MARI301_Macrofauna.R
theco
Sun Apr 30 15:59:00 2017
library(plotrix)
library(car)## Warning: package 'car' was built under R version 3.3.3library(MASS)## Warning: package 'MASS' was built under R version 3.3.3library(vegan)## Warning: package 'vegan' was built under R version 3.3.3## Loading required package: permute## Warning: package 'permute' was built under R version 3.3.3## Loading required package: lattice## This is vegan 2.4-2setwd("C:/Users/theco/Desktop/")
FaunaData<-read.csv ("faunadataF.csv",header=TRUE)
FaunaData## block treatment Edwardsia.neozelanica Abarenicola.affinis
## 1 1 black 0 0
## 2 1 blue 0 0
## 3 1 green 0 0
## 4 1 yellow 0 0
## 5 2 black 0 0
## 6 2 blue 0 1
## 7 3 black 0 0
## 8 3 blue 2 0
## 9 3 green 0 1
## 10 3 yellow 0 0
## 11 4 black 0 1
## 12 4 blue 0 0
## 13 4 green 0 1
## 14 4 yellow 0 0
## 15 5 black 0 0
## 16 5 blue 1 0
## 17 5 green 0 0
## 18 5 yellow 0 0
## 19 6 black 0 0
## 20 6 blue 0 1
## 21 6 green 0 0
## 22 6 yellow 0 0
## 23 7 black 0 0
## 24 7 blue 0 0
## 25 7 green 0 0
## 26 7 yellow 0 0
## Macroclymenella.stewartensis Family.Orbiniidae Family.Spionidae
## 1 0 0 1
## 2 0 1 0
## 3 0 1 0
## 4 0 0 0
## 5 0 6 0
## 6 0 2 0
## 7 0 1 0
## 8 0 1 0
## 9 0 5 0
## 10 0 0 0
## 11 0 0 0
## 12 1 0 2
## 13 0 5 2
## 14 0 1 1
## 15 1 0 1
## 16 0 0 0
## 17 0 0 0
## 18 0 0 0
## 19 0 0 0
## 20 3 6 1
## 21 1 4 0
## 22 1 2 0
## 23 1 0 2
## 24 2 0 1
## 25 0 0 0
## 26 0 2 0
## Family.Nephtytidae Family.Nereididae Family.Opheliidae Family.Syllidae
## 1 0 0 0 0
## 2 1 0 0 0
## 3 0 0 0 1
## 4 0 1 0 0
## 5 1 0 0 0
## 6 1 2 0 0
## 7 1 0 1 0
## 8 0 0 0 0
## 9 0 0 1 0
## 10 2 3 0 0
## 11 0 0 0 0
## 12 1 0 0 0
## 13 1 0 2 0
## 14 1 0 0 0
## 15 0 0 3 1
## 16 4 0 0 2
## 17 0 2 0 0
## 18 0 0 0 0
## 19 0 1 0 0
## 20 0 0 0 0
## 21 0 0 0 0
## 22 1 0 0 0
## 23 0 1 2 3
## 24 1 2 0 0
## 25 0 0 0 0
## 26 0 0 0 0
## Family.Capitellidae Nucula.hartvigiana Austrovenus.stutchburyi
## 1 0 0 2
## 2 0 0 0
## 3 0 0 0
## 4 1 0 0
## 5 2 0 1
## 6 0 0 0
## 7 0 0 0
## 8 0 5 0
## 9 0 0 0
## 10 0 0 1
## 11 0 4 0
## 12 0 1 0
## 13 0 0 16
## 14 0 1 0
## 15 0 0 3
## 16 0 23 0
## 17 0 11 0
## 18 0 11 1
## 19 0 0 0
## 20 2 0 1
## 21 0 0 1
## 22 0 0 0
## 23 0 4 0
## 24 0 0 3
## 25 0 9 0
## 26 0 6 0
## Paphies.australis Perrierina.turneri Arthritica.bifurca
## 1 0 6 0
## 2 0 37 0
## 3 0 0 6
## 4 0 0 0
## 5 0 1 0
## 6 0 3 0
## 7 0 5 3
## 8 0 0 0
## 9 0 1 0
## 10 0 6 3
## 11 0 14 0
## 12 0 11 5
## 13 0 37 7
## 14 0 18 0
## 15 0 4 0
## 16 1 16 10
## 17 1 5 0
## 18 0 6 0
## 19 0 58 0
## 20 0 7 0
## 21 0 11 2
## 22 0 25 2
## 23 0 21 1
## 24 0 0 0
## 25 0 8 0
## 26 0 0 1
## Macomona..Tellina..lilliana Micrelenchus.tenebrosus