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Module-5-Overall-Example.R
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Module-5-Overall-Example.R
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# The following code is implemented by Sarah Michelle Leatherman.
Input = ("
Species Temp Pulse
ex 20.8 67.9
ex 20.8 65.1
ex 24 77.3
ex 24 78.7
ex 24 79.4
ex 24 80.4
ex 26.2 85.8
ex 26.2 86.6
ex 26.2 87.5
ex 26.2 89.1
ex 28.4 98.6
ex 29 100.8
ex 30.4 99.3
ex 30.4 101.7
niv 17.2 44.3
niv 18.3 47.2
niv 18.3 47.6
niv 18.3 49.6
niv 18.9 50.3
niv 18.9 51.8
niv 20.4 60
niv 21 58.5
niv 21 58.9
niv 22.1 60.7
niv 23.5 69.8
niv 24.2 70.9
niv 25.9 76.2
niv 26.5 76.1
niv 26.5 77
niv 26.5 77.7
niv 28.6 84.7
")
data <- read.table(textConnection(Input),header=TRUE)
data$group<-factor(data$Species)
summary(data$Species)
summary(data$Species)/nrow(data)*100
# Summarize by species #
library(plyr)
ddply(data, "Species", summarise,
N = length(Pulse),
mean = mean(Pulse),
sd = sd(Pulse) )
boxplot(Pulse~Species, data = data, main = "Pulse by Species",
xlab = "Species",
ylab = "Pulse")
ddply(data, "Species", summarise,
N = length(Temp),
mean = mean(Temp),
sd = sd(Temp) )
boxplot(Temp~Species, data = data, main = "Temp by Species",
xlab = "Species",
ylab = "Temp")
# ANOVA #
m<-aov(Pulse~Species, data = data)
summary(m)
# Dummy variables #
data$n<-ifelse(data$Species == "niv", 1, 0)
m2<-lm(Pulse~n, data = data) #ex as reference
summary(m2)
# ANCOVA #
library(car)
library(lsmeans)
options(contrasts=c("contr.treatment","contr.poly"))
m3 <-lm(Pulse~n+Temp, data=data)
summary(m3)
Anova(lm(Pulse~Species+Temp, data=data), type =3)
# simple plot #
plot(x = data$Temp,
y = data$Pulse,
col = data$Species,
pch = 16,
xlab = "Temperature",
ylab = "Pulse")
legend('bottomright',
legend = levels(data$Species),
col = 1:2,
cex = 1,
pch = 16)
# simple plot with regression lines #
I.nought = -7.21091
I1 = I.nought + 0
I2 = I.nought + -10.06529
B = 3.60275
plot(x = data$Temp,
y = data$Pulse,
col = data$Species,
pch = 16,
xlab = "Temperature",
ylab = "Pulse")
legend('bottomright',
legend = levels(data$Species),
col = 1:2,
cex = 1,
pch = 16)
abline(I1, B,
lty=1, lwd=2, col = 1)
abline(I2, B,
lty=1, lwd=2, col = 2)