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.

AuthorThomas Petzoldt
Date of publication2016-03-14 07:54:21
MaintainerThomas Petzoldt <thomas.petzoldt@tu-dresden.de>
LicenseGPL (>= 2)
Version0.6.5
https://github.com/tpetzoldt/growthrates

View on CRAN

Man pages

all_easylinear: Easy Growth Rates Fit to data Frame

all_growthmodels: Fit Nonlinear Growth Models to Data Frame

all_splines: Fit Exponential Growth Model with Smoothing Spline

bactgrowth: Plate Reader Data of Bacterial Growth

cost: Cost Function for Nonlinear Fits

extract: Extract or Replace Parts of a 'multiple_fits' Object

fit_easylinear: Fit Exponential Growth Model with a Heuristic Linear Method

fit_growthmodel: Fit Nonlinear Parametric Growth Model

fit_spline: Fit Exponential Growth Model with Smoothing Spline

function_growthmodel-class: Union Class of Growth Model or Function

generics: Additional Generic Functions

grow_baranyi: The Baranyi and Roberts Growth Model

grow_exponential: Exponential Growth Model

grow_genlogistic: Generalized Logistic Growth Model

grow_gompertz: Growth Model According to Gompertz

grow_huang: Growth Model According to Huang

grow_logistic: Logistic Growth Model

grow_richards: Growth Model According to Richards

growthmodel-class: Class of Growth Model Functions

growthmodel-constructor: Create a User-defined Parametric Growth Model

growthrates-classes: S4 Classes of Package 'growthrates'

growthrates-package: Estimate Growth Rates from Experimental Data

grow_twostep: Twostep Growth Model

lm_window: Fit Exponential Growth Model with a Heuristic Linear Method

methods: Accessor Methods of Package 'growthrates'.

multisplit: Split Data Frame into Multiple Groups

names: Get Names Attributes of Growth Models

parse_formula: Simple Formula Interface

parse_formula_nonlin: Simple Formula Interface for Grouped Nonlinear Functions

plot: Plot Model Fits

Functions

all_easylinear Man page
all_easylinear.data.frame Man page
all_easylinear.formula Man page
all_growthmodels Man page
all_growthmodels.formula Man page
all_growthmodels.function Man page
all_splines Man page
all_splines.data.frame Man page
all_splines.formula Man page
bactgrowth Man page
coef,easylinear_fit-method Man page
coef,growthrates_fit-method Man page
coef,multiple_fits-method Man page
coef,smooth.spline_fit-method Man page
cost Man page
deviance,growthrates_fit-method Man page
deviance,multiple_fits-method Man page
deviance,smooth.spline_fit-method Man page
df.residual,growthrates_fit-method Man page
df.residual,smooth.spline_fit-method Man page
easylinear_fit-class Man page
fit_easylinear Man page
fit_growthmodel Man page
fit_spline Man page
function_growthmodel-class Man page
functions Man page
grow_baranyi Man page
grow_exponential Man page
grow_genlogistic Man page
grow_gompertz Man page
grow_huang Man page
grow_logistic Man page
grow_richards Man page
growthmodel Man page
growthmodel-class Man page
growthrates Man page
growthrates_fit-class Man page
growthrates-package Man page
grow_twostep Man page
lines,easylinear_fit-method Man page
lines,nonlinear_fit-method Man page
lm_parms Man page
lm_window Man page
multiple_easylinear_fits-class Man page
multiple_fits Man page
[,multiple_fits,ANY,missing-method Man page
[[,multiple_fits,ANY,missing-method Man page
multiple_fits-class Man page
multiple_nonlinear_fits-class Man page
multiple_smooth.spline_fits-class Man page
multisplit Man page
multisplit,ANY,ANY-method Man page
multisplit,data.frame,character-method Man page
multisplit,data.frame,factor-method Man page
multisplit,data.frame,formula-method Man page
multisplit,data.frame,list-method Man page
names.growthmodel Man page
names<-,multiple_fits-method Man page
names,multiple_fits-method Man page
nonlinear_fit-class Man page
obs Man page
obs,growthrates_fit-method Man page
ode_genlogistic Man page
ode_twostep Man page
parse_formula Man page
parse_formula_nonlin Man page
plot Man page
plot,easylinear_fit,missing-method Man page
plot,multiple_fits,missing-method Man page
plot,nonlinear_fit,missing-method Man page
plot,smooth.spline_fit,missing-method Man page
residuals,growthrates_fit-method Man page
residuals,multiple_fits-method Man page
results Man page
results,multiple_easylinear_fits-method Man page
results,multiple_fits-method Man page
rsquared Man page
rsquared,growthrates_fit-method Man page
rsquared,multiple_fits-method Man page
smooth.spline_fit-class Man page
summary,growthrates_fit-method Man page
summary,multiple_fits-method Man page
summary,nonlinear_fit-method Man page
summary,smooth.spline_fit-method Man page
user-defined Man page

