I'm trying to use the grofit package to compare growth rates between
bacterial cultures, but I've come across a couple glitches/things I
don't understand. I'm not sure if they're related to the package or to a
problem with my growth data, which is messy. Some strains don't follow
a proper logarithmic growth curve because they died or didn't grow over
the course of the experiment. I could remove those but it will get more
time consuming once I have more cultures going.
I've attached the 'time' matrix and 'data' data frame. This code should
fit the growth curves, but when I run it I get an error related to
`smooth.spline`:
require(grofit)
mytime <- as.matrix(read.table('time.txt'))
mydata <- read.csv('data.csv')
dimnames(mytime) <- NULL
fits <- gcFit(mytime, mydata, grofit.control(
interactive=FALSE, # don't ask if the graphs look OK
nboot.gc=1000, # number of bootstraps
fit.opt="s" # just do splines, no models
))
= 1. growth curve =================================
----------------------------------------------------
= 2. growth curve =================================
----------------------------------------------------
= 3. growth curve =================================
----------------------------------------------------
Error in smooth.spline(time, data, spar = control$smooth.gc) :
'tol' must be strictly positive and finite
Error in gcFitSpline(time.cur, data.cur, gcID, control.change) :
object 'y.spl' not found
That error usually occurs at some point, though I've run through all 17
successfully a couple times. The documentation says:
> smooth.gc: Parameter describing the smoothness of the spline fit;
> usually (not necessary) in (0;1]. Set ‘smooth.gc=NULL’ causes the
> program to query an optimal value via cross validation techniques.
> Note: This is partly experimental. In future improved implementations
> of the ‘smooth.spline’ function may lead to different results. See
> documentation of the R function ‘smooth.spline’ for further details.
> Especially for datasets with few data points the option ‘NULL’ might
> result in a too small smoothing parameter, which produces an error in
> ‘smooth.spline’. In that case the usage of a fixed value is
> recommended. Default: ‘NULL’.
I tried setting different values (0.1, 0.5, 0.9, 1, 10) and they all
cause the same error. If instead I use the `gcBootSpline` function
directly, it gives a different error about the number of bootstraps
being 0, when they clearly aren't:
fits <- gcBootSpline(mytime, mydata, grofit.control(nboot.gc=1000))
Error in gcBootSpline(mytime, mydata, grofit.control(nboot.gc =
1000)) : Number of bootstrap samples is zero! See grofit.control()
Am I using these right? Is there something about the data that would
make it un-fittable?
Jeff
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