Package: growthrates 0.8.5
growthrates: Estimate Growth Rates from Experimental Data
A collection of methods to determine growth rates from experimental data, in particular from batch experiments and plate reader trials.
Authors:
growthrates_0.8.5.tar.gz
growthrates_0.8.5.zip(r-4.5)growthrates_0.8.5.zip(r-4.4)growthrates_0.8.5.zip(r-4.3)
growthrates_0.8.5.tgz(r-4.4-x86_64)growthrates_0.8.5.tgz(r-4.4-arm64)growthrates_0.8.5.tgz(r-4.3-x86_64)growthrates_0.8.5.tgz(r-4.3-arm64)
growthrates_0.8.5.tar.gz(r-4.5-noble)growthrates_0.8.5.tar.gz(r-4.4-noble)
growthrates_0.8.5.tgz(r-4.4-emscripten)growthrates_0.8.5.tgz(r-4.3-emscripten)
growthrates.pdf |growthrates.html✨
growthrates/json (API)
| # Install 'growthrates' in R: |
| install.packages('growthrates', repos = c('https://tpetzoldt.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tpetzoldt/growthrates/issues
- antibiotic - Plate Reader Data of Bacterial Growth
- bactgrowth - Plate Reader Data of Bacterial Growth
Last updated 1 years agofrom:c22e479899. Checks:OK: 4 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 08 2024 |
| R-4.5-win-x86_64 | NOTE | Sep 08 2024 |
| R-4.5-linux-x86_64 | NOTE | Sep 08 2024 |
| R-4.4-win-x86_64 | NOTE | Sep 08 2024 |
| R-4.4-mac-x86_64 | NOTE | Sep 08 2024 |
| R-4.4-mac-aarch64 | NOTE | Sep 08 2024 |
| R-4.3-win-x86_64 | OK | Sep 08 2024 |
| R-4.3-mac-x86_64 | OK | Sep 08 2024 |
| R-4.3-mac-aarch64 | OK | Sep 08 2024 |
Exports:all_easylinearall_growthmodelsall_splinescoefcostdeviancedf.residualextcoef_logisticfit_easylinearfit_growthmodelfit_splinegrow_baranyigrow_exponentialgrow_genlogisticgrow_gompertzgrow_gompertz2grow_gompertz3grow_huanggrow_logisticgrow_richardsgrow_twostepgrowthmodellineslm_parmslm_windowmultisplitobsode_genlogisticode_twostepparse_formulaparse_formula_nonlinplotpredictresidualsresultsrsquaredsummary
Dependencies:codadeSolveFMElatticeMASSminpack.lmminqaRcpprootSolve
Estimation of Growth Rates with Package growthrates, Part 1: Introduction
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Sep 08 2024.Last update: 2023-09-19
Started: 2015-08-07
Estimation of Growth Rates with Package growthrates, Part 2: User-defined Growth Models
Rendered fromUser_models.Rmdusingknitr::rmarkdownon Sep 08 2024.Last update: 2022-08-12
Started: 2019-02-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate Growth Rates from Experimental Data | growthrates-package growthrates |
| Extract or Replace Parts of a 'multiple_fits' Object | [,multiple_fits,ANY,missing-method [[,multiple_fits,ANY,missing-method |
| Easy Growth Rates Fit to data Frame | all_easylinear all_easylinear.data.frame all_easylinear.formula |
| Fit Nonlinear Growth Models to Data Frame | all_growthmodels all_growthmodels.formula all_growthmodels.function |
| Fit Exponential Growth Model with Smoothing Spline | all_splines all_splines.data.frame all_splines.formula |
| Plate Reader Data of Bacterial Growth | antibiotic |
| Plate Reader Data of Bacterial Growth | bactgrowth |
| Extended Set of Coefficients of a Logistic Growth Model | extcoef_logistic |
| Fit Exponential Growth Model with a Heuristic Linear Method | fit_easylinear |
| Fit Nonlinear Parametric Growth Model | fit_growthmodel |
| Fit Exponential Growth Model with Smoothing Spline | fit_spline |
| Union Class of Growth Model or Function | function_growthmodel-class |
| The Baranyi and Roberts Growth Model | grow_baranyi |
| Exponential Growth Model | grow_exponential |
| Growth Model According to Gompertz | grow_gompertz |
| Growth Model According to Gompertz | grow_gompertz2 grow_gompertz3 |
| Growth Model According to Huang | grow_huang |
| Logistic Growth Model | grow_logistic |
| Growth Model According to Richards | grow_richards |
| Create a User-defined Parametric Growth Model | functions growthmodel user-defined |
| Class of Growth Model Functions | growthmodel-class |
| S4 Classes of Package 'growthrates' | easylinear_fit-class growthrates_fit-class multiple_easylinear_fits-class multiple_fits multiple_fits-class multiple_nonlinear_fits-class multiple_smooth.spline_fits-class nonlinear_fit-class smooth.spline_fit-class |
| Union Class of Linear Model or NULL | lm_or_NULL-class |
| Get Names Attributes of Growth Models | names,multiple_fits-method names.growthmodel names<-,multiple_fits-method |
| Generalized Logistic Growth Model | grow_genlogistic ode_genlogistic |
| Twostep Growth Model | grow_twostep ode_twostep |
| Plot Model Fits | lines,easylinear_fit-method lines,nonlinear_fit-method plot plot,easylinear_fit,missing-method plot,multiple_fits,missing-method plot,nonlinear_fit,missing-method plot,smooth.spline_fit,missing-method |
| Model Predictions for 'growthrates' Fits | predict,easylinear_fit-method predict,growthrates_fit-method predict,multiple_fits-method predict,nonlinear_fit-method predict,smooth.spline_fit-method |
| Accessor Methods of Package 'growthrates'. | coef,easylinear_fit-method coef,growthrates_fit-method coef,multiple_fits-method coef,smooth.spline_fit-method deviance,growthrates_fit-method deviance,multiple_fits-method deviance,smooth.spline_fit-method df.residual,growthrates_fit-method df.residual,smooth.spline_fit-method obs,growthrates_fit-method residuals,growthrates_fit-method residuals,multiple_fits-method results,multiple_easylinear_fits-method results,multiple_fits-method rsquared,growthrates_fit-method rsquared,multiple_fits-method summary,growthrates_fit-method summary,multiple_fits-method summary,nonlinear_fit-method summary,smooth.spline_fit-method |
