Package: rTPC 1.0.7

rTPC: Fitting and Analysing Thermal Performance Curves

Helps to fit thermal performance curves (TPCs). 'rTPC' contains 26 model formulations previously used to fit TPCs and has helper functions to set sensible start parameters, upper and lower parameter limits and estimate parameters useful in downstream analyses, such as cardinal temperatures, maximum rate and optimum temperature. See Padfield et al. (2021) <doi:10.1111/2041-210X.13585>.

Authors:Daniel Padfield [aut, cre], Hannah O'Sullivan [aut], Francis Windram [aut]

rTPC_1.0.7.tar.gz
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rTPC_1.0.7.tgz(r-4.5-any)rTPC_1.0.7.tgz(r-4.4-any)rTPC_1.0.7.tgz(r-4.3-any)
rTPC_1.0.7.tar.gz(r-4.5-noble)rTPC_1.0.7.tar.gz(r-4.4-noble)
rTPC_1.0.7.tgz(r-4.4-emscripten)rTPC_1.0.7.tgz(r-4.3-emscripten)
rTPC.pdf |rTPC.html✨
rTPC/json (API)
NEWS

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

Bug tracker:https://github.com/padpadpadpad/rtpc/issues

Pkgdown site:https://padpadpadpad.github.io

Datasets:
  • bacteria_tpc - Example thermal performance curves of bacterial growth
  • chlorella_tpc - Example metabolic thermal performance curves

On CRAN:

Conda:

9.10 score 25 stars 267 scripts 222 downloads 67 exports 2 dependencies

Last updated 1 days agofrom:6197191d1b. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-winNOTEMar 31 2025
R-4.5-macNOTEMar 31 2025
R-4.5-linuxNOTEMar 31 2025
R-4.4-winNOTEMar 31 2025
R-4.4-macNOTEMar 31 2025
R-4.4-linuxNOTEMar 31 2025
R-4.3-winNOTEMar 31 2025
R-4.3-macNOTEMar 31 2025

Exports:analytiskontodimas_2004ashrafi1_2018ashrafi2_2018ashrafi3_2018ashrafi4_2018ashrafi5_2018atkin_2005beta_2012betatypesimplified_2008boatman_2017briere1_1999briere1simplified_1999briere2_1999briere2simplified_1999briereextended_2021briereextendedsimplified_2021calc_paramsdelong_2017deutsch_2008eubank_1973flextpc_2024flinn_1991gaussian_1987gaussianmodified_2006get_breadthget_ctmaxget_ctminget_eget_ehget_lower_limsget_model_namesget_q10get_rmaxget_skewnessget_start_valsget_thermalsafetymarginget_thermaltoleranceget_toptget_upper_limshinshelwood_1947janisch1_1925janisch2_1925joehnk_2008johnsonlewin_1946kamykowski_1985lactin2_1995lobry_1991lrf_1991mitchell_2009modifiedgaussian_2006oneill_1972pawar_2018quadratic_2008ratkowsky_1983rezende_2019rosso_1993sharpeschoolfull_1981sharpeschoolhigh_1981sharpeschoollow_1981spain_1982stinner_1974taylorsexton_1972thomas_2012thomas_2017tomlinsonphillips_2015warrendreyer_2006weibull_1995

Dependencies:clirlang

Adding Models to rTPC

Rendered fromadding_models.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2025-02-12
Started: 2025-01-15

Bootstrapping many curves using rTPC

Daniel Padfield

Rendered frombootstrapping_many_curves.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2025-02-03
Started: 2021-07-29

Bootstrapping using rTPC

Daniel Padfield

Rendered frombootstrapping_models.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2025-02-03
Started: 2020-06-16

Bootstrapping with weights using rTPC

Daniel Padfield

Rendered fromweighted_bootstrapping.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2025-02-03
Started: 2020-07-24

Fitting many curves using rTPC

Daniel Padfield

Rendered fromfit_many_curves.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2023-08-13
Started: 2020-06-12

Fitting many models with rTPC

Daniel Padfield

Rendered fromfit_many_models.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2025-02-20
Started: 2020-06-10

Introduction to rTPC

Daniel Padfield

Rendered fromrTPC.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2024-12-15
Started: 2020-06-10

Model selection and model averaging with rTPC

Daniel Padfield

Rendered frommodel_averaging_selection.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2020-09-18
Started: 2020-06-10

Model weighting with rTPC

Daniel Padfield

Rendered frommodel_weighting.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2024-08-27
Started: 2020-06-12

