Patterns and drivers of lichen species composition in a NW-European lowland deciduous woodland complex
Supplementary Material.
Output of mixed linear models from R
Key:
Nage = age of plots in years since last cut / modification, continuous variable
gen1 = genus of trees (Fs = Fagus, Qs = Quercus, Ia = Ilex, reference level = Betula), factor
logf = log10 (fragment size, ha), continuous variable
dbh = daimater of tree at breast height, continuous
isol = isolation status of fragment (op = peripheral plantation, o = core plantation, ap = peripheral old growth, reference level = old growth core)
1.1. All data
> L1<- glmer(spp~Nage+gen1+isol+logf+dbh+(1|site), family=poisson)
> drop1(L1)
Single term deletions
Model:
spp ~ Nage + gen1 + isol + logf + dbh + (1 | site) [final best model]
Df AIC
<none> 1044.6
Nage 1 1045.1
gen1 3 1057.9
isol 3 1044.2
logf 1 1045.9
dbh 1 1045.3
> summary(L1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: spp ~ Nage + gen1 + isol + logf + dbh + (1 | site)
AIC BIC logLik deviance
1044.5948 1079.7173 -511.2974 1022.5948
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 0.01532 0.1238
Number of obs: 180, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.256905 0.855285 3.808 0.000140 ***
Nage -0.002578 0.001586 -1.625 0.104157
gen1Fs 0.130540 0.098198 1.329 0.183727
gen1Ia 0.172870 0.110547 1.564 0.117873
gen1Qs 0.335088 0.095920 3.493 0.000477 ***
isolap -0.107384 0.133344 -0.805 0.420641
isolo -1.129277 0.442589 -2.552 0.010725 *
isolop -1.254107 0.502635 -2.495 0.012593 *
logf 0.297798 0.155781 1.912 0.055923 .
dbh 0.049057 0.029415 1.668 0.095358 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
1.2. gCl: only, all trees
> gL1<- glmer(gCl~Nage+gen1+isol+logf+dbh+(1|site), family=poisson)
> drop1(L1)
Single term deletions
Model:
spp ~ Nage + gen1 + isol + logf + dbh + (1 | site)
Df AIC
<none> 1044.6
Nage 1 1045.1
gen1 3 1057.9
isol 3 1044.2
logf 1 1045.9
dbh 1 1045.3
> summary(gL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: gCl ~ Nage + gen1 + isol + logf + dbh + (1 | site) [final best model]
AIC BIC logLik deviance
791.4289 826.5514 -384.7144 769.4289
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 0.007008 0.08371
Number of obs: 180, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 5.407503 0.964290 5.608 2.05e-08 ***
Nage -0.007448 0.001792 -4.155 3.25e-05 ***
gen1Fs 0.003403 0.138177 0.025 0.980354
gen1Ia -0.937002 0.191052 -4.904 9.37e-07 ***
gen1Qs 0.186002 0.133180 1.397 0.162525
isolap -0.234463 0.154775 -1.515 0.129807
isolo -2.400104 0.513418 -4.675 2.94e-06 ***
isolop -2.090532 0.558391 -3.744 0.000181 ***
logf -0.130932** 0.176831 -0.740 0.459037
dbh -0.030530 0.048764 -0.626 0.531258
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
1.3. Tr only, all trees
> gL1<- glmer(Tr~Nage+gen1+isol+logf+dbh+(1|site), family=poisson)
> drop1(gL1)
Single term deletions
Model:
Tr ~ Nage + gen1 + isol + logf + dbh + (1 | site) [final best model]
Df AIC
<none> 799.32
Nage 1 799.02
gen1 3 816.62
isol 3 803.39
logf 1 808.13
dbh 1 806.65
> summary(gL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: Tr ~ Nage + gen1 + isol + logf + dbh + (1 | site)
AIC BIC logLik deviance
799.3171 834.4396 -388.6585 777.3171
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 0.01302 0.1141
Number of obs: 180, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.621234 1.002784 -0.620 0.535581
Nage 0.002437 0.001847 1.319 0.187040
gen1Fs 0.321011 0.158816 2.021 0.043251 *
gen1Ia 0.688459 0.169556 4.060 4.9e-05 ***
