growthrates: Estimate Growth Rates from Experimental Data
Version 0.6.5

A collection of methods to determine growth rates from experimental data, in particular from batch experiments and plate reader trials.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Petzoldt
Date of publication2016-03-14 07:54:21
MaintainerThomas Petzoldt <thomas.petzoldt@tu-dresden.de>
LicenseGPL (>= 2)
Version0.6.5
URL https://github.com/tpetzoldt/growthrates
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("growthrates")

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

[,multiple_fits,ANY,missing-method Man page
[[,multiple_fits,ANY,missing-method Man page
all_easylinear Man page Source code
all_easylinear.data.frame Man page Source code
all_easylinear.formula Man page Source code
all_growthmodels Man page Source code
all_growthmodels.formula Man page Source code
all_growthmodels.function Man page Source code
all_splines Man page Source code
all_splines.data.frame Man page Source code
all_splines.formula Man page Source code
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 Source code
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 Source code
fit_growthmodel Man page Source code
fit_spline Man page Source code
function_growthmodel-class Man page
functions Man page
grow_baranyi Man page Source code
grow_exponential Man page Source code
grow_genlogistic Man page Source code
grow_gompertz Man page Source code
grow_huang Man page Source code
grow_logistic Man page Source code
grow_richards Man page Source code
grow_twostep Man page Source code
growthmodel Man page Source code
growthmodel-class Man page
growthrates Man page
growthrates-package Man page
growthrates_fit-class Man page
is.numericOrNull Source code
lines,easylinear_fit-method Man page
lines,nonlinear_fit-method Man page
lm_parms Man page Source code
lm_window Man page Source code
multiple_easylinear_fits-class Man page
multiple_fits 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,multiple_fits-method Man page
names.growthmodel Man page Source code
names<-,multiple_fits-method Man page
nonlinear_fit-class Man page
obs Man page
obs,growthrates_fit-method Man page
ode_genlogistic Man page Source code
ode_twostep Man page Source code
parse_formula Man page Source code
parse_formula_nonlin Man page Source code
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
renameListElement Source code
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

inst
inst/doc
inst/doc/examples
inst/doc/examples/example_growthmodel.R
inst/doc/examples/import_grofit_data.R
inst/doc/examples/benchmark_compiled_ode.R
inst/doc/examples/example_huang_p_as_df.R
inst/doc/examples/example_huang.R
inst/doc/examples/example_user_defined_growthmodel.R
inst/doc/examples/example_user_defined_ode_compiled.R
inst/doc/examples/example_easylinear.R
inst/doc/examples/example_spline.R
inst/doc/examples/startvalue_heuristics.R
inst/doc/examples/example_masking.R
inst/doc/examples/example_baranyi.R
inst/doc/examples/example_user_defined_ode_model.R
inst/doc/Introduction.Rmd
inst/doc/Introduction.R
inst/doc/Introduction.pdf
inst/doc/User_models.pdf
inst/doc/User_models.R
inst/doc/User_models.Rmd
src
src/twostep.c
src/genlogistic.c
NAMESPACE
demo
demo/growthrates.R
demo/00Index
data
data/bactgrowth.txt.gz
R
R/grow_twostep.R
R/parse_formula.R
R/aac_classes.R
R/multisplit.R
R/fit_growthmodel.R
R/cost.R
R/all_growthmodels.R
R/plot.R
R/fit_spline.R
R/all_splines.R
R/growthrates-package.R
R/utilities.R
R/grow_logistic.R
R/methods.R
R/grow_gompertz.R
R/aab_growthmodel-constructor.R
R/grow_exponential.R
R/fit_easylinear.R
R/grow_genlogistic.R
R/grow_huang.R
R/extract.R
R/names.R
R/grow_baranyi.R
R/parse_formula_nonlin.R
R/all_easylinear.R
R/grow_richards.R
R/aad_set_generics.R
R/aaa_growthmodel-class.R
R/bactgrowth.R
R/lm_window.R
vignettes
vignettes/Introduction.Rmd
vignettes/growthrates.bib
vignettes/User_models.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/fit_easylinear.Rd
man/all_easylinear.Rd
man/grow_genlogistic.Rd
man/names.Rd
man/growthmodel-class.Rd
man/cost.Rd
man/parse_formula.Rd
man/parse_formula_nonlin.Rd
man/all_splines.Rd
man/lm_window.Rd
man/all_growthmodels.Rd
man/fit_growthmodel.Rd
man/grow_twostep.Rd
man/growthrates-package.Rd
man/generics.Rd
man/function_growthmodel-class.Rd
man/fit_spline.Rd
man/growthmodel-constructor.Rd
man/growthrates-classes.Rd
man/grow_logistic.Rd
man/grow_baranyi.Rd
man/grow_richards.Rd
man/grow_exponential.Rd
man/multisplit.Rd
man/methods.Rd
man/bactgrowth.Rd
man/grow_gompertz.Rd
man/grow_huang.Rd
man/plot.Rd
man/extract.Rd
growthrates documentation built on May 19, 2017, 6:36 p.m.