Readme and manuals

Help Manual

Help pageTopics
Analytis-Kontodimas model for fitting thermal performance curvesanalytiskontodimas_2004
Ashrafi I model for fitting thermal performance curvesashrafi1_2018
Ashrafi II model for fitting thermal performance curvesashrafi2_2018
Ashrafi III model for fitting thermal performance curvesashrafi3_2018
Ashrafi IV model for fitting thermal performance curvesashrafi4_2018
Ashrafi V model for fitting thermal performance curvesashrafi5_2018
Atkin model for fitting thermal performance curvesatkin_2005
Example thermal performance curves of bacterial growthbacteria_tpc
Beta model for fitting thermal performance curvesbeta_2012
Simplified Beta-type model for fitting thermal performance curvesbetatypesimplified_2008
Boatman model for fitting thermal performance curvesboatman_2017
Brière I model for fitting thermal performance curvesbriere1_1999
Simplified Brière I model for fitting thermal performance curvesbriere1simplified_1999
Brière II model for fitting thermal performance curvesbriere2_1999
Simplified Brière II model for fitting thermal performance curvesbriere2simplified_1999
Extended Brière model for fitting thermal performance curvesbriereextended_2021
Simplified Extended Brière model for fitting thermal performance curvesbriereextendedsimplified_2021
Calculate extra parameters of a thermal performance curvecalc_params
Example metabolic thermal performance curveschlorella_tpc
DeLong enzyme-assisted Arrhenius model for fitting thermal performance curvesdelong_2017
Modified deutsch model for fitting thermal performance curvesdeutsch_2008
Eubank model for fitting thermal performance curveseubank_1973
flexTPC model for fitting thermal performance curvesflextpc_2024
Flinn model for fitting thermal performance curvesflinn_1991
Gaussian model for fitting thermal performance curvesgaussian_1987
Modified gaussian model for fitting thermal performance curvesgaussianmodified_2006 modifiedgaussian_2006
Estimate thermal performance breadth of a thermal performance curveget_breadth
Estimate the critical thermal maximum of a thermal performance curveget_ctmax
Estimate the critical thermal minimum of a thermal performance curveget_ctmin
Estimate the activation energy of a thermal performance curveget_e
Estimate the deactivation energy of a thermal performance curveget_eh
Set broad lower limits on parameter valuesget_lower_lims
Lists or searches the models available in rTPCget_model_names
Estimate the q10 value of a thermal performance curveget_q10
Estimate maximum rate of a thermal performance curveget_rmax
Estimates skewness of a thermal performance curveget_skewness
Estimate start values for TPC fittingget_start_vals
Estimate thermal safety margin of a thermal performance curveget_thermalsafetymargin
Estimate thermal tolerance of a thermal performance curveget_thermaltolerance
Estimate optimum temperature of a thermal performance curveget_topt
Set broad upper limits on parameter valuesget_upper_lims
Hinshelwood model for fitting thermal performance curveshinshelwood_1947
Janisch I model for fitting thermal performance curvesjanisch1_1925
Janisch II model for fitting thermal performance curvesjanisch2_1925
Jöhnk model for fitting thermal performance curvesjoehnk_2008
Johnson-Lewin model for fitting thermal performance curvesjohnsonlewin_1946
Kamykowski model for fitting thermal performance curveskamykowski_1985
Lactin2 model for fitting thermal performance curveslactin2_1995
Lobry model for fitting thermal performance curveslobry_1991
Mitchell Angilletta model for fitting thermal performance curvesmitchell_2009
O'Neill model for fitting thermal performance curvesoneill_1972
Pawar model for fitting thermal performance curvespawar_2018
Quadratic model for fitting thermal performance curvesquadratic_2008
Ratkowsky model for fitting thermal performance curvesratkowsky_1983
Rezende model for fitting thermal performance curvesrezende_2019
Rosso model for fitting thermal performance curveslrf_1991 rosso_1993
Full Sharpe-Schoolfield model for fitting thermal performance curvessharpeschoolfull_1981
Sharpe-Schoolfield model (high temperature inactivation only) for fitting thermal performance curvessharpeschoolhigh_1981
Sharpe-Schoolfield model (low temperature inactivation only) for fitting thermal performance curvessharpeschoollow_1981
Spain model for fitting thermal performance curvesspain_1982
Stinner model for fitting thermal performance curvesstinner_1974
Taylor-Sexton model for fitting thermal performance curvestaylorsexton_1972
Thomas model (2012) for fitting thermal performance curvesthomas_2012
Thomas model (2017) for fitting thermal performance curvesthomas_2017
Tomlinson-Phillips model for fitting thermal performance curvestomlinsonphillips_2015
Warren-Dreyer model for fitting thermal performance curveswarrendreyer_2006
Weibull model for fitting thermal performance curvesweibull_1995