R/devRate_forRstudioUsers.R
In frareb/devRate: Quantify the Relationship Between Development Rate and Temperature in Ectotherms
Defines functions
devRateFindStartNls
# A wrapper for the manipulate function to get parameter estimates for NLS
#
# This is a wrapper for manipulate function using sliders for all equations
# in the devRate package in order to have good first guess estimates of the
# parameters in the NLS process (devRateModel function).
# It requiers the manipulate package to be installed in order to work:
# install.packages("manipulate")
#
# devRateFindStartNls is not part of the R CRAN package because it depends
# on the manipulate package which works only for Rstudio. This function is
# available online in the GitHub page of the devRate package.
#
# There are three parameters:
# - temp: the dataset temperatures
# - devRate: the dataset development rate
# - eq: the equation to be fitted to the dataset
#
# example:
# rawDevEggs <- matrix(c(10, 0.031, 10, 0.039, 15, 0.047, 15, 0.059, 15.5, 0.066,
# 16, 0.072, 16, 0.083, 16, 0.100, 17, 0.100, 20, 0.100, 20, 0.143, 25, 0.171,
# 25, 0.200, 30, 0.200, 30, 0.180, 50, 0.01), ncol = 2, byrow = TRUE)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = taylor_81)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = beta_16)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = ratkowsky_83)
devRateFindStartNls <- function(temp, devRate, eq){
# library(manipulate)
if (requireNamespace("manipulate", quietly = TRUE)) {
require("manipulate")
switch(EXPR = eq$id,
"eq010" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (Dmin/2 * (exp(aa*(xx - Topt)) + exp(-bb*(xx - Topt))))^(-1),
type = 'l', lwd = 3),
Dmin = slider(0, 50, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Topt = slider(0, 50, step = 0.005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
aa = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
bb = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq020" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = K / (1 + exp(aa + bb * xx)),
type = 'l', lwd = 3),
aa = slider(0, 10, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-0.5, 0, step = 0.005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
K = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq030" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = aa + bb * xx,
type = 'l', lwd = 3),
aa = slider(-1, 0, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 0.1, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq040" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = C / (1 + exp(k1 + k2 * xx)),
type = 'l', lwd = 3) +
points(x = xx, y = C / (1 + exp(k1 + k2 * (2 * Topt - xx))),
type = 'l', lwd = 3),
C = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
k1 = slider(0, 15, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
k2 = slider(-1, 0, step = 0.0005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Topt = slider(0, 50, step = 0.0005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq050" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = phi * (exp(bb * xx) - exp(bb * Tmax - (Tmax - xx)/deltaT)),
type = 'l', lwd = 3),
phi = slider(-0.5, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 0.5, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.0005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq060" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = alpha * (1/(1 + cc * exp(- bb * xx)) - exp(-((Tmax - xx)/deltaT))),
type = 'l', lwd = 3),
alpha = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-0.5, 0.5, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 500, step = 10, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.05, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0005, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq070" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = ((xx + 273.16) * exp((aa - bb/(xx + 273.16))/1.987)) / (1 + exp((cc - dd/(xx + 273.16))/1.987) + exp((ff - gg/(xx + 273.16))/1.987)),
type = 'l', lwd = 3),
aa = slider(0, 100, step = 0.1, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(-1000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(-500000, 0, step = 10, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
ff = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
gg = slider(0, 100000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq080" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = aa * (xx - Tmin)^bb * (Tmax - xx)^cc,
type = 'l', lwd = 3),
aa = slider(0, 0.01, step = 0.0000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 10, step = 0.001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(-15, 15, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
Tmax = slider(15, 50, step = 0.1, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq090" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(bb/1.987 * (1/cc - 1/(xx + 273.16))) + exp(dd/1.987 * (1/ee - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(-50000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