Cantharidus.huttoni
## 1 0 0 0
## 2 0 0 9
## 3 0 0 1
## 4 0 0 1
## 5 2 0 0
## 6 1 0 0
## 7 2 0 0
## 8 0 0 0
## 9 0 0 1
## 10 0 0 3
## 11 0 0 2
## 12 2 0 0
## 13 2 2 0
## 14 1 0 0
## 15 0 0 0
## 16 0 0 0
## 17 0 0 0
## 18 0 0 0
## 19 0 0 2
## 20 0 0 0
## 21 0 0 3
## 22 0 0 0
## 23 0 0 1
## 24 3 0 1
## 25 0 0 0
## 26 0 0 3
## Diloma.subrostrata Zethalia.zelandica Cominella.glandiformis
## 1 0 0 0
## 2 0 0 1
## 3 0 1 0
## 4 0 0 0
## 5 0 0 0
## 6 0 0 0
## 7 0 1 0
## 8 0 0 0
## 9 0 0 1
## 10 0 0 0
## 11 0 0 0
## 12 0 0 0
## 13 0 0 0
## 14 0 1 0
## 15 0 0 0
## 16 0 0 0
## 17 0 0 0
## 18 0 0 0
## 19 0 0 1
## 20 0 0 0
## 21 0 0 0
## 22 0 0 0
## 23 0 0 0
## 24 1 0 0
## 25 2 0 0
## 26 0 0 1
## Zeacumantus.subcarinatus Notoacmea.sp. Amphibola.crenata
## 1 0 0 0
## 2 0 4 0
## 3 0 0 0
## 4 0 0 0
## 5 0 0 0
## 6 0 0 0
## 7 0 0 0
## 8 0 0 0
## 9 0 0 0
## 10 0 0 0
## 11 0 0 0
## 12 0 0 0
## 13 0 1 0
## 14 0 0 0
## 15 0 0 0
## 16 2 0 0
## 17 0 0 0
## 18 0 0 0
## 19 0 0 0
## 20 0 0 0
## 21 1 2 0
## 22 0 0 0
## 23 0 0 0
## 24 0 0 0
## 25 0 4 0
## 26 0 0 0
## ORDER.HARPACTECOIDA Family.Anthuridae Zeuxo.novazealandiae
## 1 0 0 0
## 2 0 0 2
## 3 0 0 0
## 4 10 0 0
## 5 0 0 0
## 6 0 3 0
## 7 0 0 0
## 8 0 1 0
## 9 0 0 0
## 10 0 0 0
## 11 5 0 0
## 12 0 0 0
## 13 0 0 0
## 14 0 0 0
## 15 3 0 0
## 16 0 0 0
## 17 8 0 0
## 18 0 0 0
## 19 0 0 0
## 20 0 0 0
## 21 1 0 0
## 22 0 0 0
## 23 0 0 0
## 24 0 0 0
## 25 0 0 0
## 26 0 0 0
## Paracorophium.excavatum Torridoharpinia.hurleyi
## 1 0 0
## 2 0 1
## 3 0 0
## 4 0 1
## 5 0 0
## 6 0 0
## 7 0 0
## 8 0 0
## 9 0 0
## 10 0 0
## 11 1 0
## 12 0 0
## 13 0 0
## 14 0 0
## 15 0 0
## 16 1 0
## 17 1 0
## 18 0 0
## 19 0 0
## 20 0 0
## 21 0 0
## 22 0 0
## 23 1 0
## 24 0 0
## 25 0 0
## 26 2 1
## Paracalliope.novizelandiae
## 1 0
## 2 0
## 3 0
## 4 0
## 5 0
## 6 0
## 7 0
## 8 1
## 9 0
## 10 0
## 11 0
## 12 0
## 13 0
## 14 0
## 15 0
## 16 0
## 17 1
## 18 0
## 19 0
## 20 0
## 21 0
## 22 0
## 23 0
## 24 0
## 25 0
## 26 1#detach(FaunaData)
attach(FaunaData)
head(FaunaData)## block treatment Edwardsia.neozelanica Abarenicola.affinis
## 1 1 black 0 0
## 2 1 blue 0 0
## 3 1 green 0 0
## 4 1 yellow 0 0
## 5 2 black 0 0
## 6 2 blue 0 1
## Macroclymenella.stewartensis Family.Orbiniidae Family.Spionidae
## 1 0 0 1
## 2 0 1 0
## 3 0 1 0
## 4 0 0 0
## 5 0 6 0
## 6 0 2 0
## Family.Nephtytidae Family.Nereididae Family.Opheliidae Family.Syllidae
## 1 0 0 0 0
## 2 1 0 0 0
## 3 0 0 0 1
## 4 0 1 0 0
## 5 1 0 0 0
## 6 1 2 0 0
## Family.Capitellidae Nucula.hartvigiana Austrovenus.stutchburyi
## 1 0 0 2
## 2 0 0 0
## 3 0 0 0
## 4 1 0 0
## 5 2 0 1
## 6 0 0 0
## Paphies.australis Perrierina.turneri