###################################################################### ###################################################################### ###################################################################### ALTERNARIA MODELS: > model1 <- glmer(y~accession+(1|leaf)+(1|exp:box),family=binomial) > summary(model1) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ accession + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2641.8 2678.7 -1311.9 2623.8 436 Scaled residuals: Min 1Q Median 3Q Max -5.4417 -1.2880 0.1599 1.2215 5.2437 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.00809 1.0040 leaf (Intercept) 0.06717 0.2592 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.0004638 0.2192477 0.002 0.998312 accessionLA2931 0.5518345 0.1366239 4.039 5.37e-05 *** accessionLA2932 0.8755688 0.1278497 6.848 7.47e-12 *** accessionLA3111 -0.2954464 0.1236087 -2.390 0.016840 * accessionLA4107 0.8515017 0.1328940 6.407 1.48e-10 *** accessionLA4117 0.4648801 0.1302481 3.569 0.000358 *** accessionLA4330 1.3704372 0.1344934 10.190 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) aLA2931 aLA2932 aLA311 aLA410 aLA411 accssLA2931 -0.283 accssLA2932 -0.279 0.501 accssLA3111 -0.263 0.356 0.439 accssLA4107 -0.255 0.425 0.429 0.405 accssLA4117 -0.272 0.449 0.439 0.461 0.435 accssLA4330 -0.296 0.560 0.530 0.454 0.437 0.462 ###################################################################### > model2 <- glmer(y~Latitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model2) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2708.6 2725.0 -1350.3 2700.6 441 Scaled residuals: Min 1Q Median 3Q Max -5.3494 -1.2781 0.1773 1.2396 5.8381 Random effects: s Name Variance Std.Dev. exp:box (Intercept) 0.99826 0.9991 leaf (Intercept) 0.05064 0.2250 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.58161 0.20001 2.908 0.00364 ** Latitude -0.40935 0.03578 -11.441 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitude -0.020 ###################################################################### > model3 <- glmer(y~Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model3) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2815.5 2831.8 -1403.7 2807.5 441 Scaled residuals: Min 1Q Median 3Q Max -5.4153 -1.3078 0.2305 1.3728 5.2670 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.06702 1.033 leaf (Intercept) 0.06504 0.255 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.54443 0.20814 2.616 0.00891 ** Longitude 0.19097 0.03597 5.309 1.1e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Longitude -0.001 ###################################################################### > model4 <- glmer(y~Latitude+Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model4) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2703.9 2724.4 -1346.9 2693.9 440 Scaled residuals: Min 1Q Median 3Q Max -5.1867 -1.2645 0.1498 1.2628 6.0638 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.00653 1.0033 leaf (Intercept) 0.04962 0.2228 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.57568 0.20060 2.870 0.00411 ** Latitude -0.38536 0.03675 -10.485 < 2e-16 *** Longitude 0.09746 0.03750 2.599 0.00936 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Latitude -0.021 Longitude -0.009 0.243 ###################################################################### > model5 <- glmer(y~Latitude*Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model5) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude * Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2705.8 2730.4 -1346.9 2693.8 439 Scaled residuals: Min 1Q Median 3Q Max -5.1579 -1.2522 0.1635 1.2635 6.0906 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.0051 1.0026 leaf (Intercept) 0.0499 0.2234 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.58131 0.20150 2.885 0.00392 ** Latitude -0.36412 0.08364 -4.354 1.34e-05 *** Longitude 0.11176 0.06298 1.774 0.07598 . Latitude:Longitude 0.02883 0.10201 0.283 0.77744 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Latitude 0.080 Longitude 0.074 0.785 Lattd:Lngtd 0.099 0.898 0.803 ###################################################################### > summary(model6) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + Altitude + Annual.Precip + Mean.Temp.Wettest.Q + +Mean.Temp.Cold.Q + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2641.8 2678.7 -1311.9 2623.8 436 Scaled residuals: Min 1Q Median 3Q Max -5.4467 -1.2873 0.1584 1.2217 5.2477 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.00770 1.0038 leaf (Intercept) 0.06702 0.2589 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.57661 0.20343 2.834 0.00459 ** Latitude -0.47116 0.04885 -9.644 < 2e-16 *** Longitude 17.37641 2.49444 6.966 3.26e-12 *** Altitude -7.38395 1.25036 -5.905 3.52e-09 *** Annual.Precip 9.12457 1.36839 6.668 2.59e-11 *** Mean.Temp.Wettest.Q 3.19554 