Title: Highest membership coefficients
Name: Tammy L. Elliott
Date: May 22, 2016
R version 3.1
Angiosperm abundance-weighted membership coefficents
#Box plot of maximum values for only angiosperms; abundance-weighted
#dev.new(width=5.9, height=5.9)
boxplot(max.site.env, max.angio.abd, max.ph.angio.abd, col=c("grey15", "grey80", "grey50"),
cex.axis=1.15, cex.lab=1.3,yaxt="n", xaxt = "n",ylab="Highest membership coefficient across all clusters", frame=F)
axis(
1, # puts the axis at the bottom
at=1:3, # labels will be placed in the 3 categories
labels=c("Site\nEnv", "Angio\nBD", "Angio\nPhBD"), # labels will be the 3 genera
lwd=0, # width of the long axis line is zero, makes invisible
# width of the etick lines also zero, makes them invisible
cex.axis=1.15, # offset from the axis of the labels
cex.lab=1.3,
mgp=c(0,2,0) # middle zero controls distance of labels from axis
)
axis(
2,
#at=c(-4,-3,-2,-1,0,1,2,3,4),
ylim=c(0,1),
lwd=2, # width of the long axis line is zero, makes invisible
lwd.ticks=0.1, # width of the etick lines also zero, makes them invisible
tck=0.02,
cex.axis=1.15, # offset from the axis of the labels
cex.lab=1.3,
mgp=c(0,0.75,0) # middle zero controls distance of labels from axis
)
abline(h=0, col="grey20", lty=2)
Angiosperm presence-absence membership coefficents
#Box plot of maximum values for only angiosperms; presence-absence
#dev.new(width=5.9, height=5.9)
boxplot(max.site.env, max.angio.pa, max.ph.angio.pa, col=c("grey15", "grey80", "grey50"),
cex.axis=1.15, cex.lab=1.3,yaxt="n", xaxt = "n",ylab="Highest membership coefficient across all clusters", frame=F)
axis(
1, # puts the axis at the bottom
at=1:3, # labels will be placed in the 3 categories
labels=c("Site\nEnv", "Angio\nBD", "Angio\nPhBD"), # labels will be the 3 genera
lwd=0, # width of the long axis line is zero, makes invisible
# width of the etick lines also zero, makes them invisible
cex.axis=1.15, # offset from the axis of the labels
cex.lab=1.3,
mgp=c(0,2,0) # middle zero controls distance of labels from axis
)
axis(
2,
#at=c(-4,-3,-2,-1,0,1,2,3,4),
ylim=c(0,1),
lwd=2, # width of the long axis line is zero, makes invisible
lwd.ticks=0.1, # width of the etick lines also zero, makes them invisible
tck=0.02,
cex.axis=1.15, # offset from the axis of the labels
cex.lab=1.3,
mgp=c(0,0.75,0) # middle zero controls distance of labels from axis
)
abline(h=0, col="grey20", lty=2)
Anova comparing different methods for abundance-weighted analyses
ANOVA and Tukey test for abudance-weighted
#Compare with Tukey test: we can use this because there are a similar number of measurements per measurement type
(max.combined.aov <- aov(max.combined.one.col$Max.Support~ max.combined.one.col$Measurement))
## Call:
## aov(formula = max.combined.one.col$Max.Support ~ max.combined.one.col$Measurement)
##
## Terms:
## max.combined.one.col$Measurement Residuals
## Sum of Squares 23.48745 18.68102
## Deg. of Freedom 4 875
##
## Residual standard error: 0.1461155
## Estimated effects may be unbalanced
summary(max.combined.aov)
## Df Sum Sq Mean Sq F value Pr(>F)
## max.combined.one.col$Measurement 4 23.49 5.872 275 <2e-16 ***
## Residuals 875 18.68 0.021
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(posthoc.max.combined <- TukeyHSD(x=max.combined.aov, 'max.combined.one.col$Measurement', conf.level=0.95))
