Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/fitCellGrowth.R
Fit a cell growth curve
1 2 3  fitCellGrowth(x, z, model = "locfit",
locfit.h = 3 * 60 * 60, locfit.deg = 2,
relative.height.at.lag = 0.1)

x 

z 

model 
which model to fit. 
locfit.h 

locfit.deg 

relative.height.at.lag 
Parameter used by

For the nonparametric "locfit" model, local regression
is done by a call to locfit
.
The returned maximum growth rate values the maximum value
of the fitted derivative over the data points. For the
parametric models "logistic", "gompertz", "rosso" and
"baranyi", the function does a nonleast square fit by
calling nls
. Initial parameters values are
generated by guessCellGrowthParams
. The
returned maximum growth rate values the mu
parameter of these models.
Fit as returned by locfit
for the "locfit" model and as returned by
nls
for the "logistic", "gompertz", "rosso"
and "baranyi" models. The returned value also has an
attribute maxGrowthRate
valueing the inferred
maximum growth rate as well as an attribute
pointOfMaxGrowthRate
valuing the datapoint at
which the growth rate is maximal. Also, it has an
attribute max
valuing the inferred maximum among
the time points as well as pointOfMax
valuing the
datapoint of max fitted value. It gets the additional
class cellCurveFit
assigned.
Julien Gagneur and Moritz Matthey
nls
, locfit
,
baranyi
, gompertz
,
logistic
, rosso
,
guessCellGrowthParams
,
fitCellGrowths
1 2 3 4 5 6 7 8  x = 1:1000
z = gompertz(x, mu=0.01, l=200, z0=1, zmax=5) + rnorm(length(x),sd=0.1)
f = fitCellGrowth(x, z, model = "gompertz")
floc = fitCellGrowth(x, z, model = "locfit", locfit.h=500)
plot(x,z, main="simulated data\nGompertz model")
lines(x, predict(f,x), lwd=2, col="red")
lines(x, predict(floc,x), lwd=2, col="blue")
legend( "right", legend=c("gompertz fit", "locfit"), lwd=1, col=c("red","blue") )

Loading required package: locfit
locfit 1.59.1 20130322
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