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 rm(list=ls(all=TRUE)) #start with empty workspace
## Load the data
url <
"http://esapubs.org/archive/ecol/E090/184/PanTHERIA_10_WR93_Aug2008.txt"
if ( !file.exists("pantheria.txt") )
download.file(url, "pantheria.txt")
data.all < read.table("pantheria.txt", as.is=TRUE,
header=TRUE, sep="\t", check.names=FALSE,
na.strings="999")
## Subset interesting columns and rename
cols < c(Order="MSW93_Order",
Family="MSW93_Family",
Genus="MSW93_Genus",
Species="MSW93_Species",
Mass="51_AdultBodyMass_g",
Length="131_AdultHeadBodyLen_mm",
Longevity="171_MaxLongevity_m",
Metabolic.rate = "52_BasalMetRateMass_g",
Gestation.length= "91_GestationLen_d",
HomeRange = "221_HomeRange_km2",
OffspringSize="53_NeonateBodyMass_g",
PopulationDensity="211_PopulationDensity_n/km2",
AgeAtMaturation="231_SexualMaturityAge_d")
data < data.all[cols]
names(data) < names(cols)
## Convert longevity in months to years
data$Longevity < data$Longevity / 12
plot(Longevity ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Longevity (years)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(Longevity) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Carnivora
data.order < data[data$Order == "Carnivora",]
fit < lm(log10(Longevity) ~ log10(Mass), data.order)
points(Longevity ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Carnivora", line=1)
plot(Longevity ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Longevity (years)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(Longevity) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Chiroptera
data.order < data[data$Order == "Chiroptera",]
fit < lm(log10(Longevity) ~ log10(Mass), data.order)
points(Longevity ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Chiroptera", line=1)
## Repeat for another variable pair
plot(Gestation.length ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Gestation.length (d)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(Gestation.length) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Carnivora
data.order < data[data$Order == "Carnivora",]
fit < lm(log10(Gestation.length) ~ log10(Mass), data.order)
points(Gestation.length ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Carnivora", line=1)
plot(Gestation.length ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Gestation.length (d)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(Gestation.length) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Chiroptera
data.order < data[data$Order == "Chiroptera",]
fit < lm(log10(Gestation.length) ~ log10(Mass), data.order)
points(Gestation.length ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Chiroptera", line=1)
## And another variable pair
plot(OffspringSize ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Offspring size (g)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(OffspringSize) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Carnivora
data.order < data[data$Order == "Carnivora",]
fit < lm(log10(OffspringSize) ~ log10(Mass), data.order)
points(OffspringSize ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Carnivora", line=1)
plot(OffspringSize ~ Mass, data, log="xy", col="#66666666", pch=19,
xlab="Body mass (g)", ylab="Offspring size (g)", las=1)
## Add nice log10 labels to the plot
usr < par("usr")
r < round(usr[1:2])
at < seq(r[1], r[2])
lab < do.call(expression, lapply(at, function(i) bquote(10^.(i))))
axis(1, at=10^at, lab)
## Note: we use log10 here because that's what the plot uses (not
## natural logs)
fit < lm(log10(OffspringSize) ~ log10(Mass), data)
abline(fit, col="#66666666")
## Add focus group of points for Chiroptera
data.order < data[data$Order == "Chiroptera",]
fit < lm(log10(OffspringSize) ~ log10(Mass), data.order)
points(OffspringSize ~ Mass, data.order, pch=19, col="#ff000066")
abline(fit, col="#ff000066")
title(main="Chiroptera", line=1)
