Title: Percent rocks
Name: Tammy L. Elliott
Date: April 17, 2016
R version 3.2
Environmental distances ANOVA
Environmental distance Bartlett Test
bartlett.test(rocks.site.env.dist.cfuz.4.clusters$Rocks,rocks.site.env.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.site.env.dist.cfuz.4.clusters$Rocks and rocks.site.env.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = Inf, df = 3, p-value < 2.2e-16Environmental distance ANOVA
rocks.site.env.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.site.env.dist.cfuz.4.clusters)
summary(rocks.site.env.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 6047 2015.6 15.95 3.4e-09 ***
## Residuals 172 21734 126.4
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Environmental distance Tukey post-hoc
posthoc.env.dist.4<-TukeyHSD(x=rocks.site.env.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
env.dist.4.glht.out<-glht(rocks.site.env.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(env.dist.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.site.env.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 -1.240e-15 2.360e+00 0.000 1.000
## Group3 - Group1 == 0 3.720e-01 2.454e+00 0.152 0.999
## Group4 - Group1 == 0 1.365e+01 2.410e+00 5.662 <1e-06 ***
## Group3 - Group2 == 0 3.720e-01 2.390e+00 0.156 0.999
## Group4 - Group2 == 0 1.365e+01 2.346e+00 5.817 <1e-06 ***
## Group4 - Group3 == 0 1.328e+01 2.440e+00 5.441 <1e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)raoD presence absence
raoD presence absence Bartlett Test
bartlett.test(rocks.raoD.pa.dist.cfuz.4.clusters$Rocks,rocks.raoD.pa.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.raoD.pa.dist.cfuz.4.clusters$Rocks and rocks.raoD.pa.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = Inf, df = 3, p-value < 2.2e-16raoD presence absence ANOVA
rocks.raoD.pa.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.raoD.pa.dist.cfuz.4.clusters)
summary(rocks.raoD.pa.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 5052 1684.0 12.74 1.47e-07 ***
## Residuals 172 22729 132.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1raoD presence absence Tukey-Kramer
posthoc.raoD.pa.4<-TukeyHSD(x=rocks.raoD.pa.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
raoD.pa.4.glht.out<-glht(rocks.raoD.pa.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(raoD.pa.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.raoD.pa.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 2.235 2.161 1.034 0.727
## Group3 - Group1 == 0 1.742 2.525 0.690 0.900
## Group4 - Group1 == 0 15.133 2.525 5.993 <1e-04 ***
## Group3 - Group2 == 0 -0.493 2.665 -0.185 0.998
## Group4 - Group2 == 0 12.899 2.665 4.840 <1e-04 ***
## Group4 - Group3 == 0 13.392 2.968 4.512 <1e-04 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)raoD presence absence with phylogeny
raoD presence absence with phylogeny Bartlett Test
bartlett.test(rocks.raoD.pa.phy.dist.cfuz.4.clusters$Rocks,rocks.raoD.pa.phy.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.raoD.pa.phy.dist.cfuz.4.clusters$Rocks and rocks.raoD.pa.phy.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = 87.239, df = 3, p-value < 2.2e-16raoD presence absence with phylogeny ANOVA
rocks.raoD.pa.phy.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.raoD.pa.phy.dist.cfuz.4.clusters)
summary(rocks.raoD.pa.phy.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 722 240.8 1.53 0.208
## Residuals 172 27059 157.3raoD presence absence with phylogeny Tukey-Kramer
posthoc.raoD.pa.phy.4<-TukeyHSD(x=rocks.raoD.pa.phy.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
raoD.pa.phy.4.glht.out<-glht(rocks.raoD.pa.phy.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(raoD.pa.phy.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.raoD.pa.phy.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 4.8374 2.4535 1.972 0.202
## Group3 - Group1 == 0 4.1722 2.6573 1.570 0.397
## Group4 - Group1 == 0 2.1384 2.7269 0.784 0.861
## Group3 - Group2 == 0 -0.6652 2.7317 -0.244 0.995
## Group4 - Group2 == 0 -2.6990 2.7996 -0.964 0.769
## Group4 - Group3 == 0 -2.0338 2.9797 -0.683 0.903
## (Adjusted p values reported -- single-step method)raoD with abundance
raoD with abundance Bartlett Test
bartlett.test(rocks.raoD.abd.dist.cfuz.4.clusters$Rocks,rocks.raoD.abd.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.raoD.abd.dist.cfuz.4.clusters$Rocks and rocks.raoD.abd.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = Inf, df = 3, p-value < 2.2e-16raoD with abundance ANOVA
rocks.raoD.abd.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.raoD.abd.dist.cfuz.4.clusters)
summary(rocks.raoD.abd.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 1126 375.2 2.421 0.0677 .