Files

growthrates
growthrates/inst
growthrates/inst/doc
growthrates/inst/doc/examples
growthrates/inst/doc/examples/example_growthmodel.R
growthrates/inst/doc/examples/import_grofit_data.R
growthrates/inst/doc/examples/benchmark_compiled_ode.R
growthrates/inst/doc/examples/example_huang_p_as_df.R
growthrates/inst/doc/examples/example_huang.R
growthrates/inst/doc/examples/example_user_defined_growthmodel.R
growthrates/inst/doc/examples/example_user_defined_ode_compiled.R
growthrates/inst/doc/examples/example_easylinear.R
growthrates/inst/doc/examples/example_spline.R
growthrates/inst/doc/examples/startvalue_heuristics.R
growthrates/inst/doc/examples/example_masking.R
growthrates/inst/doc/examples/example_baranyi.R
growthrates/inst/doc/examples/example_user_defined_ode_model.R
growthrates/inst/doc/Introduction.Rmd
growthrates/inst/doc/Introduction.R
growthrates/inst/doc/Introduction.pdf
growthrates/inst/doc/User_models.pdf
growthrates/inst/doc/User_models.R
growthrates/inst/doc/User_models.Rmd
growthrates/src
growthrates/src/twostep.c
growthrates/src/genlogistic.c
growthrates/NAMESPACE
growthrates/demo
growthrates/demo/growthrates.R
growthrates/demo/00Index
growthrates/data
growthrates/data/bactgrowth.txt.gz
growthrates/R
growthrates/R/grow_twostep.R growthrates/R/parse_formula.R growthrates/R/aac_classes.R growthrates/R/multisplit.R growthrates/R/fit_growthmodel.R growthrates/R/cost.R growthrates/R/all_growthmodels.R growthrates/R/plot.R growthrates/R/fit_spline.R growthrates/R/all_splines.R growthrates/R/growthrates-package.R growthrates/R/utilities.R growthrates/R/grow_logistic.R growthrates/R/methods.R growthrates/R/grow_gompertz.R growthrates/R/aab_growthmodel-constructor.R growthrates/R/grow_exponential.R growthrates/R/fit_easylinear.R growthrates/R/grow_genlogistic.R growthrates/R/grow_huang.R growthrates/R/extract.R growthrates/R/names.R growthrates/R/grow_baranyi.R growthrates/R/parse_formula_nonlin.R growthrates/R/all_easylinear.R growthrates/R/grow_richards.R growthrates/R/aad_set_generics.R growthrates/R/aaa_growthmodel-class.R growthrates/R/bactgrowth.R growthrates/R/lm_window.R
growthrates/vignettes
growthrates/vignettes/Introduction.Rmd
growthrates/vignettes/growthrates.bib
growthrates/vignettes/User_models.Rmd
growthrates/MD5
growthrates/build
growthrates/build/vignette.rds
growthrates/DESCRIPTION
growthrates/man
growthrates/man/fit_easylinear.Rd growthrates/man/all_easylinear.Rd growthrates/man/grow_genlogistic.Rd growthrates/man/names.Rd growthrates/man/growthmodel-class.Rd growthrates/man/cost.Rd growthrates/man/parse_formula.Rd growthrates/man/parse_formula_nonlin.Rd growthrates/man/all_splines.Rd growthrates/man/lm_window.Rd growthrates/man/all_growthmodels.Rd growthrates/man/fit_growthmodel.Rd growthrates/man/grow_twostep.Rd growthrates/man/growthrates-package.Rd growthrates/man/generics.Rd growthrates/man/function_growthmodel-class.Rd growthrates/man/fit_spline.Rd growthrates/man/growthmodel-constructor.Rd growthrates/man/growthrates-classes.Rd growthrates/man/grow_logistic.Rd growthrates/man/grow_baranyi.Rd growthrates/man/grow_richards.Rd growthrates/man/grow_exponential.Rd growthrates/man/multisplit.Rd growthrates/man/methods.Rd growthrates/man/bactgrowth.Rd growthrates/man/grow_gompertz.Rd growthrates/man/grow_huang.Rd growthrates/man/plot.Rd growthrates/man/extract.Rd

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