cc = slider(0, 1000, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
dd = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
ee = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq091" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(dd/1.987 * (1/ee - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
dd = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
ee = slider(0, 10000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq092" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(bb/1.987 * (1/cc - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(-50000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
cc = slider(0, 1000, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq100" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tm)/To)^2),
type = 'l', lwd = 3),
Rm = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tm = slider(0, 50, step = 0.01, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
To = slider(-10, 15, step = 0.01, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq110" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2,
type = 'l', lwd = 3),
a0 = slider(-0.2, 0, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(0, 0.1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-0.005, 0, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq120" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2 + a3 * xx^3,
type = 'l', lwd = 3),
a0 = slider(-0.2, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(-0.2, 0.2, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-2, 0.1, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
a3 = slider(-0.1, 15, step = 0.00001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq130" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2 + a3 * xx^3 + a4 * xx^4,
type = 'l', lwd = 3),
a0 = slider(-1, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(-0.2, 0.5, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-0.1, 0.1, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
a3 = slider(-0.001, 0.001, step = 0.00001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
a4 = slider(-0.00001, 0.00001, step = 0.0000001, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq140" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = phi * (((xx-Tb)^2 / ((xx-Tb)^2 + aa^2)) - exp(-(Tmax - (xx-Tb))/deltaT)),
type = 'l', lwd = 3),
phi = slider(0, 2, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmax = slider(10, 50, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq150" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tmax)/To)^2),
type = 'l', lwd = 3, col = 4) +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tmax)/T1)^2),
type = 'l', lwd = 3, col = 2),
Rm = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
To = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
T1 = slider(-1, 5, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
fx <- as.function(alist(x =, eval(parse(text = eq$eqAlt[1]))))
graphics::curve(fx, add = TRUE, col = i, from = 0, to = Tmax)
fx <- as.function(alist(x =, eval(parse(text = eq$eqAlt[2]))))
graphics::curve(fx, add = TRUE, col = i, from = Tmax, to = 60)
},
"eq160" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(aa * xx) - exp(aa * Tmax - (Tmax - xx)/deltaT),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq170" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(aa * xx) - exp(aa * Tmax - (Tmax - xx)/deltaT) + bb,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
bb = slider(-2, 0, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq180" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * xx * (xx - Tmin) * (Tmax - xx)^(1 / 2),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq190" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * xx * (xx - Tmin) * (Tmax - xx)^(1 / bb),
type = 'l', lwd = 3)
},
defYlim = slider(0, 5, step = 0.0001, initial = 1),
aa = slider(0, 5, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq200" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (xx - Tmin)^2 * (Tmax - xx),
type = 'l', lwd = 3)
},
defYlim = slider(0, 5, step = 0.01, initial = 1),
aa = slider(0, 0.001, step = 0.000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq210" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (bb - xx / 10) * (xx / 10)^cc,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 0.001, step = 0.000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq220" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa / (1 + bb * xx + cc * xx^2),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 100, step = 0.0001, initial = 0.1),
bb = slider(0, 20, step = 0.0001, initial = 1),
cc = slider(0, 100, step = 0.0001, initial = 1)
)
},
"eq230" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (K / (1 + exp(-r*(xx - T0)))) * (1 - exp(-(xx - TL)/aa)) * (1-exp(-(TH - xx)/aa)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
K = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
r = slider(0, 2, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
T0 = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
TL = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
TH = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
aa = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq240" = {},
"eq250" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = cc * (1 - exp(-k1 * (xx - T1))) * (1 - exp(k2 * (xx - T2))),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
k1 = slider(0, 10, step = 0.0001, initial = 1),
k2 = slider(0, 10, step = 0.0001, initial = 1),
T1 = slider(0, 20, step = 0.0001, initial = 15),
T2 = slider(0, 100, step = 0.0001, initial = 35)
)
},
"eq260" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = phi * (exp(bb * (xx - Tb)) - ((Tm - xx)/(Tm - Tb)) * exp(-bb * (xx - Tb) / deltab) - ((xx - Tb)/(Tm - Tb)) * exp(bb * (Tm - Tb) - (Tm - xx)/deltam)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
phi = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tb = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tm = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltab = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
deltam = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq270" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (sqrt(cc) * k1 * (xx - T1) * (1 - exp(k2 * (xx - T2))))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
k1 = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(0, 100, step = 0.0001, initial = 10),
k2 = slider(0, 1, step = 0.0001, initial = 0.5),
T2 = slider(0, 100, step = 0.0001, initial = 30)
)
},
"eq280" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (2 * (xx - Tmin)^aa * (Topt - Tmin)^aa - (xx - Tmin)^(2 * aa)) / ((Topt - Tmin)^(2 * aa)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
Tmin = slider(0, 20, step = 0.0001, initial = 10),
aa = slider(0, 5, step = 0.0001, initial = 0.5),
Topt = slider(0, 100, step = 0.0001, initial = 30)
)
},
"eq290" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (bb * (xx - Tb))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
bb = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tb = slider(-10, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE))
)
},
"eq300" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = cc * (xx - T1) * (1 - exp(k * (xx - T2))),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(-10, 20, step = 0.0001, initial = 5),
k = slider(0, 1, step = 0.0001, initial = 0.5),
T2 = slider(-10, 100, step = 0.0001, initial = 20)
)
},
"eq310" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(mu) * (xx - Tb)^aa * (Tc - xx)^bb,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
mu = slider(-1, 1, step = 0.0001, initial = 0.5),
Tb = slider(-10, 20, step = 0.0001, initial = 10),
aa = slider(-1, 2, step = 0.0001, initial = 0.5),
Tc = slider(-10, 100, step = 0.0001, initial = 35),
bb = slider(-1, 1, step = 0.0001, initial = 0.5)
)
},
"eq320" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa + bb * xx + cc * exp(xx) + dd * exp(-xx),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(-1, 1, step = 0.0000001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(-500000, 0, step = 100, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq330" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = 1/( (1 + exp((cc/1.987) * ((1/dd) - (1/(xx + 273.16))) )) / (aa*(xx + 273.16)/298.15*exp( (bb/1.987)*((1/298.15) - 1/(xx + 273.16)) ) ) ),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 50000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 500000, step = 10, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq340" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (xx - Tmin) - (bb * exp(xx - Tm)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 0.6, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tm = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(-10, 20, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq350" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = rm * (T2 - xx)/(T2 - Tm) * ((xx - T1)/(Tm - T1))^((Tm - T1)/(T2 - Tm)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
rm = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(0, 50, step = 0.0001, initial = 5),
T2 = slider(0, 50, step = 0.0001, initial = 35),
Tm = slider(0, 50, step = 0.0001, initial = 20)
)
},
"eq360" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (cc * (xx - T1) * (1 - exp(k * (xx - T2))))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.05),
T1 = slider(0, 50, step = 0.0001, initial = 5),
T2 = slider(0, 50, step = 0.0001, initial = 35),
k = slider(0, 5, step = 0.0001, initial = 0.05)
)
},
{
# otherwise nothing
}
)
} else {
stop("To use this functionality, you need the package: manipulate")
}
}
frareb/devRate documentation built on Aug. 30, 2023, 5:25 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions devRateFindStartNls
