deutsch_2008: Modified deutsch model for fitting thermal performance curves

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

Modified deutsch model for fitting thermal performance curves

Description

Modified deutsch model for fitting thermal performance curves

Usage

deutsch_2008(temp, rmax, topt, ctmax, a)

Arguments

temp	temperature in degrees centigrade
rmax	maximum rate at optimum temperature
topt	optimum temperature (ºC)
ctmax	critical thermal maximum (ºC)
a	related to the full curve width

Details

Equation:

\textrm{if} \quad temp < t_{opt}: rate = r_{max} \cdot exp^{-\bigg(\frac{temp-t_{opt}}{2a}\bigg)^2}

\textrm{if} \quad temp > t_{opt}: rate = r_{max} \cdot \left(1 - \bigg(\frac{temp - t_{opt}}{t_{opt} - ct_{max}}\bigg)^2\right)

Start values in get_start_vals are derived from the data.

Limits in get_lower_lims and get_upper_lims are based on extreme values that are unlikely to occur in ecological settings.

Value

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

Note

Generally we found this model easy to fit.

References

Deutsch, C. A., Tewksbury, J. J., Huey, R. B., Sheldon, K. S., Ghalambor, C. K., Haak, D. C., & Martin, P. R. Impacts of climate warming on terrestrial ectotherms across latitude. Proceedings of the National Academy of Sciences, 105(18), 6668-6672. (2008)

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 = 'deutsch_2008')
# fit model
mod <- nls.multstart::nls_multstart(rate~deutsch_2008(temp = temp, rmax, topt, ctmax, a),
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 = 'deutsch_2008'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'deutsch_2008'),
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()

padpadpadpad/rTPC documentation built on Jan. 17, 2024, 5:33 a.m.