growth.gcFitModel: Fit nonlinear growth models to growth data

In QurvE: Robust and User-Friendly Analysis of Growth and Fluorescence Curves

Fit nonlinear growth models to growth data

Description

growth.gcFitModel determines a parametric growth model that best describes the data.

Usage

growth.gcFitModel(time, data, gcID = "undefined", control = growth.control())

Arguments

time	Vector of the independent variable (usually time).
data	Vector of dependent variable (usually growth values).
gcID	(Character) The name of the analyzed sample.
control	A grofit.control object created with growth.control, defining relevant fitting options.

Value

A gcFitModel object that contains physiological parameters and information about the best fit. Use plot.gcFitModel to visualize the parametric fit and growth equation.

raw.time	Raw time values provided to the function as time.
raw.data	Raw growth data provided to the function as data.
gcID	(Character) Identifies the tested sample.
fit.time	Fitted time values.
fit.data	Fitted growth values.
parameters	List of determined growth parameters.

• A: Maximum growth.

• dY: Difference in maximum growth and minimum growth of the fitted model.

• mu: Maximum growth rate (i.e., maximum in first derivative of the spline).

• lambda: Lag time.

• b.tangent: Intersection of the tangent at the maximum growth rate with the abscissa.

• fitpar: For some models: list of additional parameters used in the equations describing the growth curve.

• integral: Area under the curve of the parametric fit.

model	(Character) The model that obtained the fit with the lowest AIC, determined by AIC.
nls	nls object for the chosen model generated by the nls function.
reliable	(Logical) Indicates whether the performed fit is reliable (to be set manually).
fitFlag	(Logical) Indicates whether a parametric model was successfully fitted on the data.
control	Object of class grofit.control containing list of options passed to the function as control.

References

Matthias Kahm, Guido Hasenbrink, Hella Lichtenberg-Frate, Jost Ludwig, Maik Kschischo (2010). grofit: Fitting Biological Growth Curves with R. Journal of Statistical Software, 33(7), 1-21. DOI: 10.18637/jss.v033.i07

See Also

Other growth fitting functions: growth.drFit(), growth.gcBootSpline(), growth.gcFitLinear(), growth.gcFitSpline(), growth.gcFit(), growth.workflow()

Examples

# Create random growth dataset
rnd.dataset <- rdm.data(d = 35, mu = 0.8, A = 5, label = 'Test1')

# Extract time and growth data for single sample
time <- rnd.dataset$time[1,]
data <- rnd.dataset$data[1,-(1:3)] # Remove identifier columns

# Perform parametric fit
TestFit <- growth.gcFitModel(time, data, gcID = 'TestFit',
                 control = growth.control(fit.opt = 'm'))

plot(TestFit, basesize = 18, eq.size = 1.5)

QurvE documentation built on May 29, 2024, 3 a.m.