0.45874 6.966 3.26e-12 *** Mean.Temp.Cold.Q 10.15202 1.38144 7.349 2.00e-13 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Altitd Annl.P M.T.W. Latitude -0.018 Longitude 0.005 -0.266 Altitude -0.005 0.183 -0.965 Annual.Prcp 0.005 -0.269 0.998 -0.977 Mn.Tmp.Wt.Q 0.006 -0.305 0.991 -0.961 0.992 Mn.Tmp.Cl.Q 0.006 -0.318 0.976 -0.885 0.962 0.960 convergence code: 0 Model failed to converge with max|grad| = 0.0211538 (tol = 0.001, component 1) ###################################################################### > model7 <- glmer(y~Altitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model7) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Altitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2843.3 2859.7 -1417.7 2835.3 441 Scaled residuals: Min 1Q Median 3Q Max -5.3313 -1.2966 0.1592 1.4127 5.2856 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.05380 1.0265 leaf (Intercept) 0.07585 0.2754 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.54931 0.20862 2.633 0.00846 ** Altitude -0.02130 0.03504 -0.608 0.54332 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Altitude -0.008 ###################################################################### > model8 <- glmer(y~Annual.Mean.Temp+(1|leaf)+(1|exp:box),family=binomial) > summary(model8) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Mean.Temp + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2843.5 2859.9 -1417.8 2835.5 441 Scaled residuals: Min 1Q Median 3Q Max -5.4184 -1.3139 0.1501 1.4257 5.1711 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.05709 1.0281 leaf (Intercept) 0.07537 0.2745 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.54767 0.20883 2.623 0.00873 ** Annual.Mean.Temp -0.01426 0.03515 -0.406 0.68502 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Annl.Mn.Tmp 0.007 ###################################################################### > summary(model9) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Precip + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2784.2 2800.6 -1388.1 2776.2 441 Scaled residuals: Min 1Q Median 3Q Max -5.7527 -1.2374 0.1656 1.3380 5.1619 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.02473 1.0123 leaf (Intercept) 0.04949 0.2225 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.55995 0.20211 2.771 0.0056 ** Annual.Precip -0.26451 0.03447 -7.675 1.66e-14 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Annual.Prcp -0.009 ###################################################################### > model10 <- glmer(y~group+(1|leaf)+(1|exp:box),family=binomial) > summary(model10) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ group + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2705.0 2725.5 -1347.5 2695.0 440 Scaled residuals: Min 1Q Median 3Q Max -5.9267 -1.3054 0.1804 1.2950 5.7745 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.0431 1.0213 leaf (Intercept) 0.0591 0.2431 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.10176 0.20849 0.488 0.626 groupCOAST 0.75668 0.08389 9.019 <2e-16 *** groupMOUNT 0.84121 0.08175 10.291 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) gCOAST groupCOAST -0.140 groupSOUTH -0.150 0.358 ###################################################################### ###################################################################### ###################################################################### FUSARIUM MODELS: > model1 <- glmer(y~accession+(1|leaf)+(1|exp:box),family=binomial) > summary(model1) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ accession + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2307.6 2342.9 -1144.8 2289.6 367 Scaled residuals: Min 1Q Median 3Q Max -6.5032 -1.4651 -0.0526 1.3388 5.5608 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.5534 0.7439 leaf (Intercept) 0.1297 0.3602 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.07134 0.20721 -0.344 0.731 accessionLA2931 -0.10738 0.16161 -0.664 0.506 accessionLA2932 0.78253 0.17146 4.564 5.02e-06 *** accessionLA3111 1.11537 0.16826 6.629 3.38e-11 *** accessionLA4107 -0.71985 0.16189 -4.447 8.73e-06 *** accessionLA4117 -0.88139 0.17376 -5.072 3.93e-07 *** accessionLA4330 -0.02266 0.15657 -0.145 0.885 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) aLA2931 aLA2932 aLA311 aLA410 aLA411 accssLA2931 -0.374 accssLA2932 -0.373 0.549 accssLA3111 -0.370 0.514 0.525 accssLA4107 -0.386 0.450 0.444 0.480 accssLA4117 -0.388 0.426 0.435 0.418 0.514 accssLA4330 -0.407 0.462 0.449 0.424 0.544 0.598 ###################################################################### > model2 <- glmer(y~Latitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model2) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2431.3 2447.1 -1211.7 2423.3 372 Scaled residuals: Min 1Q Median 3Q Max -4.9269 -1.4834 -0.0275 1.5097 5.9388 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.5514 