gen1Qs 0.508103 0.155806 3.261 0.001110 **
isolap 0.069588 0.143733 0.484 0.628284
isolo 0.221200 0.509904 0.434 0.664428
isolop -0.636740 0.610600 -1.043 0.297036
logf 0.685654 0.183371 3.739 0.000185 ***
dbh 0.124132 0.039571 3.137 0.001707 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2.1. Beech only, all photobionts
> bL1<- glmer(tspp~Nage+isol+lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
tspp ~ Nage + isol + lfrag + dbh + (1 | site)
Df AIC
<none> 323.81
Nage 1 322.86
isol 3 324.62
lfrag 1 322.14
dbh 1 324.29
> bL1<- glmer(tspp~Nage+isol+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[drop lfrag]
Model:
tspp ~ Nage + isol + dbh + (1 | site) [final best model]
Df AIC
<none> 322.14
Nage 1 323.70
isol 3 324.84
dbh 1 322.29
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: tspp ~ Nage + isol + dbh + (1 | site)
AIC BIC logLik deviance
322.1360 336.1874 -154.0680 308.1360
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 0.009835 0.09917
Number of obs: 55, groups: site, 13
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.181036 1.036837 4.032 5.52e-05 ***
Nage -0.003941 0.002065 -1.909 0.0563 .
isolap 0.067027 0.206290 0.325 0.7452
isolo -1.486085 0.584337 -2.543 0.0110 *
isolop -1.097735 0.657677 -1.669 0.0951 .
dbh 0.091042 0.061803 1.473 0.1407
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2.2. Beech only, gCl,
> bL1<- glmer(gCl~Nage+isol+lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
gCl ~ Nage + isol + lfrag + dbh + (1 | site)
Df AIC
<none> 242.67
Nage 1 242.62
isol 3 252.13
lfrag 1 240.86
dbh 1 241.03
> bL1<- glmer(gCl~Nage+isol+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[drop lfrag]
Model:
gCl ~ Nage + isol + dbh + (1 | site)
Df AIC
<none> 240.86
Nage 1 243.78
isol 3 251.68
dbh 1 239.08
> bL1<- glmer(gCl~Nage+isol+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[drop dbh]
Model:
gCl ~ Nage + isol + (1 | site) [final best model]
Df AIC
<none> 239.08
Nage 1 241.91
isol 3 251.32
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: gCl ~ Nage + isol + (1 | site)
AIC BIC logLik deviance
239.0804 251.1244 -113.5402 227.0804
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 2.431e-11 4.931e-06
Number of obs: 55, groups: site, 13
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.615409 1.419533 3.251 0.00115 **
Nage -0.006170 0.002834 -2.177 0.02947 *
isolap -0.064207 0.290495 -0.221 0.82507
isolo -2.177060 0.819624 -2.656 0.00790 **
isolop -1.060369 0.875111 -1.212 0.22563
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2.3. Beech only, Tr
> bL1<- glmer(Tr~Nage+isol+lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
Tr ~ Nage + isol + lfrag + dbh + (1 | site)
Df AIC
<none> 256.03
Nage 1 254.06
isol 3 258.31
lfrag 1 254.34
dbh 1 256.26
> bL1<- glmer(Tr~isol+lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[drop Nage]
Model:
Tr ~ isol + lfrag + dbh + (1 | site)
Df AIC
<none> 254.06
isol 3 261.38
lfrag 1 252.94
dbh 1 254.54
> bL1<- glmer(Tr~isol+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[drop lfrag]
Model:
Tr ~ isol + dbh + (1 | site)
Df AIC
<none> 252.94
isol 3 259.38
dbh 1 252.77
[drop dbh]
> bL1<- glmer(Tr~isol+(1|site), family=poisson) [final best model]
> drop1(bL1)
Single term deletions
Model:
Tr ~ isol + (1 | site)
Df AIC
<none> 252.77
isol 3 262.18
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: Tr ~ isol + (1 | site)
AIC BIC logLik deviance
252.7666 262.8032 -121.3833 242.7666
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 1.385e-10 1.177e-05
