afmRelax: Stress relaxation/ Creep model fit

Description

Fits a viscoelastic exponential decay in a Force-Relaxation or Creep experiments as described in Nanotechnology 2010 (see references).

Usage

afmRelax(afmdata, model = c("power","exp"), nexp = 2, tmax = NULL, 
       type = c("CH","CF"), plt = TRUE, ...)

Value

An afmdata class variable which will consist on the original input

afmdata variable plus a new list named RelaxFit with the following fields:

model: The model used in the fit.

relaxModel: A nls object returned from nlsM() function.

relaxFit: The values predicted by the fit, returned from the

predict() function.

Arguments

afmdata: An object of afmdata class with a pause segment and a Time column in the data dataframe.
model: Type of model to be fitted. Could be either "power" for a power law model or "exp" for an exponential decay model.
nexp: Number of expontials in the Prony series to be fitted if model is "exp". Currently only one or two exponentials are supported. Default is 2.
tmax: Maximum time considered in the relaxation curve. It defaults to Inf, meaning that the whole pause segment is considered.
type: Type of the experiment. Can be either "CH" (Constant Height) for a force-relaxation experiment or "CF" (Constant Force) for a creep experiment. Default is type = "CH".
plt: Logical. If TRUE (default) then a plot of the pause segment with the overlay of the fit is shown.
...: Options passed to the nlsM() function from the minpack.lm package. At least should contain the starting values (start = list(...)) for the Levenberg-Mardquart nonlinear least square method. For use only if model is "exp".

References

Susana Moreno-Flores, Rafael Benitez, Maria dM Vivanco and Jose Luis Toca-Herrera (2010). "Stress relaxation and creep on living cells with the atomic force microscope: a means to calculate elastic moduli and viscosities of cell components". Nanotechnology, 21 (44), pp. 445101.

Examples

Run this code

data <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path.package("afmToolkit"))
width <- 20
mul1 <- 1
mul2 <- 10
data <- afmContactPoint(data, width = width, mul1 = mul1, mul2 = mul2)
data <- afmDetachPoint(data, width = width, mul1 = mul1, mul2 = mul2)
data <- afmBaselineCorrection(data)
data <- afmRelax(data, model = "exp", nexp = 2, type = "CH")

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