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = max.combined.one.col$Max.Support ~ max.combined.one.col$Measurement)
##
## $`max.combined.one.col$Measurement`
## diff lwr upr p adj
## Angio.PhBD-Angio.BD 0.35784375 0.31526725 0.400420236 0.0000000
## Site Env.-Angio.BD 0.30342661 0.26085011 0.346003096 0.0000000
## Vasc.BD-Angio.BD -0.03611172 -0.07868821 0.006464771 0.1399522
## Vasc.PhBD-Angio.BD 0.26659231 0.22401581 0.309168797 0.0000000
## Site Env.-Angio.PhBD -0.05441714 -0.09699363 -0.011840649 0.0045450
## Vasc.BD-Angio.PhBD -0.39395547 -0.43653196 -0.351378974 0.0000000
## Vasc.PhBD-Angio.PhBD -0.09125144 -0.13382793 -0.048674948 0.0000001
## Vasc.BD-Site Env. -0.33953833 -0.38211482 -0.296961834 0.0000000
## Vasc.PhBD-Site Env. -0.03683430 -0.07941079 0.005742192 0.1260462
## Vasc.PhBD-Vasc.BD 0.30270403 0.26012753 0.345280517 0.0000000
summary(posthoc.max.combined)
## Length Class Mode
## max.combined.one.col$Measurement 40 -none- numeric
Examine for only angiosperms
ANOVA and Tukey test for angiosperms
#Compare with Tukey test: we can use this because there are a similar number of measurements per measurement type
(max.combined.angio.aov <- aov(max.combined.angio.one.col$Max.Support~ max.combined.angio.one.col$Measurement))
## Call:
## aov(formula = max.combined.angio.one.col$Max.Support ~ max.combined.angio.one.col$Measurement)
##
## Terms:
## max.combined.angio.one.col$Measurement Residuals
## Sum of Squares 13.08742 12.67403
## Deg. of Freedom 2 525
##
## Residual standard error: 0.1553738
## Estimated effects may be unbalanced
summary(max.combined.angio.aov)
## Df Sum Sq Mean Sq F value Pr(>F)
## max.combined.angio.one.col$Measurement 2 13.09 6.544 271.1 <2e-16
## Residuals 525 12.67 0.024
##
## max.combined.angio.one.col$Measurement ***
## Residuals
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(posthoc.max.combined.angio <- TukeyHSD(x=max.combined.angio.aov, 'max.combined.angio.one.col$Measurement', conf.level=0.95))
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = max.combined.angio.one.col$Max.Support ~ max.combined.angio.one.col$Measurement)
##
## $`max.combined.angio.one.col$Measurement`
## diff lwr upr p adj
## Angio.PhBD-Angio.BD 0.35784375 0.31891467 0.39677282 0.0000000
## Site Env.-Angio.BD 0.30342661 0.26449753 0.34235568 0.0000000
## Site Env.-Angio.PhBD -0.05441714 -0.09334621 -0.01548807 0.0031126
summary(posthoc.max.combined.angio)
## Length Class Mode
## max.combined.angio.one.col$Measurement 12 -none- numeric
Anova comparing different methods for presence-absence
ANOVA and Tukey test for presence-absence
#Compare with Tukey test: we can use this because there are a similar number of measurements per measurement type
(max.combined.aov.pa <- aov(max.combined.one.col.pa$Max.Support~ max.combined.one.col.pa$Measurement))
## Call:
## aov(formula = max.combined.one.col.pa$Max.Support ~ max.combined.one.col.pa$Measurement)
##
## Terms:
## max.combined.one.col.pa$Measurement Residuals
## Sum of Squares 13.34753 16.59740
## Deg. of Freedom 4 875
##
## Residual standard error: 0.137726
## Estimated effects may be unbalanced
summary(max.combined.aov.pa)
