rm(list=ls())
setwd("C:/Users/April Mae Tabonda/Documents/MS Marine Science/Biostat/PLP/RMDs/PLP_11 Project")
getwd()
## [1] "C:/Users/April Mae Tabonda/Documents/MS Marine Science/Biostat/PLP/RMDs/PLP_11 Project"
sample.data<-read.csv("coral.csv", header=TRUE, sep=";")
str(sample.data)
## 'data.frame': 81 obs. of 7 variables:
## $ ï..DATE : Factor w/ 8 levels "01/12/2017","14/11/2017",..: 1 1 1 1 1 1 5 5 5 5 ...
## $ SITE : Factor w/ 7 levels "Balingasay","Cangaluyan",..: 1 1 1 1 1 1 2 2 2 2 ...
## $ DEPTH : Factor w/ 2 levels "deep","shallow": 1 1 1 1 1 1 1 1 1 1 ...
## $ TRANSECT : int 18 20 37 47 70 86 4 35 35 35 ...
## $ COUNT : int 2 1 1 4 1 2 2 1 1 1 ...
## $ CORAL : Factor w/ 13 levels "Acropora","Cyphastrea",..: 10 11 10 10 10 10 4 4 1 4 ...
## $ PICTURE..: Factor w/ 81 levels "PB150479","PB150483",..: 73 74 75 76 77 78 42 43 44 45 ...
head(sample.data)
## ï..DATE SITE DEPTH TRANSECT COUNT CORAL PICTURE..
## 1 01/12/2017 Balingasay deep 18 2 Porites PC010115
## 2 01/12/2017 Balingasay deep 20 1 Porites PC010128
## 3 01/12/2017 Balingasay deep 37 1 Porites PC010138
## 4 01/12/2017 Balingasay deep 47 4 Porites PC010155
## 5 01/12/2017 Balingasay deep 70 1 Porites PC010181
## 6 01/12/2017 Balingasay deep 86 2 Porites PC010203
tail(sample.data)
## ï..DATE SITE DEPTH TRANSECT COUNT CORAL PICTURE..
## 76 14/11/2017 Malwest shallow 46 10 Porites PB160451
## 77 14/11/2017 Malwest shallow 50 2 Favia PB160464
## 78 14/11/2017 Malwest shallow 52 1 Porites PB160469
## 79 14/11/2017 Malwest shallow 54 1 Porites PB160473
## 80 14/11/2017 Malwest shallow 56 1 Heliopora PB160477
## 81 14/11/2017 Malwest shallow 92 1 Heliopora PB160545
sample.data$CORAL<-factor(sample.data$CORAL, levels=c('Porites','Galaxea','Acropora','Heliopora','Montipora','Favia'),ordered=F)
sample.data
## ï..DATE SITE DEPTH TRANSECT COUNT CORAL PICTURE..
## 1 01/12/2017 Balingasay deep 18 2 Porites PC010115
## 2 01/12/2017 Balingasay deep 20 1 <NA> PC010128
## 3 01/12/2017 Balingasay deep 37 1 Porites PC010138
## 4 01/12/2017 Balingasay deep 47 4 Porites PC010155
## 5 01/12/2017 Balingasay deep 70 1 Porites PC010181
## 6 01/12/2017 Balingasay deep 86 2 Porites PC010203
## 7 17/11/2017 Cangaluyan deep 4 2 Galaxea PB169997
## 8 17/11/2017 Cangaluyan deep 35 1 Galaxea PB170044
## 9 17/11/2017 Cangaluyan deep 35 1 Acropora PB170047
## 10 17/11/2017 Cangaluyan deep 35 1 Galaxea PB170051
## 11 17/11/2017 Cangaluyan deep 57 1 <NA> PB170089
## 12 17/11/2017 Cangaluyan deep 72 1 Heliopora PB170099
## 13 17/11/2017 Cangaluyan deep 82 1 Galaxea PB170118
## 14 17/11/2017 Cangaluyan deep 82 1 <NA> PB170123
## 15 17/11/2017 Cangaluyan deep 86 3 Galaxea PB170129
## 16 28/11/2017 Caniogan shallow 20 2 Porites PB290140
## 17 28/11/2017 Caniogan shallow 22 1 Favia PB290146
## 18 28/11/2017 Caniogan shallow 76 2 Porites PB290207
## 19 29/11/2017 Cory deep 16 2 <NA> PB290032
## 20 29/11/2017 Cory deep 86 2 Montipora PB290097
## 21 29/11/2017 Cory deep 86 1 Acropora PB290099
## 22 