| reportHTML.gam {STAR} | R Documentation |
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)