rTPC and nls.multstart: a new pipeline to fit thermal performance curves in R.

Padfield, D.; O'Sullivan, H.; Pawar, S.

doi:10.1101/2020.12.16.423089

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bioRxiv · 10.1101/2020.12.16.423089

rTPC and nls.multstart: a new pipeline to fit thermal performance curves in R.

Padfield, D.·O'Sullivan, H.·Pawar, S.

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Abstract

O_LIThe quantification of thermal performance curves (TPCs) for biological rates has many applications to problems such as predicting species responses to climate change. There is currently no widely used open-source pipeline to fit mathematical TPC models to data, which limits the transparency and reproducibility of the curve fitting process underlying applications of TPCs. C_LIO_LIWe present a new pipeline in R that currently allows for reproducible fitting of 24 different TPC models using non-linear least squares (NLLS) regression. The pipeline consists of two packages - rTPC and nls. multstart - that allow multiple start values for NLLS fitting and provides helper functions for setting start parameters. This pipeline overcomes previous problems that have made NLLS fitting and estimation of key parameters difficult or unreliable. C_LIO_LIWe demonstrate how rTPC and nls.multstart can be combined with other packages in R to robustly and reproducibly fit multiple models to multiple TPC datasets at once. In addition, we show how model selection or averaging, weighted model fitting, and bootstrapping can easily be implemented within the pipeline. C_LIO_LIThis new pipeline provides a flexible and reproducible approach that makes the challenging task of fitting multiple TPC models to data accessible to a wide range of users. C_LI

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Padfield, D., O'Sullivan, H., Pawar, S.. 2020-12-16. rTPC and nls.multstart: a new pipeline to fit thermal performance curves in R.. https://doi.org/10.1101/2020.12.16.423089

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