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inst/doc/AllometryAndConversionsTutorial.R
In TrenchR: Tools for Microclimate and Biophysical Ecology
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## -----------------------------------------------------------------------------
# Load TrenchR package
library(TrenchR)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
oldpar<- par()
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "lizard"),
type = "l",
xlab = "length (m)",
ylab = "mass (g)",
ylim = c(0, 200),
xlim = c(0, 0.25),
las = 1,
bty = "L",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "salamander"),
type = "l",
col = "blue",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "frog"),
type = "l",
col = "red",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "snake"),
type = "l",
col = "green",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "turtle"),
type = "l",
col = "orange",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "insect"),
type = "l",
col = "purple",
lwd = 2)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "lizard"),
type = "l",
xlab = "mass (g)",
ylab = "",
las = 1,
bty = "L",
lwd = 2)
mtext(text = expression("surface area" ~ (m^{2})),
side = 2,
line = 3.5)
points(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "frog"),
type = "l",
lty = "dashed",
lwd = 2)
points(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "salamander"),
type = "l",
lty = "dotted",
lwd = 2)
points(x = seq(0.1, 5, 0.2),
y = surface_area_from_mass(m = seq(0.1,5,0.2),
taxon = "insect"),
type = "l",
lty = "dotdash",
lwd = 2)
box(bty = "L",
lwd = 2)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
plot(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "lizard"),
type = "l",
xlab = expression(volume ~ (m^{3})),
ylab = expression("surface area" ~ (m^{2})))
points(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "frog"),
type = "l",
lty = "dashed")
points(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "sphere"),
type = "l",
lty = "dotted")
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "lizard"),
type = "l",
xlab = "length (m)",
ylab = expression(volume ~ (m^{3})))
points(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "frog"),
type = "l",
lty = "dashed")
points(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "sphere"),
type = "l",
lty = "dotted")
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.05, 0.001),
y = surface_area_from_length(l = seq(0.01, 0.05, 0.001)),
type = "l",
xlab = "length (m)",
ylab = expression("surface area" ~ (m^{2})))
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "frog"),
type = "l",
xlab = "zenith angle (°)",
ylab = "proportion silhouette area",
ylim = range(0, 0.5))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "lizard",
raz = 0,
posture = "prostrate"),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "lizard",
raz = 0,
posture = "elevated"),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "grasshopper"),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.39),
type = "l",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35),
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.3),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.4),
type = "l",
lty = "dashed",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.05),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.4),
type = "l",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.05),
type = "l",
lty = "dotdash")
## -----------------------------------------------------------------------------
degrees_to_radians(47.608)
radians_to_degrees(0.831)
fahrenheit_to_celsius(85)
fahrenheit_to_kelvin(85)
kelvin_to_celsius(270)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
plot(x = 0:60,
y = TPC(T = 0:60,
T_opt = 30,
CT_min = 10,
CT_max = 40),
type = "l",
ylim = c(0,3),
ylab = "performance",
xlab = "temperature (°C)")
points(x = 0:60,
y = TPC_beta(T = 0:60,
shift = -1,
breadth = 0.1,
aran = 0,
tolerance = 43,
skew = 0.7),
type = "l",
lty = "dashed")
suppressWarnings(par(oldpar))
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TrenchR documentation built on Sept. 14, 2023, 1:07 a.m.
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## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## -----------------------------------------------------------------------------
# Load TrenchR package
library(TrenchR)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
oldpar<- par()
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "lizard"),
type = "l",
xlab = "length (m)",
ylab = "mass (g)",
ylim = c(0, 200),
xlim = c(0, 0.25),
las = 1,
bty = "L",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "salamander"),
type = "l",
col = "blue",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "frog"),
type = "l",
col = "red",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "snake"),
type = "l",
col = "green",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "turtle"),
type = "l",
col = "orange",
lwd = 2)
points(x = seq(0.01, 0.25, 0.01),
y = mass_from_length(l = seq(0.01, 0.25, 0.01),
taxon = "insect"),
type = "l",
col = "purple",
lwd = 2)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "lizard"),
type = "l",
xlab = "mass (g)",
ylab = "",
las = 1,
bty = "L",
lwd = 2)
mtext(text = expression("surface area" ~ (m^{2})),
side = 2,
line = 3.5)
points(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "frog"),
type = "l",
lty = "dashed",
lwd = 2)
points(x = 1:50,
y = surface_area_from_mass(m = 1:50,
taxon = "salamander"),
type = "l",
lty = "dotted",
lwd = 2)
points(x = seq(0.1, 5, 0.2),
y = surface_area_from_mass(m = seq(0.1,5,0.2),
taxon = "insect"),
type = "l",
lty = "dotdash",
lwd = 2)
box(bty = "L",
lwd = 2)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
plot(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "lizard"),
type = "l",
xlab = expression(volume ~ (m^{3})),
ylab = expression("surface area" ~ (m^{2})))
points(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "frog"),
type = "l",
lty = "dashed")
points(x = seq(0.001, 0.01, 0.001),
y = surface_area_from_volume(V = seq(0.001, 0.01, 0.001),
taxon = "sphere"),
type = "l",
lty = "dotted")
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "lizard"),
type = "l",
xlab = "length (m)",
ylab = expression(volume ~ (m^{3})))
points(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "frog"),
type = "l",
lty = "dashed")
points(x = seq(0.01, 0.05, 0.001),
y = volume_from_length(l = seq(0.01, 0.05, 0.001),
taxon = "sphere"),
type = "l",
lty = "dotted")
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0.01, 0.05, 0.001),
y = surface_area_from_length(l = seq(0.01, 0.05, 0.001)),
type = "l",
xlab = "length (m)",
ylab = expression("surface area" ~ (m^{2})))
## ---- fig.height = 3, fig.width = 4-------------------------------------------
par(mar = c(5, 5, 2, 2))
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "frog"),
type = "l",
xlab = "zenith angle (°)",
ylab = "proportion silhouette area",
ylim = range(0, 0.5))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "lizard",
raz = 0,
posture = "prostrate"),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "lizard",
raz = 0,
posture = "elevated"),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area(psi = seq(0, 90, 10),
taxon = "grasshopper"),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.39),
type = "l",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35),
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.3),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "spheroid",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.4),
type = "l",
lty = "dashed",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.05),
type = "l",
lty = "dotdash")
plot(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.4),
type = "l",
xlab = "theta (°)",
ylab = "proportion silhouette area",
ylim = c(0, 0.35))
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.2),
type = "l",
lty = "dashed")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.1),
type = "l",
lty = "dotted")
points(x = seq(0, 90, 10),
y = proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = seq(0, 90, 10),
h = 0.4,
d = 0.05),
type = "l",
lty = "dotdash")
## -----------------------------------------------------------------------------
degrees_to_radians(47.608)
radians_to_degrees(0.831)
fahrenheit_to_celsius(85)
fahrenheit_to_kelvin(85)
kelvin_to_celsius(270)
## ---- fig.height = 3, fig.width = 4-------------------------------------------
plot(x = 0:60,
y = TPC(T = 0:60,
T_opt = 30,
CT_min = 10,
CT_max = 40),
type = "l",
ylim = c(0,3),
ylab = "performance",
xlab = "temperature (°C)")
points(x = 0:60,
y = TPC_beta(T = 0:60,
shift = -1,
breadth = 0.1,
aran = 0,
tolerance = 43,
skew = 0.7),
type = "l",
lty = "dashed")
suppressWarnings(par(oldpar))
Try the TrenchR package in your browser
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