ratkowsky_1983: Ratkowsky model for fitting thermal performance curves

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

Ratkowsky model for fitting thermal performance curves

Description

Ratkowsky model for fitting thermal performance curves

Usage

ratkowsky_1983(temp, tmin, tmax, a, b)

Arguments

temp	temperature in degrees centigrade
tmin	low temperature (ºC) at which rates become negative
tmax	high temperature (ºC) at which rates become negative
a	parameter defined as sqrt(rate)/(temp - tmin)
b	empirical parameter needed to fit the data for temperatures beyond the optimum temperature

Details

Equation:

rate = (a \cdot (temp-t_{min}))^2 \cdot (1-exp(b \cdot (temp-t_{max})))^2

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

Ratkowsky, D.A., Lowry, R.K., McMeekin, T.A., Stokes, A.N., Chandler, R.E., Model for bacterial growth rate throughout the entire biokinetic temperature range. J. Bacteriol. 154: 1222–1226 (1983)

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 = 'ratkowsky_1983')
# fit model
mod <- nls.multstart::nls_multstart(rate~ratkowsky_1983(temp = temp, tmin, tmax, a, b),
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 = 'ratkowsky_1983'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'ratkowsky_1983'),
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 Jan. 17, 2024, 5:33 a.m.