Arthritica.bifurca
## 1 0 6 0
## 2 0 37 0
## 3 0 0 6
## 4 0 0 0
## 5 0 1 0
## 6 0 3 0
## Macomona..Tellina..lilliana Micrelenchus.tenebrosus Cantharidus.huttoni
## 1 0 0 0
## 2 0 0 9
## 3 0 0 1
## 4 0 0 1
## 5 2 0 0
## 6 1 0 0
## Diloma.subrostrata Zethalia.zelandica Cominella.glandiformis
## 1 0 0 0
## 2 0 0 1
## 3 0 1 0
## 4 0 0 0
## 5 0 0 0
## 6 0 0 0
## Zeacumantus.subcarinatus Notoacmea.sp. Amphibola.crenata
## 1 0 0 0
## 2 0 4 0
## 3 0 0 0
## 4 0 0 0
## 5 0 0 0
## 6 0 0 0
## ORDER.HARPACTECOIDA Family.Anthuridae Zeuxo.novazealandiae
## 1 0 0 0
## 2 0 0 2
## 3 0 0 0
## 4 10 0 0
## 5 0 0 0
## 6 0 3 0
## Paracorophium.excavatum Torridoharpinia.hurleyi
## 1 0 0
## 2 0 1
## 3 0 0
## 4 0 1
## 5 0 0
## 6 0 0
## Paracalliope.novizelandiae
## 1 0
## 2 0
## 3 0
## 4 0
## 5 0
## 6 0hist(Austrovenus.stutchburyi)
richness <- specnumber(FaunaData[3:32])
richness## [1] 3 8 5 5 6 7 7 5 6 6 6 7 11 7 7 9 7 3 4 7 9 5 10
## [24] 8 4 8black.richness=richness[treatment=="black"]
black.richness## [1] 3 6 7 6 7 4 10blue.richness=richness[treatment=="blue"]
blue.richness## [1] 8 7 5 7 9 7 8green.richness=richness[treatment=="green"]
green.richness## [1] 5 6 11 7 9 4yellow.richness=richness[treatment=="yellow"]
yellow.richness## [1] 5 6 7 3 5 8mean.richness= c(mean(black.richness), mean(blue.richness), mean(green.richness), mean(yellow.richness))
mean.richness## [1] 6.142857 7.285714 7.000000 5.666667mp<-barplot(mean.richness,axes=FALSE,axisnames=FALSE,ylim=c(0,10),xlab="Treatment",ylab="Taxon Richness", col=c("black", "blue", "green", "yellow"))
axis(1,labels=c("black","blue","green","yellow"),at=mp)
axis(2,at=seq(0,10,by=1))
box()
SE<-matrix(c(std.error(black.richness),std.error(blue.richness),std.error(green.richness),std.error(yellow.richness)),2)
segments(mp,mean.richness-SE,mp,mean.richness+SE,lwd=2)
segments(mp-0.1,mean.richness-SE,mp+0.1,mean.richness-SE,lwd=2)
segments(mp-0.1,mean.richness+SE,mp+0.1,mean.richness+SE,lwd=2)
leveneTest(richness, treatment)## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 3 0.9331 0.4414
## 22shapiro.test(richness)##
## Shapiro-Wilk normality test
##
## data: richness
## W = 0.96941, p-value = 0.608supermodel<-lm(richness~treatment)
summary(supermodel)##
## Call:
## lm(formula = richness ~ treatment)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.1429 -0.9167 -0.1429 0.8571 4.0000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6.1429 0.7629 8.052 5.29e-08 ***
## treatmentblue 1.1429 1.0788 1.059 0.301
## treatmentgreen 0.8571 1.1229 0.763 0.453
## treatmentyellow -0.4762 1.1229 -0.424 0.676
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.018 on 22 degrees of freedom
