Description Usage Arguments Value References Examples
Fits a viscoelastic exponential decay in a Force-Relaxation or Creep experiments as described in Nanotechnology 2010 (see references).
1 2 |
afmdata |
An object of |
nexp |
Number of expontials in the Prony series to be fitted. Currently only one or two exponentials are supported. Default is 2. |
tmax |
Maximum time considered in the relaxation curve. It defaults to |
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 |
plt |
Logical. If TRUE (default) then a plot of the pause segment with the overlay of the fit is shown. |
... |
Options passed to the |
An afmdata
class variable which will consist on the original input
afmdata
variable plus a new list named ExpFit
with the following
fields:
expdecayModel
: A nls object returned from nlsM()
function.
expdecayFit
: The values predicted by the fit, returned from the
predict()
function.
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.
1 2 3 4 5 6 7 8 | 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 <- afmExpDecay(data, nexp = 2, type = "CH")
|
Loading required package: ggplot2
JPK file force-save-JPK-3h.txt.gz loaded. 3 headers found.
Warning message:
In nlsLM(ForceCorrected ~ a0 + a1 * exp(-Time/tau1) + a2 * exp(-Time/tau2), :
No starting values specified for some parameters.
Initializing 'a0', 'a1', 'tau1', 'a2', 'tau2' to '1.'.
Consider specifying 'start' or using a selfStart model
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