Nothing
reportHTML.gam <- function(object,
filename,
extension="html",
directory=getwd(),
Title,
neuron,
neuronEvts,
...) {
objectN <- deparse(substitute(object))
## if neuronEvts given check that it is a named list
if (!missing(neuronEvts)) {
if (!inherits(neuronEvts,"list")) neuronEvts <- list(neuronEvts)
if (is.null(names(neuronEvts)))
stop("neuronEvts should be a named list.")
} ## End of conditional on !missing(neuronEvts)
## if neuron is missing try to figure out its value from the
## neuron variable of the "data" component of object
if (missing(neuron)) {
if (!("neuron" %in% names(object$data)))
stop("neuron is not specified and cannot be obtained from object.")
neuron <- with(object$data,unique(neuron)[1])
} ## End of conditional on missing(neuron)
if (missing(filename))
filename <- paste(objectN,"GAM analysis")
if (missing(Title))
Title <- filename
HTMLInitFile(outdir=directory,
filename=filename,
extension=extension,
Title=Title)
fullName <- paste(directory,"/",
filename,".",
extension,sep="")
## Write object's summary
HTML.title("GAM fit summary:",file=fullName,HR=3)
objectS <- summary(object)
HTML(objectS,file=fullName)
HTMLhr(file=fullName)
## add a spike train plot after time transformation
HTML.title("Spike train after time transformation:",
file=fullName,HR=3)
Lambda <- transformedTrain(object)
st <- Lambda
class(st) <- "spikeTrain"
stFigName <- paste(filename,"_TTst.png",sep="")
figFname <- paste(directory,"/",stFigName,sep="")
png(figFname,width=500,height=500)
plot(st,
xlab="Transformed time",
main=""
)
dev.off()
HTMLInsertGraph(stFigName,
file=fullName,
WidthHTML=500,
HeightHTML=500)
## add a renewal test plot after time transformation
HTMLhr(file=fullName)
HTML.title("Renewal test after time transformation:",
file=fullName,HR=3)
rtFigName <- paste(filename,"_TTrt.png",sep="")
figFname <- paste(directory,"/",rtFigName,sep="")
png(figFname,width=800,height=800)
renewalTestPlot(Lambda)
dev.off()
HTMLInsertGraph(rtFigName,
file=fullName,
WidthHTML=800,
HeightHTML=800)
## add a Ogata tests after time transformation
HTMLhr(file=fullName)
HTML.title("Ogata's tests after time transformation:",
file=fullName,HR=3)
otFigName <- paste(filename,"_TTot.png",sep="")
figFname <- paste(directory,"/",otFigName,sep="")
png(figFname,width=800,height=800)
plot(Lambda,
which=c(1,2,4,5),
ask=FALSE)
dev.off()
HTMLInsertGraph(otFigName,
file=fullName,
WidthHTML=800,
HeightHTML=800)
## Check if the Ogata tests are passed and if yes and if
## neurons is given add interaction plots
LambdaS <- summary(Lambda)
otTRUE <- LambdaS[[1]][2] &&
LambdaS[[2]][2] &&
(0.005 <= LambdaS[[3]][2]) &&
(0.995 >= LambdaS[[3]][2])
if (otTRUE && !missing(neuronEvts)) {
HTMLhr(file=fullName)
HTML.title("Interaction tests after time transformation:",
file=fullName,HR=3)
## load other neurons data
pre.Lambda <- lapply(neuronEvts,
function(l) transformedTrain(object,l)
)
names(pre.Lambda) <- names(neuronEvts)
itFigName <- paste(filename,"_TTit.png",sep="")
figFname <- paste(directory,"/",itFigName,sep="")
png(figFname,width=300*length(neuronEvts),height=1000)
layout(matrix(1:(2*length(neuronEvts)),
nrow=2)
)
sapply(seq(neuronEvts),
function(nIdx) {
theFRT <- pre.Lambda[[nIdx]] %frt% Lambda
plot(theFRT,
main=paste(names(neuronEvts)[nIdx],"/ N",neuron),
ask=FALSE,which=1)
plot(theFRT,
main=paste(names(neuronEvts)[nIdx],"/ N",neuron),
ask=FALSE,which=2)
}
)
dev.off()
HTMLInsertGraph(itFigName,
file=fullName,
WidthHTML=300*length(neuronEvts),
HeightHTML=1000)
} ## end of conditional on otTRUE && !missing(neuronEvts)
HTMLbr(1,file=fullName)
HTMLhr(file=fullName)
## End with the call used to generate the object
HTML.title(paste("Call used to generate object ",
objectN, ":",sep=""),
file=fullName,HR=3)
thisC <- object$call
HTML(thisC,file=fullName)
HTMLbr(1,file=fullName)
HTMLEndFile()
}
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