## Multiple R-squared: 0.1079, Adjusted R-squared: -0.01372
## F-statistic: 0.8872 on 3 and 22 DF, p-value: 0.4631Anova(supermodel)## Anova Table (Type II tests)
##
## Response: richness
## Sum Sq Df F value Pr(>F)
## treatment 10.842 3 0.8872 0.4631
## Residuals 89.619 22#plot(supermodel)
##Diversity has been difined as H here
H<-diversity(FaunaData[3:32])
black.H=H[treatment=="black"]
blue.H=H[treatment=="blue"]
green.H=H[treatment=="green"]
yellow.H=H[treatment=="yellow"]
##Now plotting for diversity (H)
mean.H=c (mean(black.H),mean(blue.H),mean(green.H),mean(yellow.H))
mean.H## [1] 1.308470 1.592372 1.493868 1.181951mp<-barplot(mean.H,axes=FALSE,axisnames=FALSE,ylim=c(0,2), xlab="Treatment",ylab="Taxon Diversity", col=c("black", "blue", "green", "yellow"))
axis(1,labels=c("black","blue","green","yellow"),at=mp)
axis(2,at=seq(0,10,by=0.1))
box()
SE<-matrix(c(std.error(black.H),std.error(blue.H),std.error(green.H),std.error(yellow.H)),2)
segments(mp,mean.H-SE,mp,mean.H+SE,lwd=2)
segments(mp-0.1,mean.H-SE,mp+0.1,mean.H-SE,lwd=2)
segments(mp-0.1,mean.H+SE,mp+0.1,mean.H+SE,lwd=2)
logH<-log(H)
FaunaData2 <- FaunaData[2:32]
summary(FaunaData2)## treatment Edwardsia.neozelanica Abarenicola.affinis
## black :7 Min. :0.0000 Min. :0.0000
## blue :7 1st Qu.:0.0000 1st Qu.:0.0000
## green :6 Median :0.0000 Median :0.0000
## yellow:6 Mean :0.1154 Mean :0.1923
## 3rd Qu.:0.0000 3rd Qu.:0.0000
## Max. :2.0000 Max. :1.0000
## Macroclymenella.stewartensis Family.Orbiniidae Family.Spionidae
## Min. :0.0000 Min. :0.000 Min. :0.0000
## 1st Qu.:0.0000 1st Qu.:0.000 1st Qu.:0.0000
## Median :0.0000 Median :0.500 Median :0.0000
## Mean :0.3846 Mean :1.423 Mean :0.4231
## 3rd Qu.:0.7500 3rd Qu.:2.000 3rd Qu.:1.0000
## Max. :3.0000 Max. :6.000 Max. :2.0000
## Family.Nephtytidae Family.Nereididae Family.Opheliidae Family.Syllidae
## Min. :0.0000 Min. :0.0000 Min. :0.0000 Min. :0.0000
## 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:0.0000
## Median :0.0000 Median :0.0000 Median :0.0000 Median :0.0000
## Mean :0.5769 Mean :0.4615 Mean :0.3462 Mean :0.2692
## 3rd Qu.:1.0000 3rd Qu.:0.7500 3rd Qu.:0.0000 3rd Qu.:0.0000
## Max. :4.0000 Max. :3.0000 Max. :3.0000 Max. :3.0000
## Family.Capitellidae Nucula.hartvigiana Austrovenus.stutchburyi
## Min. :0.0000 Min. : 0.000 Min. : 0.000
## 1st Qu.:0.0000 1st Qu.: 0.000 1st Qu.: 0.000
## Median :0.0000 Median : 0.000 Median : 0.000
## Mean :0.1923 Mean : 2.885 Mean : 1.115
## 3rd Qu.:0.0000 3rd Qu.: 4.000 3rd Qu.: 1.000
## Max. :2.0000 Max. :23.000 Max. :16.000
## Paphies.australis Perrierina.turneri Arthritica.bifurca
## Min. :0.00000 Min. : 0.00 Min. : 