 119 40 20 2180.262 124 34 21 2087.954 133 29 22 2308.462 111 21 23 2313.585 132 31 24 2526.923 133 27 25 2108.462 134 38 26 2123.846 168 49 27 2159.738 144 46 28 2298.200 170 40 29 2328.969 136 28 30 2021.277 137 41 31 2098.200 120 35 32 2062.308 103 26 33 1944.354 134 38 #dissimilarity > sim<-cor(MET,method="spearman") > dis<-1-sim > dis Al Li Ti Mn Cu As Pb Al 0.0000000 0.2372233 0.5757272 0.4735963 0.26892862 0.3438074 0.37561628 Li 0.2372233 0.0000000 0.5760003 0.4638951 0.31543042 0.3197032 0.33668230 Ti 0.5757272 0.5760003 0.0000000 0.4222668 0.25263333 0.3481023 0.30435507 Mn 0.4735963 0.4638951 0.4222668 0.0000000 0.26073875 0.2570617 0.25378123 Cu 0.2689286 0.3154304 0.2526333 0.2607387 0.00000000 0.2178201 0.08399498 As 0.3438074 0.3197032 0.3481023 0.2570617 0.21782013 0.0000000 0.26803176 Pb 0.3756163 0.3366823 0.3043551 0.2537812 0.08399498 0.2680318 0.00000000 > attach(CC) The following object(s) are masked from CC ( position 3 ) : PrecipitDays SnowDays SpringFreezLevel The following object(s) are masked from CC ( position 8 ) : PrecipitDays SnowDays SpringFreezLevel #fuzzy set ordination > z <- fso(~SpringFreezLevel+ PrecipitDays+SnowDays,dis,permute=1000) Error in fso.formula(~SpringFreezLevel + PrecipitDays + SnowDays, dis, : You must supply a (dis)similarity matrix ________________________________ Message: 2 Date: Tue, 20 Jul 2010 20:42:54 +0100 From: Gavin Simpson <gavin.simp...@ucl.ac.uk> Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Distance matrix based on correlation coefficient Message-ID: <1279654974.2355.49.ca...@desktop.localdomain> Content-Type: text/plain; charset="UTF-8" On Tue, 2010-07-20 at 12:12 -0700, Dragos Zaharescu wrote: > I would much appreciate if someone would enlighten me on how to calculate a > distance matrix based on correlation coefficient (Spearman)? The simple > correlation matrix seems not to work. In what sense did it not work? We aren't mind readers! Hence the posting guide asking you to provide information that will help us to help you. > I am trying to use it in FSO/MFSO to calculate the influence of > climate factors on heavy metals concentrations. Does this help at all? > dat <- data.frame(A = rnorm(10), B = rnorm(10), C = rnorm(10)) > cor(dat) A B C A 1.00000000 0.08986947 0.1224007 B 0.08986947 1.00000000 0.2667838 C 0.12240068 0.26678381 1.0000000 > 1 - cor(dat) ## dissimilarity A B C A 0.0000000 0.9101305 0.8775993 B 0.9101305 0.0000000 0.7332162 C 0.8775993 0.7332162 0.0000000 > as.dist(1 - cor(dat)) A B B 0.9101305 C 0.8775993 0.7332162 HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ------------------------------ Message: 3 Date: Tue, 20 Jul 2010 23:35:02 +0300 From: Jari Oksanen <jari.oksa...@oulu.fi> To: Gavin Simpson <gavin.simp...@ucl.ac.uk>, Dragos Zaharescu Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Distance matrix based on correlation coefficient Message-ID: <c86be326.104bb%jari.oksa...@oulu.fi> Content-Type: text/plain; charset="US-ASCII" On 20/07/10 22:42 PM, "Gavin Simpson" <gavin.simp...@ucl.ac.uk> wrote: > On Tue, 2010-07-20 at 12:12 -0700, Dragos Zaharescu wrote: >> I would much appreciate if someone would enlighten me on how to calculate a >> distance matrix based on correlation coefficient (Spearman)? The simple >> correlation matrix seems not to work. > >> 1 - cor(dat) ## dissimilarity > Actually the canonical transformation to distance is sqrt(2-2*cor(dat)). Cheers, Jari Oksanen ------------------------------ Message: 4 Date: Tue, 20 Jul 2010 21:38:23 +0100 From: Gavin Simpson <gavin.simp...@ucl.ac.uk> To: Jari Oksanen <jari.oksa...@oulu.fi> r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Distance matrix based on correlation coefficient Message-ID: <1279658303.18174.2.ca...@localhost> Content-Type: text/plain; charset="UTF-8" On Tue, 2010-07-20 at 23:35 +0300, Jari Oksanen wrote: > On 20/07/10 22:42 PM, "Gavin Simpson" <gavin.simp...@ucl.ac.uk> wrote: > > > On Tue, 2010-07-20 at 12:12 -0700, Dragos Zaharescu wrote: > >> I would much appreciate if someone would enlighten me on how to calculate a > >> distance matrix based on correlation coefficient (Spearman)? The simple > >> correlation matrix seems not to work. > > > > >> 1 - cor(dat) ## dissimilarity > > > Actually the canonical transformation to distance is sqrt(2-2*cor(dat)). > > Cheers, Jari Oksanen Of course, thanks Jari. That 1 - bit was total rubbish, not even acknowledging that cor could be negative. Not sure what came over me; I blame the heat here in London ;-) Hangs head in shame. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
