Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/reportHTML.spikeTrain.R
Performs a "standard" analysis on a spikeTrain
object, computing some
cross-correlation statistics if additional spikeTrain
objects
are provided, writes results to disk and generates a report in html format.
1 2 3 4 5 6 7 8 |
object |
a |
filename |
a character string. The generic name of all the files
(html, png as well as |
extension |
see |
directory |
the full or relative path to the directory where the
results are going to be stored. See also |
Title |
See |
forceTT |
Should a time transformation be performed and the
|
timeUnit, digits |
see |
otherST |
a named list of |
laglim |
see |
cch |
if |
doGamCheck |
if smooth estimates are requested, should function
|
k |
see |
bs |
|
nbEvtPerBin |
a number of event per bin used in a way similar to
the argument with the same name in |
... |
Not used, only there for compatibilty with the generic method definition. |
A spike train plot (plot.spikeTrain
) is performed
first. The summary (summary.spikeTrain
) is computed next
and part of its output is written to the html file. The renewal tests
are then carried out and their results added
(renewalTestPlot
). The six duration distributions are
fitted (compModels
with argument plot
set to
FALSE
) and the best one is used to apply a time transformation
to spikeTrain
. The Ogata's tests are applied
(summary.transformedTrain
) and if they are all within
the 99% confidence interval, the result of the transformation is
plotted (plot.transformedTrain
) as well as all the Q-Q
plots of compModels
. If forceTT
is set to
TRUE
(default), then these last two plots are added even if the
best model does not pass the tests.
If other spikeTrain
objects are provided as a named list via
argument otherST
, then cross-correlation/cross-intensity
functions are estimated; Two estimations methods are available, the
classical histogram and a smooth version of it. Argument cch
controls if a single estimation is performed or if both are
performed. If the smooth version is requested a summary of the
gam
fit is printed. Moreover if argument
doGamCheck
is set to TRUE
then check plots
(gam.check
) are added to the report.
A R
data file (filename.rda
) is also generated with the
following objects:
cm
: the result of compModels
.
bestFit
: the durationDistribution
object
returned obtained by fitting the best model among the 6.
Lambda
: the integrated intensity of spikeTrain
with the best model.
fct
: the matched call.
cchL
: if other trains were provided and if argument
cch
was set to "both"
or to "cch"
. A list with
as many components as the otherST
argument. Each component is
the a hist.lockedTrain
object.
scchL
: if other trains were provided and if argument
cch
was set to "both"
or to "scch"
. A list with
as many components as the otherST
argument. Each component is
the a slockedTrain
object.
Nothing is returned, an html file and figures in png format are
written to disk together with the R
variables generated during
the analysis.
Christophe Pouzat christophe.pouzat@gmail.com
as.spikeTrain
,
plot.spikeTrain
,
summary.spikeTrain
,
renewalTestPlot
,
plot.spikeTrain
,
compModels
,
transformedTrain
,
plot.transformedTrain
,
summary.transformedTrain
,
gam
,
gam.check
,
lockedTrain
,
slockedTrain
1 2 3 4 5 6 7 8 | ## load e070528spont data set
data(e070528spont)
## perform a standard analysis on neuron 1, looking for cross-correlations
## with the 3 other neurons up to lag +/- 250 ms.
## Store the results under the generic name: e070528spontN1
reportHTML(e070528spont[["neuron 1"]],"e070528spontN1",otherST=e070528spont[-1],laglim=c(-1,1)*0.25,forceTT=FALSE)
## Neuron 1 of e070528spont is exceptional in that it can be well
## described by a renewal process...
|
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