0.000
## 1st Qu.:0.00000 1st Qu.: 1.50 1st Qu.: 0.000
## Median :0.00000 Median : 6.00 Median : 0.000
## Mean :0.07692 Mean :11.54 Mean : 1.538
## 3rd Qu.:0.00000 3rd Qu.:15.50 3rd Qu.: 2.000
## Max. :1.00000 Max. :58.00 Max. :10.000
## Macomona..Tellina..lilliana Micrelenchus.tenebrosus Cantharidus.huttoni
## Min. :0.00 Min. :0.00000 Min. :0.000
## 1st Qu.:0.00 1st Qu.:0.00000 1st Qu.:0.000
## Median :0.00 Median :0.00000 Median :0.000
## Mean :0.50 Mean :0.07692 Mean :1.038
## 3rd Qu.:0.75 3rd Qu.:0.00000 3rd Qu.:1.000
## Max. :3.00 Max. :2.00000 Max. :9.000
## Diloma.subrostrata Zethalia.zelandica Cominella.glandiformis
## Min. :0.0000 Min. :0.0000 Min. :0.0000
## 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:0.0000
## Median :0.0000 Median :0.0000 Median :0.0000
## Mean :0.1154 Mean :0.1154 Mean :0.1538
## 3rd Qu.:0.0000 3rd Qu.:0.0000 3rd Qu.:0.0000
## Max. :2.0000 Max. :1.0000 Max. :1.0000
## Zeacumantus.subcarinatus Notoacmea.sp. Amphibola.crenata
## Min. :0.0000 Min. :0.0000 Min. :0
## 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:0
## Median :0.0000 Median :0.0000 Median :0
## Mean :0.1154 Mean :0.4231 Mean :0
## 3rd Qu.:0.0000 3rd Qu.:0.0000 3rd Qu.:0
## Max. :2.0000 Max. :4.0000 Max. :0
## ORDER.HARPACTECOIDA Family.Anthuridae Zeuxo.novazealandiae
## Min. : 0.000 Min. :0.0000 Min. :0.00000
## 1st Qu.: 0.000 1st Qu.:0.0000 1st Qu.:0.00000
## Median : 0.000 Median :0.0000 Median :0.00000
## Mean : 1.038 Mean :0.1538 Mean :0.07692
## 3rd Qu.: 0.000 3rd Qu.:0.0000 3rd Qu.:0.00000
## Max. :10.000 Max. :3.0000 Max. :2.00000
## Paracorophium.excavatum Torridoharpinia.hurleyi
## Min. :0.0000 Min. :0.0000
## 1st Qu.:0.0000 1st Qu.:0.0000
## Median :0.0000 Median :0.0000
## Mean :0.2308 Mean :0.1154
## 3rd Qu.:0.0000 3rd Qu.:0.0000
## Max. :2.0000 Max. :1.0000
## Paracalliope.novizelandiae
## Min. :0.0000
## 1st Qu.:0.0000
## Median :0.0000
## Mean :0.1154
## 3rd Qu.:0.0000
## Max. :1.0000dist.matrix<-vegdist(FaunaData2[,-1])
dist.matrix## 1 2 3 4 5 6 7
## 2 0.8153846
## 3 1.0000000 0.9393939
## 4 1.0000000 0.9428571 0.9166667
## 5 0.8181818 0.9130435 0.9130435 0.9259259
## 6 0.7272727 0.8550725 0.9130435 0.9259259 0.6153846
## 7 0.5652174 0.8000000 0.5833333 1.0000000 0.6296296 0.5555556
## 8 1.0000000 0.9696970 0.9000000 1.0000000 0.9130435 0.8260870 0.9166667
## 9 0.8947368 0.8787879 0.8000000 0.9166667 0.4782609 0.6521739 0.7500000
## 10 0.4814815 0.7297297 0.7142857 0.8750000 0.8064516 0.6129032 0.4375000
## 11 0.6666667 0.6144578 0.9459459 0.7073171 0.9500000 0.8000000 0.7560976
## 12 0.5625000 0.6962025 0.6969697 1.0000000 0.7777778 0.7222222 0.4054054
## 13 0.7882353 