01/12/2017 Lucero deep 24 1 Heliopora PC020244
## 23 01/12/2017 Lucero deep 35 1 Heliopora PC020250
## 24 01/12/2017 Lucero deep 47 1 <NA> PC020267
## 25 16/11/2017 Lucero shallow 4 1 Favia PB160221
## 26 16/11/2017 Lucero shallow 16 1 <NA> PB160249
## 27 16/11/2017 Lucero shallow 16 2 Porites PB160250
## 28 16/11/2017 Lucero shallow 20 1 Favia PB160259
## 29 16/11/2017 Lucero shallow 30 1 Acropora PB160279
## 30 16/11/2017 Lucero shallow 48 1 Favia PB160318
## 31 16/11/2017 Lucero shallow 64 5 Heliopora PB160353
## 32 16/11/2017 Lucero shallow 76 2 Acropora PB160379
## 33 16/11/2017 Lucero shallow 78 1 Favia PB160387
## 34 16/11/2017 Lucero shallow 84 2 Favia PB160400
## 35 16/11/2017 Lucero shallow 86 1 Heliopora PB160406
## 36 16/11/2017 Lucero shallow 96 1 Acropora PB160434
## 37 27/11/2017 Magsaysay deep 4 1 Porites PB270012
## 38 27/11/2017 Magsaysay deep 41 1 Montipora PB270048
## 39 27/11/2017 Magsaysay deep 49 1 Montipora PB270059
## 40 27/11/2017 Magsaysay deep 72 1 Montipora PB270078
## 41 27/11/2017 Magsaysay deep 78 1 Favia PB270088
## 42 27/11/2017 Magsaysay deep 92 2 Porites PB270116
## 43 27/11/2017 Magsaysay shallow 6 1 Favia PB270135
## 44 27/11/2017 Magsaysay shallow 6 2 Montipora PB270136
## 45 27/11/2017 Magsaysay shallow 16 8 Montipora PB270151
## 46 27/11/2017 Magsaysay shallow 22 1 Favia PB270161
## 47 27/11/2017 Magsaysay shallow 43 1 Montipora PB270179
## 48 27/11/2017 Magsaysay shallow 51 2 Montipora PB270194
## 49 27/11/2017 Magsaysay shallow 55 2 Montipora PB270204
## 50 27/11/2017 Magsaysay shallow 59 1 Montipora PB270220
## 51 27/11/2017 Magsaysay shallow 76 1 Montipora PB270235
## 52 27/11/2017 Magsaysay shallow 84 1 Porites PB270248
## 53 15/11/2017 Malwest deep 28 1 <NA> PB150479
## 54 15/11/2017 Malwest deep 30 1 Porites PB150483
## 55 15/11/2017 Malwest deep 32 1 Porites PB150490
## 56 15/11/2017 Malwest deep 34 2 <NA> PB150497
## 57 15/11/2017 Malwest deep 38 1 Porites PB150506
## 58 15/11/2017 Malwest deep 38 1 <NA> PB150507
## 59 15/11/2017 Malwest deep 44 1 Montipora PB150523
## 60 15/11/2017 Malwest deep 46 2 Heliopora PB150527
## 61 15/11/2017 Malwest deep 50 1 Heliopora PB150538
## 62 15/11/2017 Malwest deep 58 1 <NA> PB150554
## 63 15/11/2017 Malwest deep 58 1 <NA> PB150555
## 64 15/11/2017 Malwest deep 70 1 Heliopora PB150578
## 65 15/11/2017 Malwest deep 76 1 Heliopora PB150590
## 66 15/11/2017 Malwest deep 84 2 <NA> PB150605
## 67 15/11/2017 Malwest deep 88 1 Montipora PB150616
## 68 15/11/2017 Malwest deep 98 1 <NA> PB150639
## 69 14/11/2017 Malwest shallow 2 1 <NA> PB160356
## 70 14/11/2017 Malwest shallow 6 2 <NA> PB160362
## 71 14/11/2017 Malwest shallow 10 1 <NA> PB160371
## 72 14/11/2017 Malwest shallow 26 2 <NA> PB160408
## 73 14/11/2017 Malwest shallow 28 1 Porites PB160413
## 74 14/11/2017 Malwest shallow 30 1 Porites PB160416
## 75 14/11/2017 Malwest shallow 40 2 Porites PB160417
## 76 14/11/2017 Malwest shallow 46 10 <NA> PB160451
## 77 14/11/2017 Malwest shallow 50 2 Favia PB160464
## 78 14/11/2017 Malwest shallow 52 1 <NA> PB160469
## 79 14/11/2017 Malwest shallow 54 1 Porites PB160473
## 80 14/11/2017 Malwest shallow 56 1 Heliopora PB160477
## 81 14/11/2017 Malwest shallow 92 1 Heliopora PB160545
boxplot(COUNT~CORAL, data=sample.data)