## Residuals 172 26655 155.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1raoD with abundance Tukey
posthoc.raoD.abd.4<-TukeyHSD(x=rocks.raoD.abd.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
raoD.abd.4.glht.out<-glht(rocks.raoD.abd.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(raoD.abd.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.raoD.abd.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 -1.1669 2.6114 -0.447 0.9676
## Group3 - Group1 == 0 -5.4868 2.2879 -2.398 0.0725 .
## Group4 - Group1 == 0 -6.4681 5.8559 -1.105 0.6685
## Group3 - Group2 == 0 -4.3199 2.3365 -1.849 0.2353
## Group4 - Group2 == 0 -5.3011 5.8751 -0.902 0.7899
## Group4 - Group3 == 0 -0.9812 5.7386 -0.171 0.9981
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)raoD with abundance and phylogeny
raoD with abundance and phylogeny Bartlett Test
bartlett.test(rocks.raoD.abd.phy.dist.cfuz.4.clusters$Rocks,rocks.raoD.abd.phy.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.raoD.abd.phy.dist.cfuz.4.clusters$Rocks and rocks.raoD.abd.phy.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = Inf, df = 3, p-value < 2.2e-16raoD with abundance and phylogeny ANOVA
rocks.raoD.abd.phy.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.raoD.abd.phy.dist.cfuz.4.clusters)
summary(rocks.raoD.abd.phy.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 1148 382.7 2.472 0.0635 .
## Residuals 172 26633 154.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1raoD with abundance and phylogeny Tukey-Kramer
posthoc.raoD.abd.phy.4<-TukeyHSD(x=rocks.raoD.abd.phy.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
raoD.abd.phy.4.glht.out<-glht(rocks.raoD.abd.phy.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(raoD.abd.phy.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.raoD.abd.phy.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 5.202 2.769 1.878 0.240
## Group3 - Group1 == 0 1.646 2.759 0.597 0.933
## Group4 - Group1 == 0 6.789 2.961 2.293 0.103
## Group3 - Group2 == 0 -3.556 2.429 -1.464 0.460
## Group4 - Group2 == 0 1.588 2.656 0.598 0.932
## Group4 - Group3 == 0 5.143 2.645 1.944 0.213
## (Adjusted p values reported -- single-step method)Vascular plants percent rocks boxplots
# Show with boxplots
#dev.new(width=8, height=6)
par(mfrow=c(2,3))
par(mar=c(2.5,2.5, 1, 0.5), mai=c(0.75,0.7,0.4,0.1))
#, mgp=c(3,1.1,0.25))
boxplot(rock.site.env.dist.cfuz.4, data=rock.site.env.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.raoD.pa.dist.cfuz.4, data=rock.raoD.pa.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.raoD.pa.phy.dist.cfuz.4, data=rock.raoD.pa.phy.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.raoD.abd.dist.cfuz.4, data=rock.raoD.abd.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.raoD.abd.phy.dist.cfuz.4, data=rock.raoD.abd.phy.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))
#textClick.bold("(f)", cex=c(size=1.5, font=2))
Angiosperms only analyses
Angiosperm raoD presence-absence
Angiosperm raoD presence-absence Bartlett Test
bartlett.test(rocks.angio.raoD.pa.dist.cfuz.4.clusters$Rocks,rocks.angio.raoD.pa.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.angio.raoD.pa.dist.cfuz.4.clusters$Rocks and rocks.angio.raoD.pa.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = 217.54, df = 3, p-value < 2.2e-16Angiosperm raoD presence-absence ANOVA
rocks.angio.raoD.pa.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.angio.raoD.pa.dist.cfuz.4.clusters)
summary(rocks.angio.raoD.pa.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 2646 882.1 6.037 0.000622 ***
## Residuals 172 25135 146.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Angiosperm raoD presence-absence Tukey
posthoc.angio.raoD.pa.4<-TukeyHSD(x=rocks.angio.raoD.pa.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
angio.raoD.pa.4.glht.out<-glht(rocks.angio.raoD.pa.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(angio.raoD.pa.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.angio.raoD.pa.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 3.32537 2.87015 1.159 0.6498
## Group3 - Group1 == 0 8.88162 2.25202 3.944 <0.001 ***
## Group4 - Group1 == 0 0.01838 2.53909 0.007 1.0000
## Group3 - Group2 == 0 5.55625 3.00190 1.851 0.2497
## Group4 - Group2 == 0 -3.30699 3.22285 -1.026 0.7311
## Group4 - Group3 == 0 -8.86324 2.68712 -3.298 0.0063 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Angiosperm raoD presence-absence with phylogeny
Angiosperm raoD presence-absence with phylogeny Bartlett Test
bartlett.test(rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters$Rocks,rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters$Rocks and rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = 16.017, df = 3, p-value = 0.001125Angiosperm raoD presence-absence with phylogeny ANOVA
rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters)
summary(rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 250 83.21 0.52 0.669
