mass.t.test: perform mass univariate statistics on an erplist.
In erpR: Event-Related Potentials (ERP) Analysis, Graphics and Utility Functions

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

This function performs a series of t-tests on each timepoint comparing two sets of ERP data frames. The first set is specified by base1 and numbers1. The second is specified by base2 and numbers2. Several options are available.

mass.t.test(base1=NULL, base2=NULL, numbers1=NULL, numbers2=numbers1, startmsec=NULL, 
endmsec=NULL, paired=F, erplist1=NULL, erplist2=erplist1,  electrodes="all", 
to.exclude=NULL, interval=c(startmsec, endmsec), p.adjust.method="none", 
n.permutations=1000, p.crit=0.05, stable.diff=FALSE, crit.msec=NULL, 
crit.npoints=NULL, neighbours=NULL, min_nchans=2, na.rm=TRUE)

`base1`	a string indicating the beginning of the name of the first set of ERP data frames.
`base2`	a string indicating the beginning of the name of the second set of ERP data frames.
`numbers1`	the numbers of the subjects of the first set of ERP data frames.
`numbers2`	the numbers of the subjects of the second set of ERP data frames.
`startmsec`	the start time (in ms) of the ERP vector
`endmsec`	the end time (in ms) of the ERP vector
`paired`	logical. This argument specifies if the t-tests are paired or not.
`erplist1`	a list containing the ERP data frames specified in `base1` and `numbers1`.
`erplist2`	a list containing the ERP data frames specified in `base2` and `numbers2`.
`electrodes`	A vector with the names of the electrodes that should be influded in the analysis. Default is `"all"` and all electrodes will be used.
`to.exclude`	A vector with electrode names that should be excluded from the analsysis.
`interval`	a vector with a pair of values indicating the interval (in milliseconds) to be plotted.
`p.adjust.method`	p-value correction methods as in `p.adjust`. Alternatively `"tmax"` or `"cluster.based.permutation"` can be used to perform permutation test as in Groppe et al., 2011.
`n.permutations`	number of permutation if a permutation test is specified in `p.adjust.methods`, (currently for `"tmax"` or `"cluster.based.permutation"`) .
`p.crit`	the alpha of the t-tests. Default is 0.05.
`stable.diff`	Logical (default is `FALSE`). If `TRUE`, significant results are filtered, and only consecutive sigificant results as specified in `crit.msec` or `crit.npoints` are retained.
`crit.msec`	if `stable.diff=TRUE`, only sequences of consecutive significant timpoints during at least `crit.msec` milliseconds will be retained in the results (Overridden if `crit.npoints` is specified).
`crit.npoints`	if `stable.diff=TRUE`, only sequences of consecutive significant timpoints during at least `crit.npoints` number of timepoints will be retained in the results.
`neighbours`	An electrode by electrode matrix with 0 and 1 indicating neighbouring electrode (1 = neighbouring, 0 = not neighbouring).
`min_nchans`	Only used in cluster based permutation. The minimun number of neighbouring channels to consider a cluster. Default is 2 (i.e., a cluster must be composed by at least 2 channels).
`na.rm`	Logical. Should `NA` values be removed from the analysis?

This function perform a series of t-tests, according to a Mass Univariate Statistics approach (Groppe et al., 2011)

The function returns results in the form of a list containing a series of objects. param, contains the parameters of the call to mass.t.test. mass.t.results, contains the t.values of the results filtered according to the mass.t.results call. sig is a logical matrix containing the significant results (0 = not significant, 1 = significant). t.mat is a matrix containing all the t-values (not filtered). p.mat is a matrix containing the p.values, unfiltered. If cluster.based.permutation is chosed a different list of results is returned, with seprate results for positive and negative clusters and with cluster identity. If stable.diff=TRUE an additional object containing the list of beginning and end of signficant time windows is included in the ouput.

Giorgio Arcara

Groppe, D. M., Urbach, T. P., and Kutas, M. (2011). Mass univariate analysis of event-related brain potentials fields I: a critical tutorial review. Psychophysiology, 48(12), 1711-25.

erp, erp.t

## Not run: 
data(erplistExample)

res = mass.t.test("Exp1_word_subj", "Exp1_nonword_subj", 1:20, 1:20, startmsec=-200, endmsec=1500, 
erplist1=erplistExample, erplist2=erplistExample, paired=T)


## End(Not run)