0.3939394 0.8372093 1.0000000 0.7752809 0.8202247 0.7111111
## 14 0.5757576 0.5000000 0.8823529 1.0000000 0.7837838 0.6756757 0.5263158
## 15 0.4400000 0.8888889 0.9230769 0.8000000 0.8620690 0.7931034 0.6666667
## 16 0.8260870 0.7068966 0.8000000 1.0000000 0.9452055 0.8904110 0.7567568
## 17 0.7368421 0.8823529 1.0000000 0.5813953 0.9523810 0.7619048 0.7674419
## 18 0.4814815 0.8378378 1.0000000 1.0000000 0.8709677 0.8064516 0.6875000
## 19 0.8309859 0.3220339 0.9722222 0.9473684 0.9733333 0.8933333 0.8684211
## 20 0.4666667 0.7922078 0.9354839 0.9428571 0.4117647 0.6470588 0.6571429
## 21 0.6000000 0.5853659 0.7777778 0.9000000 0.6923077 0.7435897 0.6000000
## 22 0.7000000 0.3793103 0.8536585 1.0000000 0.8181818 0.7272727 0.6000000
## 23 0.6956522 0.5268817 0.8723404 0.9215686 0.9600000 0.8400000 0.7254902
## 24 0.7391304 0.9428571 0.9166667 0.8571429 0.7037037 0.7037037 0.7857143
## 25 0.6250000 0.6962025 1.0000000 1.0000000 0.9444444 0.8333333 0.7297297
## 26 1.0000000 0.8356164 0.7777778 0.8709677 0.8666667 0.8666667 0.8709677
## 8 9 10 11 12 13 14
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9 0.9000000
## 10 1.0000000 0.8571429
## 11 0.7837838 0.8378378 0.6444444
## 12 0.9393939 0.9393939 0.5121951 0.5200000
## 13 0.9767442 0.8139535 0.7659574 0.7087379 0.5757576
## 14 0.8823529 0.8823529 0.6666667 0.4117647 0.3617021 0.5600000
## 15 1.0000000 0.8461538 0.7058824 0.6744186 0.6923077 0.7826087 0.7500000
## 16 0.8285714 0.9714286 0.7179487 0.5632184 0.5662651 0.6470588 0.5714286
## 17 0.6923077 0.9487179 0.7021277 0.4642857 0.7692308 0.9047619 0.7735849
## 18 0.6428571 0.9285714 0.6111111 0.5555556 0.6585366 0.8510638 0.6666667
## 19 1.0000000 0.9166667 0.7750000 0.6404494 0.7411765 0.4637681 0.5813953
## 20 0.9354839 0.5483871 0.6410256 0.6666667 0.5909091 0.6907216 0.6000000
## 21 0.9444444 0.6666667 0.4545455 0.4716981 0.4285714 0.6274510 0.5200000
## 22 0.9512195 0.8536585 0.6326531 0.5172414 0.4444444 0.4392523 0.2727273
## 23 0.8297872 0.8723404 0.6727273 0.3750000 0.4666667 0.5398230 0.3442623
## 24 1.0000000 0.9166667 0.6875000 0.9512195 0.7297297 0.8444444 0.8421053
## 25 0.6969697 0.9393939 0.7073171 0.5200000 0.6086957 0.8181818 0.6170213
## 26 0.4814815 0.7037037 0.7714286 0.6818182 0.9000000 0.9354839 0.9024390
## 15 16 17 18 19 20 21
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9
