Nothing
print.yai = function(x,...)
{
if (missing(x)) stop ("x required.")
if (class(x)[1] != "yai") stop("arg class must be yai")
cat ("\nCall:\n")
print (x$call)
if (length(x$obsDropped)== 0) cat ("0 observations dropped\n")
else cat (length(x$obsDropped),"observations dropped: ",
x$obsDropped[1:min(15,length(x$obsDropped))],"...\n")
cat ("method used: ",x$method,"\n")
if (is.null(x$cancor))
{
cat ("Cancor not run\n")
}
else
{
cat ("Cancor report:\n")
print(format(data.frame(cor=x$cancor$cor, F=x$ftest$F,
Pr.F=x$ftest$pgF, Sig=c(" ","NS")[(x$ftest$pgF>x$pVal)+1]),digits=4))
cat (x$nVec,"vectors used, pVal=",x$pVal,"\n")
cat ("cancor$xcoef:\n")
print(x$cancor$xcoef[,1:x$nVec])
}
if (!is.null(x$projector))
{
cat ("Projector:\n")
print (x$projector)
}
if (is.null(x$ccaVegan))
{
cat ("CCA not run\n")
}
else
{
cat ("CCA analysis:\n")
if (!requireNamespace ("vegan")) stop("install vegan and try again")
print (x$ccaVegan)
}
if (is.null(x$ranForest))
{
cat ("randomForest not run\n")
}
else
{
cat ("randomForest analysis:\n")
if (!requireNamespace ("randomForest"))
stop("install randomForest and try again")
print(yaiRFsummary(x))
}
cat (sum(x$yDrop),"y variables dropped ",
paste(names(x$yDrop[x$yDrop]),collapse=","),"\n")
cat (sum(x$xDrop),"x variables dropped ",
paste(names(x$xDrop[x$xDrop]),collapse=","),"\n")
if (x$ann & x$method!="randomForest") cat ("Note: ann used\n") else cat ("ann not used\n")
if (length(x$neiDstTrgs)==0) cat ("No target neighbors computed.\n")
else
{
nPr=min(10,nrow(x$neiDstTrgs))
part=data.frame(x$neiDstTrgs[1:nPr,,drop=FALSE],x$neiIdsTrgs[1:nPr,,drop=FALSE],
stringsAsFactors = FALSE)
names(part)=c(colnames(x$neiDstTrgs),colnames(x$neiIdsTrgs))
cat ("First",nPr,"targets:\n")
print (part)
}
if (length(x$neiDstRefs)==0) cat ("No reference neighbors computed.\n")
else
{
nPr=min(10,nrow(x$neiDstRefs))
part=data.frame(x$neiDstRefs[1:nPr,,drop=FALSE],x$neiIdsRefs[1:nPr,,drop=FALSE],
stringsAsFactors = FALSE)
names(part)=c(colnames(x$neiDstRefs),colnames(x$neiIdsRefs))
cat ("First",nPr,"references:\n")
print (part)
}
if (!is.null(x$biasParameters))
{
cat ("Bias correction parameters:\n")
cat ("trgVal CI =",x$biasParameters$trgValCI,
" curVal =",x$biasParameters$curVal,
"\nNumber of passes used =",x$biasParameters$npasses,
" of ",x$biasParameters$oldk-1,"possible\n")
}
}
summary.yai = function (object,...) print.yai(object,...)
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