# A wrapper for the manipulate function to get parameter estimates for NLS
#
# This is a wrapper for manipulate function using sliders for all equations
# in the devRate package in order to have good first guess estimates of the
# parameters in the NLS process (devRateModel function).
# It requiers the manipulate package to be installed in order to work:
# install.packages("manipulate")
#
# devRateFindStartNls is not part of the R CRAN package because it depends
# on the manipulate package which works only for Rstudio. This function is
# available online in the GitHub page of the devRate package.
#
# There are three parameters:
# - temp: the dataset temperatures
# - devRate: the dataset development rate
# - eq: the equation to be fitted to the dataset
#
# example:
# rawDevEggs <- matrix(c(10, 0.031, 10, 0.039, 15, 0.047, 15, 0.059, 15.5, 0.066,
# 16, 0.072, 16, 0.083, 16, 0.100, 17, 0.100, 20, 0.100, 20, 0.143, 25, 0.171,
# 25, 0.200, 30, 0.200, 30, 0.180, 50, 0.01), ncol = 2, byrow = TRUE)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = taylor_81)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = beta_16)
# devRateFindStartNls(temp = rawDevEggs[, 1], devRate = rawDevEggs[, 2], eq = ratkowsky_83)
devRateFindStartNls <- function(temp, devRate, eq){
# library(manipulate)
if (requireNamespace("manipulate", quietly = TRUE)) {
require("manipulate")
switch(EXPR = eq$id,
"eq010" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (Dmin/2 * (exp(aa*(xx - Topt)) + exp(-bb*(xx - Topt))))^(-1),
type = 'l', lwd = 3),
Dmin = slider(0, 50, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Topt = slider(0, 50, step = 0.005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
aa = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
bb = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq020" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = K / (1 + exp(aa + bb * xx)),
type = 'l', lwd = 3),
aa = slider(0, 10, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-0.5, 0, step = 0.005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
K = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq030" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = aa + bb * xx,
type = 'l', lwd = 3),
aa = slider(-1, 0, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 0.1, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq040" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = C / (1 + exp(k1 + k2 * xx)),
type = 'l', lwd = 3) +
points(x = xx, y = C / (1 + exp(k1 + k2 * (2 * Topt - xx))),
type = 'l', lwd = 3),
C = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
k1 = slider(0, 15, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
k2 = slider(-1, 0, step = 0.0005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Topt = slider(0, 50, step = 0.0005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq050" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = phi * (exp(bb * xx) - exp(bb * Tmax - (Tmax - xx)/deltaT)),
type = 'l', lwd = 3),
phi = slider(-0.5, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 0.5, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.0005, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0005, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq060" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = alpha * (1/(1 + cc * exp(- bb * xx)) - exp(-((Tmax - xx)/deltaT))),
type = 'l', lwd = 3),
alpha = slider(0, 1, step = 0.005, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-0.5, 0.5, step = 0.0005, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 500, step = 10, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.05, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0005, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq070" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = ((xx + 273.16) * exp((aa - bb/(xx + 273.16))/1.987)) / (1 + exp((cc - dd/(xx + 273.16))/1.987) + exp((ff - gg/(xx + 273.16))/1.987)),
type = 'l', lwd = 3),
aa = slider(0, 100, step = 0.1, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(-1000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(-500000, 0, step = 10, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
ff = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
gg = slider(0, 100000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq080" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = aa * (xx - Tmin)^bb * (Tmax - xx)^cc,
type = 'l', lwd = 3),
aa = slider(0, 0.01, step = 0.0000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 10, step = 0.001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(-15, 15, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
Tmax = slider(15, 50, step = 0.1, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq090" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(bb/1.987 * (1/cc - 1/(xx + 273.16))) + exp(dd/1.987 * (1/ee - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(-50000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
cc = slider(0, 1000, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
dd = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
ee = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq091" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(dd/1.987 * (1/ee - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
dd = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