## Residuals 172 27531 160.07Angiosperm raoD presence-absence with phylogeny Tukey-Kramer Test
posthoc.angio.raoD.pa.phy.4<-TukeyHSD(x=rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
angio.raoD.pa.phy.4.glht.out<-glht(rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(angio.raoD.pa.phy.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.angio.raoD.pa.phy.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 -1.2553 2.5582 -0.491 0.961
## Group3 - Group1 == 0 -1.6792 2.6240 -0.640 0.919
## Group4 - Group1 == 0 1.6275 2.8996 0.561 0.943
## Group3 - Group2 == 0 -0.4239 2.5726 -0.165 0.998
## Group4 - Group2 == 0 2.8828 2.8532 1.010 0.743
## Group4 - Group3 == 0 3.3067 2.9123 1.135 0.667
## (Adjusted p values reported -- single-step method)Angiosperm raoD with abundance
Angiosperm raoD with abundance Bartlett Test
bartlett.test(rocks.angio.raoD.abd.dist.cfuz.4.clusters$Rocks,rocks.angio.raoD.abd.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.angio.raoD.abd.dist.cfuz.4.clusters$Rocks and rocks.angio.raoD.abd.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = 22.641, df = 3, p-value = 4.797e-05Angiosperm raoD with abundance ANOVA
rocks.angio.raoD.abd.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.angio.raoD.abd.dist.cfuz.4.clusters)
summary(rocks.angio.raoD.abd.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 560 186.7 1.18 0.319
## Residuals 172 27221 158.3Angiosperm raoD with abundance Tukey-Kramer Test
posthoc.angio.raoD.abd.4<-TukeyHSD(x=rocks.angio.raoD.abd.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
angio.raoD.abd.4.glht.out<-glht(rocks.angio.raoD.abd.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(angio.raoD.abd.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.angio.raoD.abd.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 -2.33166 2.11371 -1.103 0.670
## Group3 - Group1 == 0 -0.08276 3.26216 -0.025 1.000
## Group4 - Group1 == 0 5.80296 5.03362 1.153 0.639
## Group3 - Group2 == 0 2.24890 3.10679 0.724 0.879
## Group4 - Group2 == 0 8.13462 4.93435 1.649 0.334
## Group4 - Group3 == 0 5.88571 5.52464 1.065 0.694
## (Adjusted p values reported -- single-step method)Angiosperm raoD with abundance and phylogeny
Angiosperm raoD with abundance and phylogeny Bartlett Test
bartlett.test(rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters$Rocks,rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters$Group)##
## Bartlett test of homogeneity of variances
##
## data: rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters$Rocks and rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters$Group
## Bartlett's K-squared = 56.092, df = 3, p-value = 4.015e-12Angiosperm raoD with abundance and phylogeny ANOVA
rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters.aov<-aov(Rocks~Group, data=rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters)
summary(rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters.aov)## Df Sum Sq Mean Sq F value Pr(>F)
## Group 3 211 70.3 0.439 0.726
## Residuals 172 27570 160.3Angiosperm raoD with abundance and phylogeny Tukey-Kramer test
posthoc.angio.raoD.abd.phy.4<-TukeyHSD(x=rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters.aov, "Group", conf.level=0.95)
angio.raoD.abd.phy.4.glht.out<-glht(rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters.aov, linfct=mcp(Group="Tukey"))
summary(angio.raoD.abd.phy.4.glht.out)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = Rocks ~ Group, data = rocks.angio.raoD.abd.phy.dist.cfuz.4.clusters)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Group2 - Group1 == 0 1.3101 2.5506 0.514 0.955
## Group3 - Group1 == 0 0.1576 2.5713 0.061 1.000
## Group4 - Group1 == 0 -2.3239 3.3059 -0.703 0.894
## Group3 - Group2 == 0 -1.1524 2.4147 -0.477 0.963
## Group4 - Group2 == 0 -3.6339 3.1856 -1.141 0.661
## Group4 - Group3 == 0 -2.4815 3.2022 -0.775 0.864
## (Adjusted p values reported -- single-step method)Boxplots for Angiosperms
# Show with boxplots
#dev.new(width=8, height=6)
par(mfrow=c(2,3))
par(mar=c(2.5,2.5, 1, 0.5), mai=c(0.75,0.7,0.4,0.1))
#, mgp=c(3,1.1,0.25))
boxplot(rock.site.env.dist.cfuz.4, data=rock.site.env.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.angio.raoD.pa.dist.cfuz.4, data=rock.angio.raoD.pa.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.angio.raoD.pa.phy.dist.cfuz.4, data=rock.angio.raoD.pa.phy.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.angio.raoD.abd.dist.cfuz.4, data=rock.angio.raoD.abd.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
boxplot(rock.angio.raoD.abd.phy.dist.cfuz.4, data=rock.angio.raoD.abd.phy.dist.cfuz.4,frame.plot=FALSE,axes=FALSE,
notch=FALSE,at =c(1,2,3,4), col=c("grey80", "grey30", "grey60", "grey10"),ylab="Rocks (% cover)", beside=TRUE,
cex.lab=1.5, cex.axis=1.1,cex.names=1.75, lwd=1, ylim=c(0,100))
axis(side=2, lwd=2)
mtext(c("Group 1", "Group 2", "Group 3", "Group 4"), side = 1, at =c(1,2,3,4), cex=0.7, line=1)
#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))