Package: devRate 0.2.6

devRate: 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) <doi:10.1111/2041-210X.12935>, Rebaudo and Rabhi (2018) <doi:10.1111/eea.12693>, and Regnier et al. (2021) <doi:10.1093/ee/nvab115>. An example can be found in Rebaudo et al. (2017) <doi:10.1007/s13355-017-0480-5>.

Authors:Francois Rebaudo [aut, cre], Baptiste Regnier [aut], Camila Benavides [ctb], Tanusson Selvarajah [ctb], Nicolas Bonnal [ctb], Badre Rabhi [ctb], Quentin Struelens [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
devRate/json (API)

# Install 'devRate' in R:
install.packages('devRate', repos = c('https://frareb.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/frareb/devrate/issues

Datasets:
  • analytis_77 - Analytis equation of development rate as a function of temperature.
  • bayoh_03 - Bayoh and Lindsay equation of development rate as a function of temperature.
  • beta_16 - Beta2 equation of development rate as a function of temperature.
  • beta_95 - Beta equation of development rate as a function of temperature.
  • bieri1_83 - Bieri equation 1 of development rate as a function of temperature.
  • briere1_99 - Briere et al equation 1 of development rate as a function of temperature.
  • briere2_99 - Briere et al equation 2 of development rate as a function of temperature.
  • campbell_74 - Campbell et al. equation of development rate as a function of temperature.
  • damos_08 - Simplified beta type equation of development rate as a function of temperature.
  • damos_11 - Inverse second-order polynomial equation of development rate as a function of temperature.
  • davidson_44 - Davidson equation of development rate as a function of temperature.
  • devRateEqList - The list of all available equations of development rate as a function of temperature.
  • devRateEqStartVal - Default starting values for each equation listed in the devRateEqList object.
  • exTropicalMoth - Tropical moth development rate at constant temperatures.
  • harcourtYee_82 - Harcourt and Yee equation of development rate as a function of temperature.
  • hilbertLogan_83 - Holling type III equation of development rate as a function of temperature.
  • janisch_32 - Janisch equation of development rate as a function of temperature (Analytis modification).
  • kontodimas_04 - Kontodimas et al. equation of development rate as a function of temperature.
  • lactin1_95 - Lactin et al. equation 1 of development rate as a function of temperature.
  • lactin2_95 - Lactin et al. equation 2 of development rate as a function of temperature.
  • lamb_92 - Lamb equation of development rate as a function of temperature.
  • logan10_76 - Logan et al. equation 10 of development rate as a function of temperature.
  • logan6_76 - Logan et al. equation 6 of development rate as a function of temperature.
  • perf2_11 - Performance-2 equation of development rate as a function of temperature.
  • poly2 - Second-order polynomial equation of development rate as a function of temperature.
  • poly4 - Fourth-order polynomial equation of development rate as a function of temperature.
  • ratkowsky_82 - Ratkowsky equation of development rate as a function of temperature (Shi modification).
  • ratkowsky_83 - Ratkowsky equation of development rate as a function of temperature (Shi 2016 modification).
  • regniere_12 - Regniere equation of development rate as a function of temperature.
  • rootsq_82 - Root square equation of development rate as a function of temperature.
  • schoolfield_81 - Schoolfield et al. equation of development rate as a function of temperature.
  • schoolfieldHigh_81 - Schoolfield et al. equation of development rate as a function of temperature for intermediate to high temperatures only.
  • schoolfieldLow_81 - Schoolfield et al. equation of development rate as a function of temperature for intermediate to low temperatures only.
  • sharpeDeMichele_77 - Sharpe and DeMichele equation of development rate as a function of temperature.
  • shi_11 - Shi equation of development rate as a function of temperature.
  • stinner_74 - Stinner et al equation of development rate as a function of temperature.
  • taylor_81 - Taylor equation of development rate as a function of temperature.
  • wagner_88 - Hagstrum et Milliken equation of development rate as a function of temperature retrieved from Wagner 1984.
  • wang_82 - Wang et al. equation of development rate as a function of temperature.
  • wangengel_98 - Wang and Engel equation of development rate as a function of temperature.

