R: Generates a Report in HTML Format from a STAR gam Object
reportHTML.gam
R Documentation
Generates a Report in
HTML Format from a STAR gam Object
Description
Writes the result of a gam fit in an html file.
Usage
## S3 method for class 'gam'
reportHTML(object, filename, extension = "html",
directory = getwd(), Title,
neuron, neuronEvts, ...)
Arguments
object
an object returned by gam.
filename
a character string. The generic name of all the files
(html, png as well as R data files which will be
generated. See also HTMLInitFile.
extension
see HTMLInitFile.
directory
the full or relative path to the directory where the
results are going to be stored. See also HTMLInitFile.
Title
See HTMLInitFile. If missing a default
value baed on filename is provided.
neuron
a character string describing to which the analysis
refers and used for the titles of the interaction plots (see plot.frt).
neuronEvts
a named list with the event variable from the
data frame returned by mkGLMdf and corresponding to the
other neurons recorded simultaneously. One list element per neuron.
...
Not used, only there for compatibilty with the generic
method definition.
Details
A summary (summary.gam) of object is added
to the report. A plot of the spike train after time transformation
transformedTrain comes next followed by a renewal test
plot (renewalTestPlot) of the spike train on the time
transformed scale. The "usual" Ogata's tests plots
(plot.transformedTrain) are added. Then if other trains
are provided as a named list via argument neuronEvts,
interactions plots (plot.frt) are built showing both the
survivor function and the Berman's test. The report ends with the
call which generated object.
Value
Nothing is returned, an html file and figures in png format are
written to disk.
## Not run:
## load e070528spont data set
data(e070528spont)
## make a data frame for gam using a 2 ms bin width
spontDF <- mkGLMdf(e070528spont,0.002,0,60)
## make data frames specific of each neuron
n1.spontDF <- spontDF[spontDF$neuron=="1",]
n2.spontDF <- spontDF[spontDF$neuron=="2",]
n3.spontDF <- spontDF[spontDF$neuron=="3",]
n4.spontDF <- spontDF[spontDF$neuron=="4",]
## save space by removing the now redundant spontDF
rm(spontDF)
## fit neuron 1 using the gam representation of a
## renewal process and a binomial model
n1.spontFit1 <- gam(event ~ s(lN.1,k=25,bs="cr"),data=n1.spontDF,family=binomial())
## create a list with the discretized spike times of the 3 other neurons
preN1 <- list(n2=with(n2.spontDF,event),n3=with(n3.spontDF,event),n4=with(n4.spontDF,event))
## generate the report
reportHTML(n1.spontFit1,"e070528spontN1gFit",neuron="1",neuronEvts=preN1)
## End(Not run)