tomlinsonphillips_2015: Tomlinson-Phillips model for fitting thermal performance...

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

Tomlinson-Phillips model for fitting thermal performance curves

Description

Tomlinson-Phillips model for fitting thermal performance curves

Usage

tomlinsonphillips_2015(temp, a, b, c)

Arguments

temp	temperature in degrees centigrade
a	parameter similar to R at Tmin
b	shape parameter indicating the slope of the upwards part of the curve
c	peak position parameter, similar to Topt

Details

Equation:

rate = a \cdot [\exp{(b \cdot T) - \exp{(T-c)}}]

Start values in get_start_vals are derived from the data or sensible values from the literature.

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.

Value

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

Note

Generally we found this model somewhat difficult to fit.

Author(s)

Francis Windram

References

Tomlinson, S. & Phillips, R. D. Differences in metabolic rate and evaporative water loss associated with sexual dimorphism in thynnine wasps. J. Insect Physiol. 78, 62–68 (2015).

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 = 'tomlinsonphillips_2015')
# fit model
mod <- nls.multstart::nls_multstart(rate~tomlinsonphillips_2015(temp = temp, a, b, c),
data = d,
iter = c(3,3,3),
start_lower = start_vals - 10,
start_upper = start_vals + 10,
lower = get_lower_lims(d$temp, d$rate, model_name = 'tomlinsonphillips_2015'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'tomlinsonphillips_2015'),
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 Feb. 21, 2025, 5:30 a.m.