Visreg plots
Ang
30 October, 2015
Data
env<-read.csv("/Users/Ang/Documents/Tesis New/Landscape/env.csv")
env2<-na.omit(env)Abundance
abEnv2<- glmmadmb(Tot.Abund~Leaves+Time+Patch.Area+Fixed.edge+Prox.Index+Dist.finger+Real.For.cover+DBH+(1|Site),data=env2,zeroInflation=TRUE,family="nbinom")overdisp_fun(abEnv2)## chisq ratio rdf p
## 184.1330578 0.9442721 195.0000000 0.7008723Anova(abEnv2)## Analysis of Deviance Table (Type II tests)
##
## Response: Tot.Abund
## Df Chisq Pr(>Chisq)
## Leaves 1 0.0040 0.94988
## Time 1 15.8513 6.852e-05 ***
## Patch.Area 1 2.8235 0.09289 .
## Fixed.edge 1 0.6281 0.42806
## Prox.Index 1 1.1845 0.27645
## Dist.finger 1 1.2930 0.25550
## Real.For.cover 1 4.0502 0.04417 *
## DBH 1 4.2915 0.03830 *
## Residuals 193
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1summary(abEnv2)##
## Call:
## glmmadmb(formula = Tot.Abund ~ Leaves + Time + Patch.Area + Fixed.edge +
## Prox.Index + Dist.finger + Real.For.cover + DBH + (1 | Site),
## data = env2, family = "nbinom", zeroInflation = TRUE)
##
## AIC: 1615
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.66e+00 4.01e-01 4.15 3.4e-05 ***
## LeavesStandard -9.61e-03 1.53e-01 -0.06 0.950
## TimeLate 6.13e-01 1.54e-01 3.98 6.9e-05 ***
## Patch.Area 1.99e-06 1.19e-06 1.68 0.093 .
## Fixed.edge -1.73e-03 2.18e-03 -0.79 0.428
## Prox.Index -2.69e-05 2.47e-05 -1.09 0.276
## Dist.finger 2.04e-03 1.80e-03 1.14 0.255
## Real.For.cover 2.07e-02 1.03e-02 2.01 0.044 *
## DBH 1.82e-02 8.78e-03 2.07 0.038 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Number of observations: total=205, Site=12
## Random effect variance(s):
## Group=Site
## Variance StdDev
## (Intercept) 2.061e-09 4.54e-05
##
## Negative binomial dispersion parameter: 0.90322 (std. err.: 0.092491)
## Zero-inflation: 1e-06 (std. err.: 3.1411e-08 )
##
## Log-likelihood: -795.492Abundance plots
Richness
richEnv2<- glmmadmb(Rich~Leaves+Time+Fixed.edge+Dist.finger+Real.For.cover+DBH+(1|Site),data=env2,zeroInflation=TRUE,family="nbinom")
overdisp_fun(richEnv2) ## chisq ratio rdf p
## 161.1012296 0.8177727 197.0000000 0.9711303Anova(richEnv2)## Analysis of Deviance Table (Type II tests)
##
## Response: Rich
## Df Chisq Pr(>Chisq)
## Leaves 1 0.5547 0.456413
## Time 1 28.5249 9.25e-08 ***
## Fixed.edge 1 0.4150 0.519421
## Dist.finger 1 4.2415 0.039447 *
## Real.For.cover 1 0.6069 0.435939
## DBH 1 9.4202 0.002146 **
## Residuals 195
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1summary(richEnv2)##
## Call:
## glmmadmb(formula = Rich ~ Leaves + Time + Fixed.edge + Dist.finger +
## Real.For.cover + DBH + (1 | Site), data = env2, family = "nbinom",
## zeroInflation = TRUE)
##
## AIC: 706.8
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.189593 0.205790 0.92 0.3569
## LeavesStandard 0.068332 0.091750 0.74 0.4564
## TimeLate 0.513984 0.096236 5.34 9.3e-08 ***
## Fixed.edge -0.000664 0.001030 -0.64 0.5194
## Dist.finger 0.001437 0.000698 2.06 0.0394 *
## Real.For.cover 0.003359 0.004312 0.78 0.4359
## DBH 0.013000 0.004236 3.07 0.0021 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Number of observations: total=205, Site=12
## Random effect variance(s):
## Group=Site
## Variance StdDev
## (Intercept) 3.674e-08 0.0001917
##
## Negative binomial dispersion parameter: 403.43 (std. err.: 0.82086)
## Zero-inflation: 1e-06 (std. err.: 1.3463e-07 )
##
## Log-likelihood: -343.401Richness plots
