Hi Listers, I am trying to better understand how spatial autocorrelation is determined. I have attached 2 txt files one is a fish species x sites abundance table and the other is a distance file with the lat and longs for each site (converted to cartesian coords). I have run the tests for spatial correlation using the methodology from the Borcard et al. Use R! book.
The result was no significant spatial correlation. However an nmds ordination of the fish data shows 3 very strongly clustered groups of sites which corresponds to 3 oceanic islands. A permutation analysis of the fish resemblance matrix with a distance matrix was also highly significant with a rho=0.646 spearmans rank correlation. To my mind I would have thought that with such strong groupings in the data that spatial correlation would be present at the scale of islands? Can someone help me explain this result? My analysis below fish_hellinger <- decostand (fish,"hellinger") fish.xy # spatial dataset space_ed.txt #test for overall trend lineartest <- anova(rda(fish_hellinger,fish.xy)) Permutation test for rda under reduced model Model: rda(X = fish_hellinger, Y = fish.xy) Df Var F N.Perm Pr(>F) Model 2 0.17148 8.6098 199 0.005 ** ##significant linear trend Residual 14 0.13942 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # fit linear trend to the fish data and then extract residuals for subsequent use in spatial analysis > fish_hellinger_detrended <- resid(lm(as.matrix(fish_hellinger)~ .,data=fish.xy)) # make a distance matrix from the residuals data for input to the correlogram call > fish_hellinger_D1 <- dist(fish_hellinger_detrended) # perform the mantel-based test for spatial correlation > (fish_correlogram <- mantel.correlog(fish_hellinger_D1,XY=fish.xy,nperm=99)) Mantel Correlogram Analysis Call: mantel.correlog(D.eco = fish_hellinger_D1, XY = fish.xy, nperm = 99) class.index n.dist Mantel.cor Pr(Mantel) Pr(corrected) D.cl.1 118.013676 462.000000 -0.042424 0.11 0.11 D.cl.2 352.037024 0.000000 NA NA NA D.cl.3 586.060371 0.000000 NA NA NA D.cl.4 820.083719 0.000000 NA NA NA D.cl.5 1054.107067 384.000000 0.033639 0.30 NA D.cl.6 1288.130414 0.000000 NA NA NA D.cl.7 1522.153762 0.000000 NA NA NA D.cl.8 1756.177109 320.000000 NA NA NA D.cl.9 1990.200457 0.000000 NA NA NA D.cl.10 2224.223804 0.000000 NA NA NA D.cl.11 2458.247152 240.000000 NA NA NA -- cheers Andy Andrew Halford Ph.D Research Scientist (Kimberley Marine Parks) Dept. Parks and Wildlife Western Australia Ph: +61 8 9219 9795 Mobile: +61 (0) 468 419 473
