Quantify the Relationship Between Development Rate and Temperature in Ectotherms

A set of functions to quantify the relationship between development rate and temperature and to build phenological models. The package comprises a set of models and estimated parameters borrowed from a literature review in ectotherms. The methods and literature review are described in Rebaudo et al. (2018) and Rebaudo and Rabhi (2018) . An example can be found in Rebaudo et al. (2017) .


Purpose of the package

The devRate package allows quantifying the relationship between development rate and temperature in ectotherm organisms.

How to use the package

You can use the package:

  • to get development rate curves as a function of temperature for a specific organism (hundred of examples from the literature are included in the package);
  • to know which equations exists and which are most used in the literature; and
  • to relate development rate with temperature from your empirical data, using the equations from the package database.

Installation instructions

install.packages("devRate")

Overview

The devRate package provides three categories of functions:

  • to find development rate information about a specific organism (Order, Family, Genus, species)
  • to relate development rate and temperature; and
  • to plot your empirical datasets and the associated fitted model, and/or to plot development curves from the literature.

Author's affiliation

UMR EGCE, Univ. ParisSud, CNRS, IRD, Univ. ParisSaclay, Gif-sur-Yvette, France

To cite this package please use citation("devRate") and/or Rebaudo F, Struelens Q, Dangles O. Modelling temperature-dependent development rate and phenology in arthropods: The devRate package for r. Methods Ecol Evol. 2017;00:1-7. https://doi.org/10.1111/2041-210X.12935

News

devRate 0.1.6

  • fix bug in devRatePlotInfo for eq. with NA parameter values
  • fix bug in devRatePlotInfo for eq. briere2_99
  • README and devRate package info updated

devRate 0.1.5

  • main vignette improved
  • new sec01 vignette for model evaluation
  • CITATION file
  • BDD update: 37 models ; 2249 entries ; 799 species

devRate 0.1.4

  • fixed typos and misspellings in the documentation
  • vignette improved and output is generated automatically
  • devRateFind function returns number of parameters and enforce single value

devRate 0.1.3

  • typos and grammatical errors in manual fixed
  • example from the vignette included in the package
  • vignette with more information and interpretation
  • devRateFind function now returns a data.frame
  • new function to model phenology from the package database
  • BDD modif: refs with new column entries
  • BDD update: 35 models and 619 entries ; 138 species

devRate 0.1.2.

  • equations in latex in PDF manual using \eqn{latex}{ascii}
  • fixed some typos in manual
  • linear models with auto-starting values

devRate 0.1.1.

  • vignette improved
  • help page for function devRateMap improved
  • new devRatePrint function (custom output for nls object)
  • bug in phenological model corrected
  • Sharpe and DeMichele equation now in Celsius: transformed into Kelvins within the equation (cf. Sharpe and DeMichele 1977)
  • Structural equations of each regression model in the package manual
  • testing units using testthat package
  • BDD update: 35 models ; 543 entries ; 131 species

devRate 0.1.0.

  • Initial submission

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("devRate")

0.1.8 by Francois Rebaudo, 14 days ago


https://github.com/frareb/devRate/


Report a bug at https://github.com/frareb/devRate/issues


Browse source code at https://github.com/cran/devRate


Authors: Francois Rebaudo [aut, cre] (2016-2018), Camila Benavides [ctb] (M2 student; 2018), Tanusson Selvarajah [ctb] (L2 student; 2018), Nicolas Bonnal [ctb] (M1 student; 2018), Badre Rabhi [ctb] (L2 student; 2017), Quentin Struelens [ctb] (VIA; 2016)


Documentation:   PDF Manual  


GPL-2 license


Suggests knitr, rmarkdown, testthat


See at CRAN