pawar_2018 {rTPC} | R Documentation |
Pawar model for fitting thermal performance curves
Description
Pawar model for fitting thermal performance curves
Usage
pawar_2018(temp, r_tref, e, eh, topt, tref)
Arguments
temp |
temperature in degrees centigrade |
r_tref |
rate at the standardised temperature, tref |
e |
activation energy (eV) |
eh |
high temperature de-activation energy (eV) |
topt |
optimum temperature (ºC) |
tref |
standardisation temperature in degrees centigrade. Temperature at which rates are not inactivated by high temperatures |
Details
This model is a modified version of sharpeschoolhigh_1981
that explicitly models the optimum temperature.
Equation:
rate= \frac{r_{tref} \cdot exp^{\frac{-e}{k} (\frac{1}{temp + 273.15}-\frac{1}{t_{ref} + 273.15})}}{1 + (\frac{e}{eh - e}) \cdot exp^{\frac{e_h}{k}(\frac{1}{t_opt + 273.15}-\frac{1}{temp + 273.15})}}
where k
is Boltzmann's constant with a value of 8.62e-05.
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.
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.
Author(s)
Daniel Padfield
References
Kontopoulos, Dimitrios - Georgios, Bernardo García-Carreras, Sofía Sal, Thomas P. Smith, and Samraat Pawar. Use and Misuse of Temperature Normalisation in Meta-Analyses of Thermal Responses of Biological Traits. PeerJ. 6 (2018),
Examples
# load in ggplot
library(ggplot2)
library(nls.multstart)
# 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 = 'pawar_2018')
# fit model
mod <- nls_multstart(rate~pawar_2018(temp = temp, r_tref, e, eh, topt, tref = 20),
data = d,
iter = c(3,3,3,3),
start_lower = start_vals - 10,
start_upper = start_vals + 10,
lower = get_lower_lims(d$temp, d$rate, model_name = 'pawar_2018'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'pawar_2018'),
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()