rTPC (version 1.0.4)

weibull_1995: Weibull model for fitting thermal performance curves

Description

Weibull model for fitting thermal performance curves

Usage

weibull_1995(temp, a, topt, b, c)

Value

a numeric vector of rate values based on the temperatures and parameter values provided to the function

Arguments

temp

temperature in degrees centigrade

a

scale the height of the curve

topt

optimum temperature

b

defines the breadth of the curve

c

defines the curve shape

Details

Equation: $$rate=a\cdot (\frac{c-1}{c}{)}^{\frac{1-c}{c}}(\frac{temp-t_{opt}}{b}+(\frac{c-1}{c}{)}^{\frac{1}{c}}{)}^{c-1}ex{p}^{-(\frac{temp-t_{opt}}{b}+(\frac{c-1}{c}{)}^{\frac{1}{c}}{)}^c}+\frac{c-1}{c}$$

Start values in get_start_vals are derived from the data.

Limits in get_lower_lims and get_upper_lims are derived from the data or based extreme values that are unlikely to occur in ecological settings.

References

Angilletta Jr, Michael J. Estimating and comparing thermal performance curves. Journal of Thermal Biology 31.7 (2006): 541-545.

Examples

# load in ggplot
library(ggplot2)

# subset for the first TPC curve
data('chlorella_tpc')
d <- subset(chlorella_tpc, curve_id == 1)

# get start values and fit model
start_vals <- get_start_vals(d$temp, d$rate, model_name = 'weibull_1995')
# fit model
mod <- nls.multstart::nls_multstart(rate~weibull_1995(temp = temp, a, topt, b, c),
data = d,
iter = c(4,4,4,4),
start_lower = start_vals - 10,
start_upper = start_vals + 10,
lower = get_lower_lims(d$temp, d$rate, model_name = 'weibull_1995'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'weibull_1995'),
supp_errors = 'Y',
convergence_count = FALSE)

# look at model fit
summary(mod)

# get predictions
preds <- data.frame(temp = seq(min(d$temp), max(d$temp), length.out = 100))
preds <- broom::augment(mod, newdata = preds)

# plot
ggplot(preds) +
geom_point(aes(temp, rate), d) +
geom_line(aes(temp, .fitted), col = 'blue') +
theme_bw()