LUT_GIBB LUT_FULV CHL_STRO SCA_PRAS NAS_LITU KYP_VAIG LUT_BOHA SCA_RUBR NAS_UNIC HIP_HARI APH_FURC NAS_ELEG CHL_ENNE KYP_CINE NAS_BREV CEP_ARGU BOL_MURI LUT_KASM CHL_MICR LET_OBSE LUT_DECU VAR_LOUT CET_BICO LUT_MONO NAS_VLAM HIP_LONG CHE_UNDU GRA_ALBO NAS_CAES ACA_XANT LUT_RIVU CEP_MINI COR_AYGU COR_GAIM LET_XANT TRI_OBES NAS_FAGE PMS_LAEV LET_ERUS LET_OLIV CAC_MELA CAC_AMBL EPI_FUSC NAS_HEXA PMS_AREO APR_VIRE SCA_GHOB SCA_XANT EPI_TAUV EPI_POLY EPI_MACR LET_EHUS AET_ROGA NAS_TONG VAR_ALBI LET_HARA SYM_NEMA Coc1 1 6 16 5 9 0 6 1 20 17 0 9 0 14 3 0 0 0 0 10 0 1 0 3 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 Coc4 0 0 1 24 12 0 0 7 4 24 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 2 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 Coc8 5 21 22 19 15 6 4 6 8 11 0 28 0 3 7 0 0 0 0 5 0 1 0 2 0 0 2 0 0 0 0 0 2 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 Coc12 0 0 40 20 6 0 0 5 6 19 0 16 4 0 0 0 0 0 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 Coc13 13 43 31 2 7 59 4 7 8 44 0 9 43 49 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 6 0 0 2 0 0 1 0 0 0 0 2 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 Coc16 96 89 34 30 4 4 0 3 3 20 0 5 8 5 0 0 0 0 0 6 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 4 0 Coc18 3 3 20 26 13 0 1 0 0 15 0 8 0 0 0 1 0 0 0 0 0 1 0 3 8 0 1 1 0 0 0 0 1 0 0 2 0 0 0 0 0 5 3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 Coc23 45 10 47 210 8 18 5 4 1 14 0 9 94 14 0 0 1 0 0 0 0 0 0 6 0 0 1 0 0 0 0 0 2 0 1 5 0 0 0 0 2 1 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 Coc25 0 186 22 15 5 0 0 5 8 16 0 3 11 0 0 0 2 0 0 0 0 2 0 0 0 0 5 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 Coc28 44 452 78 30 10 0 1 4 9 20 0 16 12 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 5 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Coc34 5 13 21 17 6 0 7 2 5 29 0 15 10 0 0 1 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 Coc35 0 2 17 21 12 0 3 3 38 9 0 17 0 0 14 2 2 2 0 8 0 1 0 0 2 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 2 2 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 X1 0 0 1 0 0 38 13 11 0 0 14 0 1 17 6 4 0 0 0 0 0 1 0 0 3 0 0 12 15 0 0 5 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 X2 0 0 0 0 7 12 11 12 0 0 13 0 0 6 0 5 0 0 0 0 0 3 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 X4 0 0 0 0 8 16 3 16 1 0 22 1 0 1 0 5 0 13 0 0 0 3 0 0 0 0 0 2 0 1 0 10 0 3 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 X7 0 0 2 0 2 0 5 21 0 0 21 0 0 0 8 11 0 0 2 0 0 6 0 0 0 0 0 0 0 0 1 0 1 2 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 X9 0 0 8 0 7 1 3 29 0 0 29 0 5 0 1 5 0 0 0 0 0 9 0 0 0 0 0 0 26 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 X10 2 0 3 3 5 6 10 15 0 0 20 0 0 0 2 10 0 0 0 0 0 5 1 0 3 0 1 4 3 0 0 5 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 X11 1 0 7 3 10 8 17 13 0 0 24 0 0 2 2 0 0 0 0 0 0 4 0 0 0 0 0 10 5 0 0 10 0 4 0 0 0 0 0 0 0 0 0 1 0 0 0 6 0 0 0 0 0 0 0 0 0 X12 0 0 2 0 9 0 6 16 0 0 21 0 0 0 0 5 0 0 0 0 0 5 1 0 0 0 0 5 2 0 0 6 2 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 1 0 0 X14 0 0 0 1 19 36 4 101 4 0 20 0 0 0 2 1 0 0 0 0 0 3 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 4 0 0 0 X16 0 0 0 0 8 16 8 16 2 0 26 0 0 8 8 4 0 0 0 0 0 3 0 0 2 0 0 5 4 0 0 5 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 X18 0 0 4 0 8 5 10 31 4 0 45 