Package: rTPC 1.0.6

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]

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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'))

Peer review:

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

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

On CRAN:

8.36 score 22 stars 217 scripts 209 downloads 43 exports 0 dependencies

Last updated 3 months agofrom:4f8c41521f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:ashrafi1_2018beta_2012boatman_2017briere2_1999calc_paramsdelong_2017deutsch_2008flinn_1991gaussian_1987get_breadthget_ctmaxget_ctminget_eget_ehget_lower_limsget_model_namesget_q10get_rmaxget_skewnessget_start_valsget_thermalsafetymarginget_thermaltoleranceget_toptget_upper_limshinshelwood_1947joehnk_2008johnsonlewin_1946kamykowski_1985lactin2_1995lrf_1991modifiedgaussian_2006oneill_1972pawar_2018quadratic_2008ratkowsky_1983rezende_2019sharpeschoolfull_1981sharpeschoolhigh_1981sharpeschoollow_1981spain_1982thomas_2012thomas_2017weibull_1995

Dependencies:

Bootstrapping many curves using rTPC

Daniel Padfield

Rendered frombootstrapping_many_curves.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-08-13
Started: 2021-07-29

Bootstrapping using rTPC

Daniel Padfield

Rendered frombootstrapping_models.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-08-13
Started: 2020-06-16

Bootstrapping with weights using rTPC

Daniel Padfield

Rendered fromweighted_bootstrapping.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-08-13
Started: 2020-07-24

Fitting many curves using rTPC

Daniel Padfield

Rendered fromfit_many_curves.Rmdusingknitr::rmarkdownon Oct 25 2024.

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

Fitting many models with rTPC

Daniel Padfield

Rendered fromfit_many_models.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-09-08
Started: 2020-06-10

Introduction to rTPC

Daniel Padfield

Rendered fromrTPC.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2021-12-03
Started: 2020-06-10

Model selection and model averaging with rTPC

Daniel Padfield

Rendered frommodel_averaging_selection.Rmdusingknitr::rmarkdownon Oct 25 2024.

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

Model weighting with rTPC

Daniel Padfield

Rendered frommodel_weighting.Rmdusingknitr::rmarkdownon Oct 25 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Ashrafi1 model for fitting thermal performance curvesashrafi1_2018
Example thermal performance curves of bacterial growthbacteria_tpc
Beta model for fitting thermal performance curvesbeta_2012
Boatman model for fitting thermal performance curvesboatman_2017
Briere2 model for fitting thermal performance curvesbriere2_1999
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
Flinn model for fitting thermal performance curvesflinn_1991
Gaussian model for fitting thermal performance curvesgaussian_1987
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 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
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-Rosso-Flandros (LRF) model for fitting thermal performance curveslrf_1991
Modified gaussian model for fitting thermal performance curvesmodifiedgaussian_2006
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
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
Thomas model (2012) for fitting thermal performance curvesthomas_2012
Thomas model (2017) for fitting thermal performance curvesthomas_2017
Weibull model for fitting thermal performance curvesweibull_1995