## Df Sum Sq Mean Sq F value Pr(>F)
## max.combined.one.col.pa$Measurement 4 13.35 3.337 175.9 <2e-16 ***
## Residuals 875 16.60 0.019
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(posthoc.max.combined.pa <- TukeyHSD(x=max.combined.aov.pa, 'max.combined.one.col.pa$Measurement', conf.level=0.95))
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = max.combined.one.col.pa$Max.Support ~ max.combined.one.col.pa$Measurement)
##
## $`max.combined.one.col.pa$Measurement`
## diff lwr upr
## max.ph.angio.pa-max.angio.pa 0.29078930 0.250657412 0.330921197
## max.ph.vasc.pa-max.angio.pa 0.06876294 0.028631047 0.108894832
## max.site.env-max.angio.pa 0.27386658 0.233734686 0.313998471
## max.vasc.pa-max.angio.pa 0.03663049 -0.003501399 0.076762385
## max.ph.vasc.pa-max.ph.angio.pa -0.22202636 -0.262158257 -0.181894472
## max.site.env-max.ph.angio.pa -0.01692273 -0.057054619 0.023209166
## max.vasc.pa-max.ph.angio.pa -0.25415881 -0.294290704 -0.214026919
## max.site.env-max.ph.vasc.pa 0.20510364 0.164971746 0.245235531
## max.vasc.pa-max.ph.vasc.pa -0.03213245 -0.072264339 0.007999446
## max.vasc.pa-max.site.env -0.23723609 -0.277367977 -0.197104193
## p adj
## max.ph.angio.pa-max.angio.pa 0.0000000
## max.ph.vasc.pa-max.angio.pa 0.0000321
## max.site.env-max.angio.pa 0.0000000
## max.vasc.pa-max.angio.pa 0.0926534
## max.ph.vasc.pa-max.ph.angio.pa 0.0000000
## max.site.env-max.ph.angio.pa 0.7782440
## max.vasc.pa-max.ph.angio.pa 0.0000000
## max.site.env-max.ph.vasc.pa 0.0000000
## max.vasc.pa-max.ph.vasc.pa 0.1849082
## max.vasc.pa-max.site.env 0.0000000
summary(posthoc.max.combined.pa)
## Length Class Mode
## max.combined.one.col.pa$Measurement 40 -none- numeric
ANOVA and Tukey test for angiosperms - presence-absence
#Compare with Tukey test: we can use this because there are a similar number of measurements per measurement type
(max.combined.angio.aov.pa <- aov(max.combined.angio.one.col.pa$Max.Support~ max.combined.angio.one.col.pa$Measurement))
## Call:
## aov(formula = max.combined.angio.one.col.pa$Max.Support ~ max.combined.angio.one.col.pa$Measurement)
##
## Terms:
## max.combined.angio.one.col.pa$Measurement Residuals
## Sum of Squares 9.377732 10.741637
## Deg. of Freedom 2 525
##
## Residual standard error: 0.1430394
## Estimated effects may be unbalanced
summary(max.combined.angio.aov.pa)
## Df Sum Sq Mean Sq F value
## max.combined.angio.one.col.pa$Measurement 2 9.378 4.689 229.2
## Residuals 525 10.742 0.020
## Pr(>F)
## max.combined.angio.one.col.pa$Measurement <2e-16 ***
## Residuals
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(posthoc.max.combined.angio.pa <- TukeyHSD(x=max.combined.angio.aov.pa, 'max.combined.angio.one.col.pa$Measurement', conf.level=0.95))
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = max.combined.angio.one.col.pa$Max.Support ~ max.combined.angio.one.col.pa$Measurement)
##
## $`max.combined.angio.one.col.pa$Measurement`
## diff lwr upr p adj
## Angio.PhBD-Angio.BD 0.29078930 0.2549506 0.32662797 0.0000000
## Site Env.-Angio.BD 0.27386658 0.2380279 0.30970525 0.0000000
## Site Env.-Angio.PhBD -0.01692273 -0.0527614 0.01891594 0.5084094
summary(posthoc.max.combined.angio.pa)
## Length Class Mode
## max.combined.angio.one.col.pa$Measurement 12 -none- numeric