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0 0 0 0 0 0 0 0 0 X19 1 0 0 0 7 3 9 29 0 0 10 0 0 0 1 3 0 0 0 0 0 7 0 1 0 0 0 0 1 0 0 0 0 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 X20 0 0 0 0 11 52 18 29 2 0 19 0 0 0 4 0 0 2 0 0 0 7 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 X21 16 0 0 0 14 40 14 15 1 0 21 2 0 2 3 6 0 1 0 0 0 14 0 0 0 0 0 3 2 0 0 0 0 2 0 1 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 X22 0 0 0 0 14 48 18 17 1 0 30 0 0 0 0 7 0 12 0 0 0 2 0 0 0 0 0 0 0 2 0 3 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 X24 0 0 2 5 6 12 8 7 0 0 26 0 0 2 0 7 0 0 0 0 0 5 0 0 0 0 0 4 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 1 0 0 0 0 Cl1 11 0 0 4 9 0 22 0 21 0 3 0 0 0 4 11 12 23 10 0 8 0 10 0 15 9 1 0 0 41 0 0 1 0 4 0 13 6 3 1 0 1 0 8 1 3 0 0 0 0 0 0 0 0 0 0 0 Cl2 2 0 0 2 19 0 6 0 7 0 3 0 0 0 0 12 10 70 4 1 8 1 7 0 6 2 4 2 0 0 0 0 1 2 1 1 1 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 Cl3 3 0 0 0 21 0 1 0 1 0 7 0 0 0 41 4 0 0 6 0 9 2 25 0 3 0 2 0 0 0 0 0 1 2 2 0 0 0 8 4 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 Cl5 83 0 0 1 19 0 18 5 10 0 7 0 0 0 19 15 0 1 29 0 41 0 7 0 0 9 6 0 0 0 0 0 0 2 1 1 0 5 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 Cl6 70 0 0 1 46 0 46 4 0 0 4 0 0 0 12 7 0 0 12 0 21 1 12 0 6 7 9 0 0 0 4 0 2 1 1 3 2 2 2 1 0 2 0 1 1 0 0 1 0 0 0 0 0 0 0 0 2 Imp1 61 0 0 0 2 3 13 0 15 0 4 0 0 0 5 12 7 7 6 1 13 3 10 0 3 2 5 0 0 18 6 0 5 1 0 1 0 1 0 3 0 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 Imp2 9 0 0 2 18 2 9 4 1 0 6 0 0 1 0 2 1 0 31 0 13 0 3 1 0 18 6 0 0 0 1 0 2 0 2 0 0 3 0 2 0 0 1 0 2 3 0 0 0 0 0 0 1 0 0 0 0 Imp4 6 0 0 2 22 0 9 0 20 0 7 0 0 0 9 12 0 0 24 0 13 4 16 0 0 0 3 0 0 0 0 0 2 3 0 0 0 0 1 6 0 0 0 0 6 0 0 0 0 5 0 0 0 0 0 0 0 Imp7 15 0 0 0 6 0 11 1 47 0 4 0 0 4 13 10 0 0 16 0 15 0 10 0 6 2 5 0 0 3 14 0 0 0 2 2 0 7 1 2 0 2 0 1 0 1 0 0 2 0 0 5 1 0 0 0 0 Imp9 195 0 0 0 16 6 13 6 32 0 1 0 0 6 16 10 11 0 5 0 5 2 11 0 0 7 4 0 0 3 0 0 2 0 0 3 8 3 0 3 0 3 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0
LAT LONG Coc1 10780.76 -1335.326 Coc4 10779.5 -1335.06 Coc8 10785.59 -1337.317 Coc12 10780.08 -1336.277 Coc13 10777.29 -1342.804 Coc16 10777.62 -1345.016 Coc18 10778.98 -1339.375 Coc23 10780.52 -1337.295 Coc25 10778.78 -1348.324 Coc28 10780.47 -1350.227 Coc34 10784.83 -1336.664 Coc35 10785.78 -1338.755 X1 11750.95 -1155.076 X2 11754.07 -1156.99 X4 11750.57 -1158.306 X7 11747.88 -1162.078 X9 11749.43 -1155.939 X10 11763.62 -1151.669 X11 11764.79 -1151.835 X12 11766.23 -1151.47 X14 11767.03 -1153.384 X16 11767.1 -1155.994 X18 11766.98 -1158.239 X19 11765.28 -1159.777 X20 11763.99 -1162.885 X21 11762.99 -1166.181 X22 11759.46 -1156.282 X24 11762.2 -1153.782 Cl1 13287.19 -1908.418 Cl2 13286.38 -1907.632 Cl3 13288.95 -1911.594 Cl5 13283.59 -1909.513 Cl6 13282.85 -1911.118 Imp1 13241.55 -1935.344 Imp2 13242.79 -1935.809 Imp4 13243.45 -1937.547 Imp7 13237.1 -1941.398 Imp9 13235.16 -1944.386
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