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#' Performs a Single Dimension Exploration (SDE) analysis in the
#' given multigroup data matrix.
#' Show SDE graphical output.
#'
#' @param mydata data set
#' @param groups is a vector of classes
#' @param plt grafics
#' @import gplots
#' @import ggrepel
#' @import ggplot2
#' @import qgraph
#' @import mgm
#' @return \strong{return an grafics} .
#'
#'
#' @examples
#'sim.list2<-fun.sim(g=c(20,50,10),mean1=0.5,d=0,sds2=c(1,1,1,1),corr=c(0.1,0.5,0.5,0),
#'n.var=c(20,20))
#'datos2 <- as.data.frame(sim.list2$x)
#'datos2<-subset(datos2,select=-grp)
#'grupos <- sim.list2$grp
#'grupos<-factor(grupos,labels=c(1,2,3))
#'sde.method(mydata=datos2,groups=grupos,plt=FALSE)
#' @export
sde.method<-function(mydata,groups,plt=FALSE){
X<-list();Xn<-list()
n<-list();nn<-list();
u<-list();un<-list();
A<-list();z<-list();
B<-list();BB<-list();
gcor<-list();
for(i in 1:length(levels(groups))){
X[[i]]<-as.matrix(mydata[groups==i,])
Xn[[i]]<-as.matrix(mydata[groups!=i,])
n[i]<-nrow(as.matrix(X[[i]]))
nn[i]<-nrow(as.matrix(Xn[[i]]))
u[[i]]<-as.matrix(rep(1,n[i]),n[i],1)
un[[i]]<-as.matrix(rep(1,nn[i]),nn[i],1)
A[[i]]<- X[[i]]-u[[i]]%*%t(un[[i]])%*%Xn[[i]]/nn[[i]]
z[[i]]<-t(A[[i]])%*%u[[i]]
B[[i]]<-z[[i]]%*%t(z[[i]])
if(plt==TRUE){
# BB<-Reduce("+",B)
BB<-as.matrix(as.data.frame(B[[i]]))
res<-eigen(BB)
eigenvals<-res$values
eigenvecs<-res$vectors
Y<-as.matrix(mydata)%*%eigenvecs
as.matrix(cbind(Y[,i],as.matrix(mydata)))
datos2<-as.matrix(cbind(Y[,i],as.matrix(mydata)))
nc<-dim(datos2)[2]
type<-rep("g",nc)
level<-rep(1,nc)
group_list <- list("grupo1v"=c(1),
"grupo2v"=c(2,4,5,6),
"grupo3v" = c(7),
"grupo3v"=c(3))
# define nice colors
group_cols <- c("#E35959","#8FC45A","#4B71B3","#E8ED61")
fit <- mgm(datos2, type,level, lamda.sel="EBIC", k=2)
gcor[[i]]<-fit$pairwise$wadj
qgraph(fit$pairwise$wadj,
edge.color = fit$pairwise$edgecolor,
layout = "spring"
)
}
}
r<-list(B)
r
class(r) = c("sde")
return(r)
#G <- do.call(rbind, lapply(gcor, matrix, ncol = ncol(as.matrix(mydata)),byrow = F))
# G<-as.matrix(G)
}
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