lactin2_1995 | R Documentation |
Lactin2 model for fitting thermal performance curves
lactin2_1995(temp, a, b, tmax, delta_t)
temp |
temperature in degrees centigrade |
a |
constant that determines the steepness of the rising portion of the curve |
b |
constant that determines the height of the overall curve |
tmax |
the temperature at which the curve begins to decelerate beyond the optimum (ºC) |
delta_t |
thermal safety margin (ºC) |
Equation:
rate= = exp^{a \cdot temp} - exp^{a \cdot t_{max} - \bigg(\frac{t_{max} - temp}{\delta _{t}}\bigg)} + b
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.
a numeric vector of rate values based on the temperatures and parameter values provided to the function
Generally we found this model easy to fit.
Lactin, D.J., Holliday, N.J., Johnson, D.L. & Craigen, R. Improved rate models of temperature-dependent development by arthropods. Environmental Entomology 24, 69-75 (1995)
# 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 = 'lactin2_1995')
# fit model
mod <- nls.multstart::nls_multstart(rate~lactin2_1995(temp = temp, a, b, tmax, delta_t),
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 = 'lactin2_1995'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'lactin2_1995'),
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()
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