atkin_2005: Atkin model for fitting thermal performance curves

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

Atkin model for fitting thermal performance curves

Description

Atkin model for fitting thermal performance curves

Usage

atkin_2005(temp, r0, a, b)

Arguments

temp	temperature in degrees centigrade
r0	scaling parameter, the minimum trait value
a	arbitrary scaling parameter
b	arbitrary scaling parameter

Details

Equation:

rate = B_0 \cdot (a - b \cdot T)^{\frac{T}{10}}

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.

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)

Francis Windram

References

Atkin, OK, Bruhn D, Tjoelker MG. Response of Plant Respiration to Changes in Temperature: Mechanisms and Consequences of Variations in Q10 Values and Acclimation. In Plant Respiration. 2005.

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 = 'atkin_2005')
# fit model
mod <- nls.multstart::nls_multstart(rate~atkin_2005(temp = temp, r0, a, b),
data = d,
iter = 200,
start_lower = start_vals - 10,
start_upper = start_vals + 10,
lower = get_lower_lims(d$temp, d$rate, model_name = 'atkin_2005'),
upper = get_upper_lims(d$temp, d$rate, model_name = 'atkin_2005'),
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 Feb. 21, 2025, 5:30 a.m.