ee = slider(0, 10000, step = 1, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq092" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = (p25 * (xx + 273.16)/298 * exp(aa/1.987 * (1/298 - 1/(xx + 273.16)))) / (1 + exp(bb/1.987 * (1/cc - 1/(xx + 273.16)))),
type = 'l', lwd = 3),
p25 = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(-50000, 0, step = 1, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
cc = slider(0, 1000, step = 0.1, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq100" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tm)/To)^2),
type = 'l', lwd = 3),
Rm = slider(0, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tm = slider(0, 50, step = 0.01, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
To = slider(-10, 15, step = 0.01, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq110" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2,
type = 'l', lwd = 3),
a0 = slider(-0.2, 0, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(0, 0.1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-0.005, 0, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq120" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2 + a3 * xx^3,
type = 'l', lwd = 3),
a0 = slider(-0.2, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(-0.2, 0.2, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-2, 0.1, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
a3 = slider(-0.1, 15, step = 0.00001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq130" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = a0 + a1 * xx + a2 * xx^2 + a3 * xx^3 + a4 * xx^4,
type = 'l', lwd = 3),
a0 = slider(-1, 1, step = 0.001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
a1 = slider(-0.2, 0.5, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
a2 = slider(-0.1, 0.1, step = 0.00001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
a3 = slider(-0.001, 0.001, step = 0.00001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
a4 = slider(-0.00001, 0.00001, step = 0.0000001, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
}, # linear model: no need for starting estimates
"eq140" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = phi * (((xx-Tb)^2 / ((xx-Tb)^2 + aa^2)) - exp(-(Tmax - (xx-Tb))/deltaT)),
type = 'l', lwd = 3),
phi = slider(0, 2, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
aa = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmax = slider(10, 50, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE))
)
},
"eq150" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, max(devRate, na.rm = TRUE)),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
} +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tmax)/To)^2),
type = 'l', lwd = 3, col = 4) +
points(x = xx, y = Rm * exp(-1/2 * ((xx - Tmax)/T1)^2),
type = 'l', lwd = 3, col = 2),
Rm = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 50, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
To = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
T1 = slider(-1, 5, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
fx <- as.function(alist(x =, eval(parse(text = eq$eqAlt[1]))))
graphics::curve(fx, add = TRUE, col = i, from = 0, to = Tmax)
fx <- as.function(alist(x =, eval(parse(text = eq$eqAlt[2]))))
graphics::curve(fx, add = TRUE, col = i, from = Tmax, to = 60)
},
"eq160" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(aa * xx) - exp(aa * Tmax - (Tmax - xx)/deltaT),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq170" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(aa * xx) - exp(aa * Tmax - (Tmax - xx)/deltaT) + bb,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
deltaT = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
bb = slider(-2, 0, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq180" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * xx * (xx - Tmin) * (Tmax - xx)^(1 / 2),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.01, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq190" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * xx * (xx - Tmin) * (Tmax - xx)^(1 / bb),
type = 'l', lwd = 3)
},
defYlim = slider(0, 5, step = 0.0001, initial = 1),
aa = slider(0, 5, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
bb = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq200" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (xx - Tmin)^2 * (Tmax - xx),
type = 'l', lwd = 3)
},
defYlim = slider(0, 5, step = 0.01, initial = 1),
aa = slider(0, 0.001, step = 0.000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tmin = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tmax = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq210" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (bb - xx / 10) * (xx / 10)^cc,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 0.001, step = 0.000001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE))
)
},
"eq220" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa / (1 + bb * xx + cc * xx^2),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 100, step = 0.0001, initial = 0.1),
bb = slider(0, 20, step = 0.0001, initial = 1),
cc = slider(0, 100, step = 0.0001, initial = 1)
)
},
"eq230" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (K / (1 + exp(-r*(xx - T0)))) * (1 - exp(-(xx - TL)/aa)) * (1-exp(-(TH - xx)/aa)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
K = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
r = slider(0, 2, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
T0 = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
