Nama : Didit Abdillah Jum’at, 25 Juli 2020

No. RAG : RAG0007

R-ARM Group Pertemuan 3

# R-ARM (Aquatic Resources Management) Group #
# #
# Fungsi Sederhana dan Penyajian Data #
# Oleh : Didit Abdillah #
# 25 Juli 2020 #

setwd("E:/ORGANISASI/R ARM MSP IPB/R-ARM Group Pertemuan 3")

kelimpahan <- read.table(file="Data.txt", header = TRUE)
names(kelimpahan)

str(kelimpahan)

n <- mean(kelimpahan$total)
n1 <- mean(kelimpahan$total[kelimpahan$transek==1])
n2 <- mean(kelimpahan$total[kelimpahan$transek==2])
n3 <- mean(kelimpahan$total[kelimpahan$transek==3])
n4 <- mean(kelimpahan$total[kelimpahan$transek==4])
n5 <- mean(kelimpahan$total[kelimpahan$transek==5])
n6 <- mean(kelimpahan$total[kelimpahan$transek==6])
n7 <- mean(kelimpahan$total[kelimpahan$transek==7])
n8 <- mean(kelimpahan$total[kelimpahan$transek==8])
c(n, n1, n2, n3, n4, n5, n6, n7, n8)

tapply(kelimpahan$total, kelimpahan$transek, mean)

tapply(X=kelimpahan$total, INDEX= kelimpahan$transek, FUN=mean)

rataan <- tapply(kelimpahan$total, kelimpahan$transek, mean)

sd <- tapply(kelimpahan$total, kelimpahan$transek, sd)
n <- tapply(kelimpahan$total, kelimpahan$transek, length)
cbind(rataan, sd, n)

sapply(kelimpahan[,5:9], FUN= mean)

lapply(kelimpahan[,5:9], FUN= mean)

sapply(cbind(kelimpahan$ikan, kelimpahan$bivalv, kelimpahan$gastrop, kelimpahan$kerang,

kelimpahan$total), FUN= mean)

sapply(data.frame(cbind(kelimpahan$ikan, kelimpahan$bivalv, kelimpahan$gastrop,

kelimpahan$kerang, kelimpahan$total)), FUN= mean)

#SUMMARY

z <- cbind(kelimpahan$ikan, kelimpahan$bivalv, kelimpahan$gastrop, kelimpahan$kerang,

kelimpahan$total)
colnames (z) <- c("total", "ikan", "bivalvia", "gastropod", "kerang")
summary (z)
Nama : Didit Abdillah Jum’at, 25 Juli 2020
No. RAG : RAG0007

summary(kelimpahan[ , c("total", "ikan", "bivalv", "gastrop", "kerang")])

summary(kelimpahan[ , c(5,6,7,8,9)])
summary(kelimpahan[ , c(5:9)])

table(kelimpahan$transek)

#PLOT

#Fungsi Plot

plot(kelimpahan$cover, kelimpahan$total)

plot(kelimpahan$total, kelimpahan$cover)

plot(x=kelimpahan$total, y=kelimpahan$cover)

plot(cover~total, data=kelimpahan)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100))

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main= "Scatter plot",
xlim= c(min(kelimpahan$cover), max(kelimpahan$cover)),
ylim= c(min(kelimpahan$total), max(kelimpahan$total)))

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab= "Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(min(kelimpahan$cover, na.rm=TRUE), max(kelimpahan$cover, na.rm=TRUE)),
ylim= c(min(kelimpahan$cover, na.rm=TRUE), max(kelimpahan$cover, na.rm=TRUE)))

#Merubah karakter plot

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=19)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=kelimpahan$transek)

kelimpahan$Tahun2 <- kelimpahan$Tahun

kelimpahan$Tahun2 [kelimpahan$Tahun == 2010] <- 1
Nama : Didit Abdillah Jum’at, 25 Juli 2020
No. RAG : RAG0007

kelimpahan$Tahun2 [kelimpahan$Tahun == 2020] <- 16

kelimpahan$Tahun2

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=kelimpahan$Tahun2)

#Merubah warna plot

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), col=3)

kelimpahan$Col2 <- kelimpahan$Tahun

kelimpahan$Col2 [kelimpahan$Tahun ==2010] <-1
kelimpahan$Col2 [kelimpahan$Tahun ==2020] <-2

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), col=kelimpahan$Col2)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=16, cex=1.5)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=16, cex=kelimpahan$Col2)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=16, col=kelimpahan$Col2, cex=kelimpahan$Col2)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100), pch=kelimpahan$transek, col=kelimpahan$Col2,
cex=kelimpahan$Col2)

#Menambah Baris
plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100))
garis <-loess (total ~ cover, data=kelimpahan)
Nama : Didit Abdillah Jum’at, 25 Juli 2020
No. RAG : RAG0007

fit <- fitted(garis)

lines(kelimpahan$cover, fit)

plot(x=kelimpahan$cover, y=kelimpahan$total,
xlab="Tutupan Karang (%)", ylab= "Kelimpahan Total (indiv)",
main="Scatter plot",
xlim= c(20,60), ylim= c(50,100))
garis <-loess (total ~ cover, data=kelimpahan)
fit <- fitted(garis)
ord1 <- order(kelimpahan$cover)
lines(kelimpahan$cover [ord1], fit [ord1], lwd = 3, lty = 2)