0.7426 leaf (Intercept) 0.1237 0.3517 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.07975 0.17691 -0.451 0.652 Latitude 0.37407 0.04360 8.580 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitude -0.002 ###################################################################### > model3 <- glmer(y~Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model3) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2490.8 2506.6 -1241.4 2482.8 372 Scaled residuals: Min 1Q Median 3Q Max -4.8989 -1.6188 -0.0947 1.5725 5.9917 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.6347 0.7967 leaf (Intercept) 0.1266 0.3558 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.07607 0.18652 -0.408 0.683 Longitude -0.17681 0.04468 -3.957 7.59e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Longitude -0.005 ###################################################################### > model4 <- glmer(y~Latitude+Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model4) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2420.6 2440.3 -1205.3 2410.6 371 Scaled residuals: Min 1Q Median 3Q Max -4.6864 -1.5344 -0.0669 1.4973 5.7199 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.5519 0.7429 leaf (Intercept) 0.1277 0.3573 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.07337 0.17768 -0.413 0.679679 Latitude 0.36510 0.04345 8.403 < 2e-16 *** Longitude -0.16190 0.04544 -3.563 0.000366 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Latitude -0.001 Longitude -0.007 0.045 ###################################################################### > model5 <- glmer(y~Latitude*Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model5) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude * Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2419.1 2442.6 -1203.5 2407.1 370 Scaled residuals: Min 1Q Median 3Q Max -4.9754 -1.5042 -0.0639 1.4891 5.8880 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.5437 0.7374 leaf (Intercept) 0.1256 0.3544 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.02205 0.17850 -0.124 0.9017 Latitude 0.56144 0.11292 4.972 6.62e-07 *** Longitude -0.05252 0.07362 -0.713 0.4756 Latitude:Longitude 0.24894 0.13199 1.886 0.0593 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Latitude 0.141 Longitude 0.117 0.735 Lattd:Lngtd 0.153 0.923 0.786 ###################################################################### > summary(model6) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + Altitude + Annual.Precip + Mean.Temp.Wettest.Q + +Mean.Temp.Cold.Q + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2641.8 2678.7 -1311.9 2623.8 436 Scaled residuals: Min 1Q Median 3Q Max -5.4467 -1.2873 0.1584 1.2217 5.2477 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 1.00770 1.0038 leaf (Intercept) 0.06702 0.2589 Number of obs: 445, groups: exp:box, 28; leaf, 16 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.57661 0.20343 2.834 0.00459 ** Latitude -0.47116 0.04885 -9.644 < 2e-16 *** Longitude 17.37641 2.49444 6.966 3.26e-12 *** Altitude -7.38395 1.25036 -5.905 3.52e-09 *** Annual.Precip 9.12457 1.36839 6.668 2.59e-11 *** Mean.Temp.Wettest.Q 3.19554 0.45874 6.966 3.26e-12 *** Mean.Temp.Cold.Q 10.15202 1.38144 7.349 2.00e-13 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Altitd Annl.P M.T.W. Latitude -0.018 Longitude 0.005 -0.266 Altitude -0.005 0.183 -0.965 Annual.Prcp 0.005 -0.269 0.998 -0.977 Mn.Tmp.Wt.Q 0.006 -0.305 0.991 -0.961 0.992 Mn.Tmp.Cl.Q 0.006 -0.318 0.976 -0.885 0.962 0.960 convergence code: 0 ###################################################################### > model7 <- glmer(y~Altitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model7) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Altitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2503.5 2519.2 -1247.7 2495.5 372 Scaled residuals: Min 1Q Median 3Q Max -5.4274 -1.6173 -0.0704 1.6169 5.8371 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.6577 0.8110 leaf (Intercept) 0.1291 0.3594 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.08463 0.18936 -0.447 0.6549 Altitude 0.07119 0.04078 1.746 0.0809 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Altitude -0.009 ###################################################################### > model8 <- glmer(y~Annual.Mean.Temp+(1|leaf)+(1|exp:box),family=binomial) > summary(model8) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Mean.Temp + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2506.5 2522.2 -1249.3 2498.5 372 Scaled residuals: Min 1Q Median 3Q Max -5.2536 -1.6174 -0.0154 1.5954 5.7910 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.651 0.8069 leaf (Intercept) 0.129 0.3592 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.081598 0.188638 -0.433 0.665 Annual.Mean.Temp 0.006754 0.041525 0.163 0.871 Correlation of Fixed Effects: (Intr) Annl.Mn.Tmp 0.009 ###################################################################### > model9 <- glmer(y~Annual.Precip+(1|leaf)+(1|exp:box),family=binomial) > summary(model9) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Precip + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2457.1 2472.8 -1224.5 2449.1 372 Scaled residuals: Min 1Q Median 3Q Max -6.0011 -1.5828 -0.0729 1.4843 6.5681 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.6805 0.8249 leaf (Intercept) 0.1201 0.3465 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.08346 0.19036 -0.438 0.661 Annual.Precip 0.29096 0.04221 6.893 5.45e-12 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Annual.Prcp 0.002 ###################################################################### > model10 <- glmer(y~group+(1|leaf)+(1|exp:box),family=binomial) > summary(model10) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ group + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 2489.7 2509.3 -1239.8 2479.7 371 Scaled residuals: Min 1Q Median 3Q Max -5.5457 -1.5795 -0.1208 1.6033 5.9027 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.5790 0.7609 leaf (Intercept) 0.1216 0.3487 Number of obs: 376, groups: exp:box, 25; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) 0.1605 0.1881 0.853 0.39354 groupCOAST -0.3008 0.0993 -3.029 0.00245 ** groupSOUTH -0.4869 0.1172 -4.156 3.24e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) gCOAST groupCOAST -0.237 groupSOUTH -0.268 0.451 ###################################################################### ###################################################################### ###################################################################### PHYTOPHTHORA MODELS: > model1 <- glmer(y~accession+(1|leaf)+(1|exp:box),family=binomial) > summary(model1) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ accession + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1893.3 1928.6 -937.6 1875.3 366 Scaled residuals: Min 1Q Median 3Q Max -6.5314 -1.2215 -0.1257 1.1224 5.0222 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.80113 0.8951 leaf (Intercept) 0.01756 0.1325 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.7864 0.2135 -3.683 0.00023 *** accessionLA2931 0.2604 0.1584 1.644 0.10017 accessionLA2932 0.7301 0.1685 4.334 1.47e-05 *** accessionLA3111 -0.2629 0.1705 -1.542 0.12305 accessionLA4107 0.2602 0.1732 1.502 0.13303 accessionLA4117 0.4233 0.1648 2.569 0.01020 * accessionLA4330 1.2323 0.1634 7.541 4.68e-14 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) aLA2931 aLA2932 aLA311 aLA410 aLA411 accssLA2931 -0.378 accssLA2932 -0.383 0.520 accssLA3111 -0.380 0.524 0.516 accssLA4107 -0.405 0.476 0.504 0.528 accssLA4117 -0.402 0.446 0.470 0.468 0.570 accssLA4330 -0.386 0.430 0.449 0.421 0.526 0.578 ###################################################################### > model2 <- glmer(y~Latitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model2) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1958.3 1974.0 -975.1 1950.3 371 Scaled residuals: Min 1Q Median 3Q Max -4.6759 -1.3209 -0.2128 1.1116 4.7940 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.80345 0.8964 leaf (Intercept) 0.02615 0.1617 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39145 0.18502 -2.116 0.0344 * Latitude -0.23864 0.04479 -5.328 9.96e-08 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitude -0.002 ###################################################################### > model3 <- glmer(y~Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model3) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1965.8 1981.6 -978.9 1957.8 371 Scaled residuals: Min 1Q Median 3Q Max -5.0753 -1.3791 -0.3591 1.1371 5.3956 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.74427 0.8627 leaf (Intercept) 0.02074 0.1440 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39605 0.17780 -2.227 0.0259 * Longitude 0.20705 0.04494 4.607 4.08e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Longitude -0.001 ###################################################################### > model4 <- glmer(y~Latitude+Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model4) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1945.4 1965.1 -967.7 1935.4 370 Scaled residuals: Min 1Q Median 3Q Max -4.9145 -1.3187 -0.1906 1.1048 4.8487 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.77501 0.8803 leaf (Intercept) 0.02279 0.1510 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.38984 0.18148 -2.148 0.031705 * Latitude -0.21451 0.04548 -4.716 2.4e-06 *** Longitude 0.17551 0.04545 3.862 0.000113 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Latitude -0.002 Longitude -0.001 0.133 ###################################################################### > model5 <- glmer(y~Latitude*Longitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model5) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude * Longitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1947.4 1971.0 -967.7 1935.4 369 Scaled residuals: Min 1Q Median 3Q Max -4.9075 -1.3222 -0.1861 1.1005 4.8358 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.77543 0.8806 leaf (Intercept) 0.02284 0.1511 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39398 0.18346 -2.147 0.0318 * Latitude -0.23136 0.11665 -1.984 0.0473 * Longitude 0.16665 0.07254 2.297 0.0216 * Latitude:Longitude -0.02029 0.12935 -0.157 0.8754 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Latitude 0.132 Longitude 0.112 0.750 Lattd:Lngtd 0.145 0.921 0.779 # ###################################################################### > summary(model6) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Latitude + Longitude + Altitude + Annual.Precip + Mean.Temp.Wettest.Q + +Mean.Temp.Cold.Q + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1893.3 1928.6 -937.6 1875.3 366 Scaled residuals: Min 1Q Median 3Q Max -6.5163 -1.2214 -0.1277 1.1226 5.0198 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.80104 0.8950 leaf (Intercept) 0.01758 0.1326 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39830 0.18346 -2.171 0.0299 * Latitude -0.29494 0.06275 -4.700 2.60e-06 *** Longitude 17.31035 3.10750 5.571 2.54e-08 *** Altitude -6.52528 1.58251 -4.123 3.73e-05 *** Annual.Precip 8.31471 1.60703 5.174 2.29e-07 *** Mean.Temp.Wettest.Q 3.07197 0.56647 5.423 5.86e-08 *** Mean.Temp.Cold.Q 10.59706 1.65222 6.414 1.42e-10 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Latitd Longtd Altitd Annl.P M.T.W. Latitude 0.002 Longitude -0.005 -0.142 Altitude 0.004 0.046 -0.966 Annual.Prcp -0.005 -0.146 0.998 -0.978 Mn.Tmp.Wt.Q -0.006 -0.172 0.991 -0.961 0.992 Mn.Tmp.Cl.Q -0.006 -0.218 0.973 -0.882 0.959 0.958 convergence code: 0 Model failed to converge with max|grad| = 0.0387411 (tol = 0.001, component 1) ###################################################################### > model7 <- glmer(y~Altitude+(1|leaf)+(1|exp:box),family=binomial) > summary(model7) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Altitude + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1985.1 2000.8 -988.5 1977.1 371 Scaled residuals: Min 1Q Median 3Q Max -4.8646 -1.3484 -0.2168 1.1001 5.2965 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.77068 0.8779 leaf (Intercept) 0.02417 0.1555 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39874 0.18121 -2.200 0.0278 * Altitude 0.05855 0.04157 1.409 0.1590 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Altitude -0.002 ###################################################################### > model8 <- glmer(y~Annual.Mean.Temp+(1|leaf)+(1|exp:box),family=binomial) > summary(model8) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Mean.Temp + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1984.1 1999.8 -988.0 1976.1 371 Scaled residuals: Min 1Q Median 3Q Max -4.8805 -1.3470 -0.2208 1.1091 5.3436 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.76660 0.8756 leaf (Intercept) 0.02389 0.1546 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39853 0.18073 -2.205 0.0274 * Annual.Mean.Temp -0.07312 0.04246 -1.722 0.0850 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Annl.Mn.Tmp 0.002 ###################################################################### > model9 <- glmer(y~Annual.Precip+(1|leaf)+(1|exp:box),family=binomial) > summary(model9) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ Annual.Precip + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1968.4 1984.1 -980.2 1960.4 371 Scaled residuals: Min 1Q Median 3Q Max -4.7967 -1.3323 -0.1464 1.0735 4.8749 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.78719 0.8872 leaf (Intercept) 0.02423 0.1556 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.39639 0.18299 -2.166 0.0303 * Annual.Precip -0.17844 0.04185 -4.264 2e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) Annual.Prcp 0.003 ###################################################################### > model10 <- glmer(y~group+(1|leaf)+(1|exp:box),family=binomial) > summary(model10) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: binomial ( logit ) Formula: y ~ group + (1 | leaf) + (1 | exp:box) AIC BIC logLik deviance df.resid 1930.2 1949.8 -960.1 1920.2 370 Scaled residuals: Min 1Q Median 3Q Max -5.1703 -1.3067 -0.2075 1.0639 5.4537 Random effects: Groups Name Variance Std.Dev. exp:box (Intercept) 0.80278 0.8960 leaf (Intercept) 0.02359 0.1536 Number of obs: 375, groups: exp:box, 26; leaf, 17 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.8105 0.1932 -4.195 2.73e-05 *** groupCOAST 0.5333 0.1090 4.894 9.88e-07 *** groupSOUTH 0.8713 0.1180 7.386 1.51e-13 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) gCOAST groupCOAST -0.240 groupSOUTH -0.263 0.454