flinn_1991 {rTPC} | R Documentation |
Flinn model for fitting thermal performance curves
Description
Flinn model for fitting thermal performance curves
Usage
flinn_1991(temp, a, b, c)
Arguments
temp |
temperature in degrees centigrade |
a |
parameter that controls the height of the curve |
b |
parameter that controls the slope of the initial increase of the curve |
c |
parameter that controls the position and steepness of the decline of the curve |
Details
Equation:
rate= \frac{1}{1+a+b \cdot temp+c \cdot temp^2}
Start values in get_start_vals
are derived from previous methods from 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
Flinn PW Temperature-dependent functional response of the parasitoid Cephalonomia waterstoni (Gahan) (Hymenoptera, Bethylidae) attacking rusty grain beetle larvae (Coleoptera, Cucujidae). Environmental Entomology, 20, 872–876, (1991)
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 = 'flinn_1991')
# fit model
mod <- nls.multstart::nls_multstart(rate~flinn_1991(temp = temp, a, b, c),
data = d,
iter = c(4,4,4),
start_lower = start_vals - 1,
start_upper = start_vals + 1,
lower = get_lower_lims(d$temp, d$rate, model_name = 'flinn_1991'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'flinn_1991'),
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()