On CRAN:

Conda:

5.66 score 4 stars 16 scripts 214 downloads 3 mentions 28 exports 0 dependencies

Last updated from:944917b7c8. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK137
source / vignettesOK242
linux-release-x86_64ERROR111
macos-release-arm64OK150
macos-oldrel-arm64OK117
windows-develOK109
windows-releaseOK135
windows-oldrelOK99
wasm-releaseOK332

Exports:devRateFinddevRateIBMdevRateIBMdataBasedevRateIBMgendevRateIBMparamdevRateIBMPlotdevRateInfodevRateMapdevRateModeldevRateModelAlldevRatePlotdevRatePlotInfodevRatePrintdevRateQlBiodevRateQlStatdRGetMetricsdRGetMetricsInfoha_ahmad2024_lsha_bartekova2006ha_foley1981ha_jallow2001ha_kay1981_lsha_kay1981_nlsha_mironidis2008_lsha_mironidis2008_nlsha_noorulane2018_lsha_noorulane2018_nlsha_qureshi1999_ls

Dependencies:

Using the devRate package to simulate the phenology of Helicoverpa armigera
1. Models published in the literature | 2. Simulating phenology | 2.1. Temperature time series | 2.2. Model selection and computation | 2.2.1. Simulation using a single model | 2.2.2. Simulation using different models | 2.3. Simulation results and comparison | Legal information
Rendered fromhelicoverpa_armigera.Rmdusingknitr::rmarkdown

Last update: 2025-10-09
Started: 2025-07-07

Using devRate package to fit development rate models to an empirical dataset
Organizing the dataset | Finding models in the literature | Fitting models to empirical datasets | Models comparison | Forecasting phenologies from empirical temperature
Rendered fromquickUserGuide.Rmdusingknitr::rmarkdown

Last update: 2020-06-09
Started: 2017-11-02

Guía metodológica para el uso del paquete R devRate
Recordatorios sobre biología de insectos | Datos del laboratorio | Seleccionar un modelo y ajustarlo | El modelo lineal | Los modelos no lineales | Construir modelos fenológicos | Límites | Conclusión
Rendered fromguiaDelUsuario.Rmdusingknitr::rmarkdown

Last update: 2020-06-09
Started: 2018-04-30

Model evaluation
Nonlinear models | Datasets | Fitting the six models to the eight empirical datasets | [1] Briere-1 model | [2] Briere-2 model | [3] Lactin model | [4] Performance-2 Model | [5] Beta model | [6] Ratkowsky model | Organizing models' results | [1] RSS | [2] R squared | [3] R squared adjusted | [4] RMSE | [5] AIC corrected | [6] AIC | Visualization | Conclusion
Rendered frommodelEvaluation.Rmdusingknitr::rmarkdown