Number of obs: 55, groups: site, 13
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.63665 0.08192 19.978 <2e-16 ***
isolap 0.35578 0.22840 1.558 0.1193
isolo -0.36368 0.14158 -2.569 0.0102 *
isolop -1.63665 0.71184 -2.299 0.0215 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
3.1. Oak only, all photobionts
> bL1<- glmer(tspp~Nage+isol+Lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
tspp ~ Nage + isol + Lfrag + dbh + (1 | site)
Df AIC
<none> 434.25
Nage 1 437.61
isol 3 440.42
Lfrag 1 433.19
dbh 1 432.26
> bL1<- glmer(tspp~Nage+isol+Lfrag+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[dbh dropped]
Model:
tspp ~ Nage + isol + Lfrag + (1 | site)
Df AIC
<none> 432.26
Nage 1 435.67
isol 3 438.54
Lfrag 1 431.20
> bL1<- glmer(tspp~Nage+isol+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[Lfrag dropped]
Model:
tspp ~ Nage + isol + (1 | site)
Df AIC
<none> 431.20
Nage 1 438.28
isol 3 443.47
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: tspp ~ Nage + isol + (1 | site) [final best model]
AIC BIC logLik deviance
431.1955 445.2583 -209.5977 419.1955
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 2.304e-11 4.8e-06
Number of obs: 77, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.492430 0.589728 7.618 2.58e-14 ***
Nage -0.003634 0.001175 -3.092 0.001989 **
isolap -0.308213 0.092873 -3.319 0.000904 ***
isolo -1.507521 0.334901 -4.501 6.75e-06 ***
isolop -1.576158 0.378304 -4.166 3.09e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
3.2.Oaks only, gCl
> bL1<- glmer(gCl~Nage+isol+Lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
gCl ~ Nage + isol + Lfrag + dbh + (1 | site)
Df AIC
<none> 364.59
Nage 1 376.67
isol 3 376.07
Lfrag 1 363.87
dbh 1 365.86
> bL1<- glmer(gCl~Nage+isol+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
[Lfrag dropped]
Model:
gCl ~ Nage + isol + dbh + (1 | site) [final best model]
Df AIC
<none> 363.87
Nage 1 375.20
isol 3 374.59
dbh 1 365.97
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: gCl ~ Nage + isol + dbh + (1 | site)
AIC BIC logLik deviance
363.8746 380.2812 -174.9373 349.8746
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 2.826e-12 1.681e-06
Number of obs: 77, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 5.673603 0.936503 6.058 1.38e-09 ***
Nage -0.007335 0.001823 -4.024 5.73e-05 ***
isolap -0.176167 0.145957 -1.207 0.227442
isolo -2.349413 0.539038 -4.359 1.31e-05 ***
isolop -2.121115 0.573718 -3.697 0.000218 ***
dbh -0.137167 0.068377 -2.006 0.044851 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
3.2. Oaks only, Tr
> bL1<- glmer(Tr~Nage+isol+Lfrag+dbh+(1|site), family=poisson)
> drop1(bL1)
Single term deletions
Model:
Tr ~ Nage + isol + Lfrag + dbh + (1 | site) [final best model]
Df AIC
<none> 328.74
Nage 1 331.81
isol 3 329.83
Lfrag 1 336.32
dbh 1 331.58
> summary(bL1)
Generalized linear mixed model fit by maximum likelihood ['glmerMod']
Family: poisson ( log )
Formula: Tr ~ Nage + isol + Lfrag + dbh + (1 | site)
AIC BIC logLik deviance
328.7420 347.4924 -156.3710 312.7420
Random effects:
Groups Name Variance Std.Dev.
site (Intercept) 3.95e-14 1.987e-07
Number of obs: 77, groups: site, 15
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.074222 1.126904 -0.953 0.34046
Nage 0.004567 0.002056 2.221 0.02633 *
isolap -0.189674 0.139567 -1.359 0.17414
isolo 0.575499 0.553836 1.039 0.29875
isolop 0.108206 0.675689 0.160 0.87277
Lfrag 0.664085 0.226413 2.933 0.00336 **
dbh 0.129245 0.058355 2.215 0.02677 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1