TL = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
TH = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
aa = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq240" = {},
"eq250" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = cc * (1 - exp(-k1 * (xx - T1))) * (1 - exp(k2 * (xx - T2))),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
k1 = slider(0, 10, step = 0.0001, initial = 1),
k2 = slider(0, 10, step = 0.0001, initial = 1),
T1 = slider(0, 20, step = 0.0001, initial = 15),
T2 = slider(0, 100, step = 0.0001, initial = 35)
)
},
"eq260" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = phi * (exp(bb * (xx - Tb)) - ((Tm - xx)/(Tm - Tb)) * exp(-bb * (xx - Tb) / deltab) - ((xx - Tb)/(Tm - Tb)) * exp(bb * (Tm - Tb) - (Tm - xx)/deltam)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
phi = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tb = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tm = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE)),
deltab = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 11], na.rm = TRUE)),
deltam = slider(0, 10, step = 0.0001, initial = mean(eq$startVal[, 12], na.rm = TRUE))
)
},
"eq270" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (sqrt(cc) * k1 * (xx - T1) * (1 - exp(k2 * (xx - T2))))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
k1 = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(0, 100, step = 0.0001, initial = 10),
k2 = slider(0, 1, step = 0.0001, initial = 0.5),
T2 = slider(0, 100, step = 0.0001, initial = 30)
)
},
"eq280" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (2 * (xx - Tmin)^aa * (Topt - Tmin)^aa - (xx - Tmin)^(2 * aa)) / ((Topt - Tmin)^(2 * aa)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
Tmin = slider(0, 20, step = 0.0001, initial = 10),
aa = slider(0, 5, step = 0.0001, initial = 0.5),
Topt = slider(0, 100, step = 0.0001, initial = 30)
)
},
"eq290" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (bb * (xx - Tb))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
bb = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
Tb = slider(-10, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE))
)
},
"eq300" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = cc * (xx - T1) * (1 - exp(k * (xx - T2))),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(-10, 20, step = 0.0001, initial = 5),
k = slider(0, 1, step = 0.0001, initial = 0.5),
T2 = slider(-10, 100, step = 0.0001, initial = 20)
)
},
"eq310" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = exp(mu) * (xx - Tb)^aa * (Tc - xx)^bb,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
mu = slider(-1, 1, step = 0.0001, initial = 0.5),
Tb = slider(-10, 20, step = 0.0001, initial = 10),
aa = slider(-1, 2, step = 0.0001, initial = 0.5),
Tc = slider(-10, 100, step = 0.0001, initial = 35),
bb = slider(-1, 1, step = 0.0001, initial = 0.5)
)
},
"eq320" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa + bb * xx + cc * exp(xx) + dd * exp(-xx),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(-1, 1, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(-1, 1, step = 0.0000001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(-500000, 0, step = 100, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq330" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = 1/( (1 + exp((cc/1.987) * ((1/dd) - (1/(xx + 273.16))) )) / (aa*(xx + 273.16)/298.15*exp( (bb/1.987)*((1/298.15) - 1/(xx + 273.16)) ) ) ),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 1, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 50000, step = 10, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
cc = slider(0, 500000, step = 10, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
dd = slider(0, 1000, step = 1, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq340" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = aa * (xx - Tmin) - (bb * exp(xx - Tm)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
aa = slider(0, 0.6, step = 0.0001, initial = mean(eq$startVal[, 7], na.rm = TRUE)),
bb = slider(0, 20, step = 0.0001, initial = mean(eq$startVal[, 8], na.rm = TRUE)),
Tm = slider(0, 100, step = 0.0001, initial = mean(eq$startVal[, 9], na.rm = TRUE)),
Tmin = slider(-10, 20, step = 0.0001, initial = mean(eq$startVal[, 10], na.rm = TRUE))
)
},
"eq350" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = rm * (T2 - xx)/(T2 - Tm) * ((xx - T1)/(Tm - T1))^((Tm - T1)/(T2 - Tm)),
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
rm = slider(0, 1, step = 0.0001, initial = 0.5),
T1 = slider(0, 50, step = 0.0001, initial = 5),
T2 = slider(0, 50, step = 0.0001, initial = 35),
Tm = slider(0, 50, step = 0.0001, initial = 20)
)
},
"eq360" = {
manipulate(
{
plot(x = temp, y = devRate, xlab = "Temperature", ylab = "Development rate",
ylim = c(0, defYlim),
lwd = 2, pch = 3)
xx <- seq(from = min(temp, na.rm = TRUE) - 2, to = max(temp, na.rm = TRUE) + 2, by = 0.1)
points(x = xx, y = (cc * (xx - T1) * (1 - exp(k * (xx - T2))))^2,
type = 'l', lwd = 3)
},
defYlim = slider(0, 10, step = 0.0001, initial = 1),
cc = slider(0, 1, step = 0.0001, initial = 0.05),
T1 = slider(0, 50, step = 0.0001, initial = 5),
T2 = slider(0, 50, step = 0.0001, initial = 35),
k = slider(0, 5, step = 0.0001, initial = 0.05)
)
},
{
# otherwise nothing
}
)
} else {
stop("To use this functionality, you need the package: manipulate")
}
}
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