Last update: 2020-05-19
Started: 2017-11-02

Readme and manuals

Help Manual

Help pageTopics
Analytis equation of development rate as a function of temperature.analytis_77
Bayoh and Lindsay equation of development rate as a function of temperature.bayoh_03
Beta2 equation of development rate as a function of temperature.beta_16
Beta equation of development rate as a function of temperature.beta_95
Bieri equation 1 of development rate as a function of temperature.bieri1_83
Briere et al equation 1 of development rate as a function of temperature.briere1_99
Briere et al equation 2 of development rate as a function of temperature.briere2_99
Campbell et al. equation of development rate as a function of temperature.campbell_74
Simplified beta type equation of development rate as a function of temperature.damos_08
Inverse second-order polynomial equation of development rate as a function of temperature.damos_11
Davidson equation of development rate as a function of temperature.davidson_44
devRate: A package to quantify the relationship between development rate and temperature in ectotherms.devRate-package devRate
The list of all available equations of development rate as a function of temperature.devRateEqList
Default starting values for each equation listed in the devRateEqList object.devRateEqStartVal
Find models for speciesdevRateFind
Forecast ectotherm phenology as a function of temperature and development rate modelsdevRateIBM
Forecast ectotherm phenology as a function of temperature and development rate models available in the package databasedevRateIBMdataBase
Number of generationsdevRateIBMgen
Forecast ectotherm phenology as a function of temperature and development rate models using known parametersdevRateIBMparam
Plot phenology tabledevRateIBMPlot
Display information about an equationdevRateInfo
Predict development rate from a matrix of temperaturesdevRateMap
Compute non-linear regressiondevRateModel
Fitting all models listed in devRateEqList to a development rate datasetdevRateModelAll
Plot the empirical points and the regressiondevRatePlot
Plot thermal performance curves from the literaturedevRatePlotInfo
Report model output from the NLS fitdevRatePrint
Biological likelihood of nls fitsdevRateQlBio
Statistical indices of the nls goodness-of-fitdevRateQlStat
Life traits from Thermal Performance CurvedRGetMetrics
Life traits from the ectotherm databasedRGetMetricsInfo
Tropical moth development rate at constant temperatures.exTropicalMoth
Ahmad linear thermal performance curve for the development of Helicoverpa armigeraha_ahmad2024_ls
Bartekova and Praslicka linear thermal performance curve for the developmentof Helicoverpa armigeraha_bartekova2006
Foley linear thermal performance curve for the post-diapausing and non-diapausing pupae development of Helicoverpa armigeraha_foley1981
Jallow and Matsumura linear thermal performance curve for the development of Helicoverpa armigeraha_jallow2001
Kay linear thermal performance curve for the egg development of Helicoverpa armigeraha_kay1981_ls
Kay non-linear Davidson thermal performance curve for the egg development of Helicoverpa armigeraha_kay1981_nls
Mironidis and Savopoulou-Soultani linear thermal performance curve for the development of Helicoverpa armigeraha_mironidis2008_ls
Mironidis and Savopoulou-Soultani non-linear Lactin-2 thermal performance curve for the development of Helicoverpa armigeraha_mironidis2008_nls
Noor-ul-Ane et al. linear thermal performance curve for the development of Helicoverpa armigeraha_noorulane2018_ls
Noor-ul-Ane et al. non-linear thermal performance curve for the development of Helicoverpa armigeraha_noorulane2018_nls
Qureshi et al. linear thermal performance curve for the development of Helicoverpa armigeraha_qureshi1999_ls
Harcourt and Yee equation of development rate as a function of temperature.harcourtYee_82
Holling type III equation of development rate as a function of temperature.hilbertLogan_83
Janisch equation of development rate as a function of temperature (Analytis modification).janisch_32
Kontodimas et al. equation of development rate as a function of temperature.kontodimas_04
Lactin et al. equation 1 of development rate as a function of temperature.lactin1_95
Lactin et al. equation 2 of development rate as a function of temperature.lactin2_95
Lamb equation of development rate as a function of temperature.lamb_92
Logan et al. equation 10 of development rate as a function of temperature.logan10_76
Logan et al. equation 6 of development rate as a function of temperature.logan6_76
Performance-2 equation of development rate as a function of temperature.perf2_11
Second-order polynomial equation of development rate as a function of temperature.poly2
Fourth-order polynomial equation of development rate as a function of temperature.poly4
Ratkowsky equation of development rate as a function of temperature (Shi modification).ratkowsky_82
Ratkowsky equation of development rate as a function of temperature (Shi 2016 modification).ratkowsky_83
Regniere equation of development rate as a function of temperature.regniere_12
Root square equation of development rate as a function of temperature.rootsq_82
Schoolfield et al. equation of development rate as a function of temperature.schoolfield_81
Schoolfield et al. equation of development rate as a function of temperature for intermediate to high temperatures only.schoolfieldHigh_81
Schoolfield et al. equation of development rate as a function of temperature for intermediate to low temperatures only.schoolfieldLow_81
Sharpe and DeMichele equation of development rate as a function of temperature.sharpeDeMichele_77
Shi equation of development rate as a function of temperature.shi_11
Stinner et al equation of development rate as a function of temperature.stinner_74
Taylor equation of development rate as a function of temperature.taylor_81
Hagstrum et Milliken equation of development rate as a function of temperature retrieved from Wagner 1984.wagner_88
Wang et al. equation of development rate as a function of temperature.wang_82
Wang and Engel equation of development rate as a function of temperature.wangengel_98