#PIE CHART

setwd("E:/ORGANISASI/R ARM MSP IPB/R-ARM Group Pertemuan 3")

ikan <- read.table(file= "jenis ikan.txt", header=TRUE)
names(ikan)
str(ikan)

jumlah <-rowSums(ikan[, 2:16])

names(jumlah) <- ikan[,1]
jumlah

par(mfrow = c(2,2), mar = c(3,3,2,1))

pie(jumlah, main = "Ordinary pie chart")
pie(jumlah, col= gray(seq(0.4, 1.0, length=6)), clockwise= TRUE, main = "Grey colours")
pie(jumlah, col= rainbow(6), clockwise = TRUE, main= "Rainbow colours")
library(plotrix)
pie3D(jumlah, labels= names(jumlah), explode=0.1, main= "3D pie chart", labelcex= 0.6)

#BAR CHART AND STRIP CHART

#Bar Chart
parasit <- read.table(file="ikan dengan parasit.txt", header= TRUE)
berparasit <- rowSums(parasit[,2:16])
names(berparasit) <- parasit[,1]
berparasit

par(mfrow = c(2,2), mar= c(3,3,2,1))

barplot(jumlah, main= "Ikan Air Tawar di Sungai")
perbandingan <- cbind(jumlah, berparasit)
barplot(perbandingan, main= "Perbandingan Ikan")
barplot(t(perbandingan), col= gray(c(0.5,1)))
barplot(t(perbandingan), beside = TRUE)

perbandingan

t(perbandingan)
par(mfrow=c(1,1))

setwd("E:/ORGANISASI/R ARM MSP IPB/R-ARM Group Pertemuan 3")

Nama : Didit Abdillah Jum’at, 25 Juli 2020
No. RAG : RAG0007

kelimpahan <- read.table(file="Data.txt", header = TRUE)

rataan <- tapply(kelimpahan$total, kelimpahan$transek, mean)
sd <- tapply(kelimpahan$total, kelimpahan$transek, sd)
TKB <- cbind(rataan, sd)
TKB

barplot(rataan)
par(mfrow= c(1,2), mar= c(3,3,2,1))
bp <- barplot(rataan, xlab= "Transek", ylab="Jumlah Ikan", ylim= c(0,100), col= rainbow(8))
arrows(bp, rataan, bp, rataan+sd, lwd=1.5, angle = 90, length=0.1)
box()

le <- tapply(kelimpahan$total, INDEX = kelimpahan$transek, FUN= length)

se <- sd/sqrt(le)
stripchart(kelimpahan$total ~ kelimpahan$transek, vert=TRUE, pch=1, method= "jitter", jit = 0.05,
xlab= "Transek", ylab= "Jumlah Ikan")
points(1:8, rataan, pch=16, cex=1.5)
arrows(1:8, rataan, 1:8, rataan + se, lwd=1.5, angle= 90, length= 0.1)
arrows(1:8, rataan, 1:8, rataan - se, lwd=1.5, angle= 90, length= 0.1)
par(mfrow = c(1,1), mar = c(3,3,2,1))

#BOXPLOT#

setwd("E:/ORGANISASI/R ARM MSP IPB/R-ARM Group Pertemuan 3")

kelimpahan <- read.table(file="Data.txt", header = TRUE)
boxplot(kelimpahan$total)

par(mfrow = c(2,2), mar= c(3,3,2,1))

boxplot(total ~ Tahun, data = kelimpahan)
boxplot(total ~ jarak, data = kelimpahan)
boxplot(total ~ Tahun*jarak, data = kelimpahan)
boxplot(total ~ Tahun*jarak, names= c("2010/D", "2020/D", "2010/J", "2020/J"), data=kelimpahan)
par(mfrow= c(1,1))
boxplot(total ~ transek, data = kelimpahan)
boxplot(total ~ transek, data = kelimpahan, col = "grey", xlab= "Transek", ylab = "Kelimpahan Total")

#CLEVELAND DOTPLOTS#

setwd("E:/ORGANISASI/R ARM MSP IPB/R-ARM Group Pertemuan 3")

kelimpahan <- read.table(file="Data.txt", header = TRUE)
dotchart (kelimpahan$total, xlab = "Kelimpahan", ylab= "Transek")
dotchart (kelimpahan$total, groups = factor(kelimpahan$transek))
par(mfrow= c(1,2))
dotchart(kelimpahan$total, groups=factor(kelimpahan$transek), xlab= "Kelimpahan", ylab=
"Transek")
dotchart(kelimpahan$total, groups=kelimpahan$transek, gdata= rataan, gpch= 19, xlab=
"Kelimpahan", ylab= "Transek")
legend("bottomright", c("values", "mean"), pch= c(1,19), bg= "white")