gampsth: Smooth Peri Stimulus Time Histogram Related Functions and...
In STAR: Spike Train Analysis with R

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

Function gampsth computes a smooth psth, while method print.gampsth prints and summary.gampsth summarises the gamObject contained in the returned gampsth object and plot.gampsth plots it.

gampsth(repeatedTrain, binSize = 0.025, k = 100,
      bs = "tp", plot = TRUE,...)
## S3 method for class 'gampsth'
print(x, ...)
## S3 method for class 'gampsth'
summary(object, ...)
## S3 method for class 'gampsth'
plot(x, stimTimeCourse = NULL, colStim = "grey80",
           colCI = NULL, xlab, ylab, main, xlim, ylim,
           lwd = 2, col = 1, ...)

`repeatedTrain`	a `repeatedTrain` object or a list which can be coerced to such an object.
`binSize`	the bin size (in s) used to generate the observations on which the gam fit will be performed. See details below.
`k`	the dimension of the basis used to represent the smooth psth. See `s`.
`bs`	the type of splines used. See `s`.
`plot`	corresponding argument of `hist`. Should a plot be generated or not?
`object`	a `gampsth` object.
`x`	a `gampsth` object.
`stimTimeCourse`	`NULL` (default) or a two elements vector specifying the time boundaries (in s) of a stimulus presentation.
`colStim`	the background color used for the stimulus.
`colCI`	if not `NULL` (default) a confidence band is plotted with the specified color; two dashed lines are plotted otherwise.
`xlim`	a numeric (default value supplied). See `plot`.
`ylim`	a numeric (default value supplied). See `plot`.
`xlab`	a character (default value supplied). See `plot`.
`ylab`	a character (default value supplied). See `plot`.
`main`	a character (default value supplied). See `plot`.
`lwd`	line width used to plot the estimated density. See `plot`.
`col`	color used to plot the estimated density. See `plot`.
`...`	in `gampsth`, if `plot` is set to `TRUE` then the ... are passed to `plot.gampsth`. In `plot.gampsth` they are passed to `plot` which is called internally. They are not used otherwise.

For gampsth, the raw data contained in repeatedTrain are pre-processed with hist using a bin size given by argument binSize. This binSize should be small "enough". That is, the rate of the aggregated train created by collapsing the spike times of the different trials onto a single "pseudo" spike train, should not change too much on the scale of binSize (see Ventura et al (2002) Sec. 4.2 p8 for more details).

When plot is set to FALSE in gampsth, a list of class gampsth is returned and no plot is generated. This list has the following components:

`freq`	a vector containing the instantaneous firing rate in the middle of the "thin" bins used for preprocessing.
`ciUp`	a vector with the upper limit of a pointwise 95% confidence interval. Check `predict.gam` for details.
`ciLow`	a vector with the lower limit of a pointwise 95% confidence interval.
`breaks`	a vector with 2 elements the ealiest and the latest spike in `repeatedTrain`.
`mids`	a numeric vector with the mid points of the bins.
`counts`	a vector with the actual number of spikes in each bin.
`nbTrials`	the number of trials in `repeatedTrain`.
`lambdaFct`	a function of a single time argument returning the estimated intensity (or instantaneous rate) at its argument.
`LambdaFct`	a function of a single time argument returning the integrale of estimated intensity (or instantaneous rate) at its argument. That is, the integrated intensity. `integrate` is used by this function.
`call`	the matched call.

When plot is set to TRUE nothing is returned and a plot is generated as a side effect. Of course the same occurs upon calling plot.gampsth with a gampsth object argument.

print.gampsth returns the result of print.gam applied to the gamObject generated by gampsth and stored in the environment of both lambdaFct and LambdaFct.

summary.gampsth returns the result of summary.gam applied to the gamObject generated by gampsth and stored in the environment of both lambdaFct and LambdaFct.

Most of the components of the list returned by gampsth are not of direct interest for the user but they are used by, for instance, reportHTML.repeatedTrain.

Christophe Pouzat christophe.pouzat@gmail.com

Ventura, V., Carta, R., Kass, R. E., Gettner, S. N. and Olson, C. R. (2002) Statistical analysis of temporal evolution in single-neuron firing rates. Biostatistics 3: 1–20.

Kass, R. E., Ventura, V. and Cai, C. (2003) Statistical smoothing of neuronal data. Network: Computation in Neural Systems 14: 5–15.

Wood S.N. (2006) Generalized Additive Models: An Introduction with R. Chapman and Hall/CRC Press.

psth, plot.psth, gam, print.gam, summary.gam, gam.check, reportHTML.repeatedTrain,

## Not run: 
## Get the e070528citronellal data set into workspace
data(e070528citronellal)
## Compute gampsth without a plot for neuron 1
## using a cubic regression spline
n1CitrGAMPSTH <- gampsth(e070528citronellal[[1]],plot=FALSE,bs="cr")
## plot the result
plot(n1CitrGAMPSTH,stim=c(6.14,6.64),colCI=2)
## get a summary of the gam fit
summary(n1CitrGAMPSTH)
## perhaps get a more complete check wit gam.check
n1CitrGAMPSTHgo <- gamObj(n1CitrGAMPSTH)
gam.check(n1CitrGAMPSTHgo)
## It does not look too bad
## Now take a look at the observation on which the gam
## was actually performed
plot(n1CitrGAMPSTH$mids,n1CitrGAMPSTH$counts,type="l")
## put dots at the positions of the knots
X <- n1CitrGAMPSTHgo$smooth[[1]][["xp"]]
rug(X,col=2)
## Add the estimated smooth psth after proper scaling
theBS <- diff(n1CitrGAMPSTH[["mids"]])[1]
Y <- n1CitrGAMPSTH$lambdaFct(n1CitrGAMPSTH$mids)*theBS*n1CitrGAMPSTH$nbTrials
lines(n1CitrGAMPSTH$mids,Y,col=4,lwd=2)

## End(Not run)