library(ggplot2)
coral.bp<-ggplot(sample.data,
aes(y=COUNT, x=CORAL, fill=CORAL)) +
geom_boxplot()
coral.bp
coral.bp + ggtitle("Percentage of Drupella spp. found in different corals")
plot(tapply(sample.data$COUNT, sample.data$CORAL,mean),
+tapply(sample.data$COUNT, sample.data$CORAL,var))
sample.data.aov<-aov(COUNT~CORAL, data=sample.data)
plot(sample.data.aov)
anova(sample.data.aov)
## Analysis of Variance Table
##
## Response: COUNT
## Df Sum Sq Mean Sq F value Pr(>F)
## CORAL 5 3.020 0.60397 0.4542 0.8085
## Residuals 56 74.464 1.32971
pacman::p_load(multcomp)
fit1<-summary(glht(sample.data.aov,linfct=mcp(CORAL="Tukey")))
fit1
##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: aov(formula = COUNT ~ CORAL, data = sample.data)
##
## Linear Hypotheses:
## Estimate Std. Error t value Pr(>|t|)
## Galaxea - Porites == 0 4.444e-02 5.829e-01 0.076 1.000
## Acropora - Porites == 0 -3.556e-01 5.829e-01 -0.610 0.989
## Heliopora - Porites == 0 -1.010e-01 4.413e-01 -0.229 1.000
## Montipora - Porites == 0 2.906e-01 4.197e-01 0.692 0.981
## Favia - Porites == 0 -3.556e-01 4.548e-01 -0.782 0.968
## Acropora - Galaxea == 0 -4.000e-01 7.293e-01 -0.548 0.994
## Heliopora - Galaxea == 0 -1.455e-01 6.220e-01 -0.234 1.000
## Montipora - Galaxea == 0 2.462e-01 6.068e-01 0.406 0.998
## Favia - Galaxea == 0 -4.000e-01 6.316e-01 -0.633 0.987
## Heliopora - Acropora == 0 2.545e-01 6.220e-01 0.409 0.998
## Montipora - Acropora == 0 6.462e-01 6.068e-01 1.065 0.889
## Favia - Acropora == 0 7.772e-16 6.316e-01 0.000 1.000
## Montipora - Heliopora == 0 3.916e-01 4.724e-01 0.829 0.959
## Favia - Heliopora == 0 -2.545e-01 5.038e-01 -0.505 0.996
## Favia - Montipora == 0 -6.462e-01 4.850e-01 -1.332 0.759
## (Adjusted p values reported -- single-step method)
fit2<-aov(lm(COUNT~CORAL, data=sample.data))
tukeyfit3<-TukeyHSD(fit2)
plot(tukeyfit3,las=1,col="red")
pacman::p_load(agricolae)
fit4<-aov(COUNT~CORAL, data=sample.data)
HSD.test(fit4,"CORAL")
outfit4<-HSD.test(fit4, "CORAL", group=TRUE)
outfit4
## $statistics
## MSerror Df Mean CV
## 1.329715 56 1.516129 76.05768
##
## $parameters
## test name.t ntr StudentizedRange alpha
## Tukey CORAL 6 4.172863 0.05
##
## $means
## COUNT std r Min Max Q25 Q50 Q75
## Acropora 1.200000 0.4472136 5 1 2 1 1 1
## Favia 1.200000 0.4216370 10 1 2 1 1 1
## Galaxea 1.600000 0.8944272 5 1 3 1 1 2
## Heliopora 1.454545 1.2135598 11 1 5 1 1 1
## Montipora 1.846154 1.9081472 13 1 8 1 1 2
## Porites 1.555556 0.7838234 18 1 4 1 1 2
##
## $comparison
## NULL
##
## $groups
## COUNT groups
## Montipora 1.846154 a
## Galaxea 1.600000 a
## Porites 1.555556 a
## Heliopora 1.454545 a
## Acropora 1.200000 a
## Favia 1.200000 a
##
## attr(,"class")
## [1] "group"