reportHTML.gam: Generates a Report in HTML Format from a STAR gam Object
In STAR: Spike Train Analysis with R

Description Usage Arguments Details Value Author(s) See Also Examples

Writes the result of a gam fit in an html file.

## S3 method for class 'gam'
reportHTML(object, filename, extension = "html",
           directory = getwd(), Title,
           neuron, neuronEvts, ...)

`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.

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.

Nothing is returned, an html file and figures in png format are written to disk.

Christophe Pouzat christophe.pouzat@gmail.com

mkGLMdf, gam, gam.check, frt, transformedTrain, plot.transformedTrain, summary.transformedTrain

## 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)