## 10
## 11
## 12
## 13
## 14
## 15
## 16 0.8684211
## 17 0.6888889 0.5955056
## 18 0.7058824 0.5641026 0.3191489
## 19 0.8974359 0.7377049 0.8681319 0.8500000
## 20 0.6216216 0.8271605 0.8000000 0.6410256 0.8313253
## 21 0.6666667 0.6744186 0.7818182 0.6818182 0.7045455 0.4468085
## 22 0.7872340 0.5824176 0.8333333 0.7551020 0.4623656 0.6153846 0.4385965
## 23 0.6603774 0.5051546 0.6666667 0.6363636 0.5353535 0.6896552 0.5555556
## 24 0.6666667 0.9729730 0.9069767 0.9375000 0.9473684 0.7714286 0.8500000
## 25 0.7948718 0.5903614 0.4615385 0.2682927 0.8117647 0.6818182 0.5918367
## 26 1.0000000 0.7922078 0.6521739 0.6571429 0.9240506 0.8947368 0.7209302
## 22 23 24 25
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9
## 10
## 11
## 12
## 13
## 14
## 15
## 16
## 17
## 18
## 19
## 20
## 21
## 22
## 23 0.3235294
## 24 0.9111111 0.8431373
## 25 0.7037037 0.6000000 0.9459459
## 26 0.8750000 0.7407407 0.9354839 0.7000000mds.data<-metaMDS(dist.matrix)## Run 0 stress 0.2114047
## Run 1 stress 0.2135415
## Run 2 stress 0.2432216
## Run 3 stress 0.2199
## Run 4 stress 0.2105724
## ... New best solution
## ... Procrustes: rmse 0.1019993 max resid 0.4344562
## Run 5 stress 0.2452305
## Run 6 stress 0.2147514
## Run 7 stress 0.2105794
## ... Procrustes: rmse 0.006938949 max resid 0.02323346
## Run 8 stress 0.2143602
## Run 9 stress 0.2572257
## Run 10 stress 0.2344393
## Run 11 stress 0.2158026
## Run 12 stress 0.2538338
## Run 13 stress 0.2329013
## Run 14 stress 0.2270163
## Run 15 stress 0.2395825
## Run 16 stress 0.220286
## Run 17 stress 0.2722497
## Run 18 stress 0.217284
## Run 19 stress 0.2608365
## Run 20 stress 0.220808
## *** No convergence -- monoMDS stopping criteria:
## 20: stress ratio > sratmaxmds.data##
## Call:
## metaMDS(comm = dist.matrix)
##
## global Multidimensional Scaling using monoMDS
##
## Data: dist.matrix
## Distance: bray
##
## Dimensions: 2
## Stress: 0.2105724
## Stress type 1, weak ties
## No convergent solutions - best solution after 20 tries
## Scaling: centring, PC rotation
## Species: scores missingordiplot(mds.data,choices=c(1,2),type="p")## Warning in ordiplot(mds.data, choices = c(1, 2), type = "p"): Species
## scores not available
colvec <- c("blue", "green2", "yellow2", "black")
ordiplot(mds.data, type="n")## Warning in ordiplot(mds.data, type = "n"): Species scores not available#text(mds.data, display="sites", col=colvec[treatment])
text(mds.data, col=colvec[treatment]) # labels=FaunaData$block,
#, main="Stressplot\nStress = 0.2488"
stressplot(mds.data,dist.matrix, p.col=colvec[treatment], l.col="red2")
mds.stats<-metaMDS(FaunaData2[,-1],trace=F)
mds.stats##
## Call:
## metaMDS(comm = FaunaData2[, -1], trace = F)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(sqrt(FaunaData2[, -1]))
## Distance: bray
##
## Dimensions: 2
## Stress: 0.2488008
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'wisconsin(sqrt(FaunaData2[, -1]))'