fit_devmodels: Fit Thermal Performance Curves

Description

Fit nonlinear regression models to data representing how development rate changes with temperature (known as Thermal Performance Curves), based on nls.multstart::nls_multstart() approach to development rate data across temperatures. The fitting procedure is built upon previous packages for starting values estimation, namely rTPC and devRate.

Usage

fit_devmodels(temp = NULL, dev_rate = NULL, model_name = NULL)

Value

A table in tibble format with estimates and standard errors for each parameter of the models specified by the user that have adequately converged. Models are sorted based on their Akaike Information Criterion (AIC) values, with the best fitting models shown first. Fitted models are also provided in list format in the model_list column and can be accessed using get_fitted_model() for for further inspection. It is important to consider ecological criteria alongside statistical information. For additional help in model selection, we recommend using plot_devmodels() and consulting relevant literature.

Arguments

temp: a vector of temperatures used in the experiment. It should have at least four different temperatures and must contain only numbers without any missing values.
dev_rate: a vector of estimated development rates corresponding to each temperature. These rates are calculated as the inverse of the number of days to complete the transition from the beginning of a certain life stage to the beginning of the following at each temperature. It must be numeric and of the same length as temp.
model_name: a string or a vector that specifies the model(s) to use for fitting the Thermal Performance Curves. Options include "all" or specific models listed in available_models. These models typically exhibit a common unimodal, left-skewed shape.

References

Angilletta, M.J., (2006). Estimating and comparing thermal performance curves. J. Therm. Biol. 31: 541-545. (for model selection in TPC framework)

Padfield, D., O'Sullivan, H. and Pawar, S. (2021). rTPC and nls.multstart: A new pipeline to fit thermal performance curves in R. Methods Ecol Evol. 12: 1138-1143.

Rebaudo, F., Struelens, Q. and Dangles, O. (2018). Modelling temperature-dependent development rate and phenology in arthropods: The devRate package for R. Methods Ecol Evol. 9: 1144-1150.

Satar, S. and Yokomi, R. (2002). Effect of temperature and host on development of Brachycaudus schwartzi (Homoptera: Aphididae). Ann. Entomol. Soc. Am. 95: 597-602.

Examples

Run this code

data("aphid")

fitted_tpcs <- fit_devmodels(temp = aphid$temperature,
                             dev_rate = aphid$rate_value,
                             model_name = c("lactin2", "briere2",
                                            "mod_weibull")
                             )
head(fitted_tpcs)