rezende_2019 {rTPC} | R Documentation |
Rezende model for fitting thermal performance curves
Description
Rezende model for fitting thermal performance curves
Usage
rezende_2019(temp, q10, a, b, c)
Arguments
temp |
temperature in degrees centigrade |
q10 |
defines the fold change in performance as a result of increasing the temperature by 10 ºC |
a |
parameter describing shifts in rate |
b |
parameter threshold temperature (ºC) beyond which the downward curve starts |
c |
parameter controlling the rate of decline beyond the threshold temperature, b |
Details
Equation:
\textrm{if} \quad temp < b: rate = a \cdot 10 ^{\frac{\log_{10} (q_{10})}{(\frac{10}{temp})}}
\textrm{if} \quad temp > b: rate = a \cdot 10 ^{\frac{\log_{10} (q_{10})}{(\frac{10}{temp})}} \cdot \bigg(1-c \cdot (b-temp)^2 \bigg)
Start values in get_start_vals
are derived from the data and previous values in the literature.
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
Rezende, Enrico L., and Francisco Bozinovic. Thermal performance across levels of biological organization. Philosophical Transactions of the Royal Society B 374.1778 (2019): 20180549.
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 = 'rezende_2019')
# fit model
mod <- nls.multstart::nls_multstart(rate~rezende_2019(temp = temp, q10, a, 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 = 'rezende_2019'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'rezende_2019'),
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()