Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
tidy.opts = list(width.cutoff = 70),
tidy = TRUE
)
## ----eval=FALSE---------------------------------------------------------------
# library(devtools)
# install_github("thebrisklab/singR")
#
## ----eval=FALSE---------------------------------------------------------------
# ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
# ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
# ld: library not found for -lgfortran
# clang: error: linker command failed with exit code 1 (use -v to see invocation)
## ----eval=FALSE---------------------------------------------------------------
# FLIBS = -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm
## ----eval=FALSE---------------------------------------------------------------
# FLIBS = -L/usr/local/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/usr/local/gfortran/lib -lgfortran -lm
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# library(singR)
# data(exampledata)
# data <- exampledata
#
# lgrid = 33
# par(mfrow = c(2,4))
# # Components for X
# image(matrix(data$sjX[1,], lgrid, lgrid), col = heat.colors(12),
# xaxt = "n", yaxt = "n",main=expression("True S"["Jx"]*", 1"))
# image(matrix(data$sjX[2,], lgrid, lgrid), col = heat.colors(12),
# xaxt = "n", yaxt = "n",main=expression("True S"["Jx"]*", 2"))
# image(matrix(data$siX[1,], lgrid, lgrid), col = heat.colors(12),
# xaxt = "n", yaxt = "n",main=expression("True S"["Ix"]*", 1"))
# image(matrix(data$siX[2,], lgrid, lgrid), col = heat.colors(12),
# xaxt = "n", yaxt = "n",main=expression("True S"["Ix"]*", 2"))
#
# # Components for Y
# image(vec2net(data$sjY[1,]), col = heat.colors(12), xaxt = "n", yaxt = "n",
# main=expression("True S"["Jy"]*", 1"))
# image(vec2net(data$sjY[2,]), col = heat.colors(12), xaxt = "n", yaxt = "n",
# main=expression("True S"["Jy"]*", 2"))
# image(vec2net(data$siY[1,]), col = heat.colors(12), xaxt = "n", yaxt = "n",
# main=expression("True S"["Iy"]*", 1"))
# image(vec2net(data$siY[2,]), col = heat.colors(12), xaxt = "n", yaxt = "n",
# main=expression("True S"["Iy"]*", 2"))
## ----origin,echo=FALSE,out.width = "100%",fig.cap="True loadings in example 1."----
knitr::include_graphics("figs/Original.png",dpi = NA)
## ----eval=FALSE,tidy=TRUE-----------------------------------------------------
# example1=singR(dX = data$dX,dY = data$dY,individual = T)
#
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# n.comp.X = NG_number(data$dX)
# n.comp.Y = NG_number(data$dY)
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# # JB on X
# estX_JB = lngca(xData = data$dX, n.comp = n.comp.X, whiten = 'sqrtprec',
# restarts.pbyd = 20, distribution='JB')
# Uxfull <- estX_JB$U
# Mx_JB = est.M.ols(sData = estX_JB$S, xData = data$dX)
#
# # JB on Y
# estY_JB = lngca(xData = data$dY, n.comp = n.comp.Y, whiten = 'sqrtprec',
# restarts.pbyd = 20, distribution='JB')
# Uyfull <- estY_JB$U
# My_JB = est.M.ols(sData = estY_JB$S, xData = data$dY)
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# matchMxMy = greedymatch(scale(Mx_JB,scale = F), scale(My_JB,scale = F), Ux = Uxfull, Uy = Uyfull)
# permJoint <- permTestJointRank(matchMxMy$Mx,matchMxMy$My)
# joint_rank = permJoint$rj
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# # Center X and Y
# dX=data$dX
# dY=data$dY
# n = nrow(dX)
# pX = ncol(dX)
# pY = ncol(dY)
# dXcentered <- dX - matrix(rowMeans(dX), n, pX, byrow = F)
# dYcentered <- dY - matrix(rowMeans(dY), n, pY, byrow = F)
#
# # For X
# # Scale rowwise
# est.sigmaXA = tcrossprod(dXcentered)/(pX-1)
# whitenerXA = est.sigmaXA%^%(-0.5)
# xDataA = whitenerXA %*% dXcentered
# invLx = est.sigmaXA%^%(0.5)
#
# # For Y
# # Scale rowwise
# est.sigmaYA = tcrossprod(dYcentered)/(pY-1)
# whitenerYA = est.sigmaYA%^%(-0.5)
# yDataA = whitenerYA %*% dYcentered
# invLy = est.sigmaYA%^%(0.5)
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# # Calculate the Sx and Sy.
# Sx=matchMxMy$Ux[1:joint_rank,] %*% xDataA
# Sy=matchMxMy$Uy[1:joint_rank,] %*% yDataA
#
# JBall = calculateJB(Sx)+calculateJB(Sy)
#
# # Penalty used in curvilinear algorithm:
# rho = JBall/10
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# # alpha=0.8 corresponds to JB weighting of skewness and kurtosis (can customize to use different weighting):
# alpha = 0.8
# #tolerance:
# tol = 1e-10
#
# out <- curvilinear_c(invLx = invLx, invLy = invLy, xData = xDataA,
# yData = yDataA, Ux = matchMxMy$Ux, Uy = matchMxMy$Uy,
# rho = rho, tol = tol, alpha = alpha,
# maxiter = 1500, rj = joint_rank)
## ----eval=FALSE, tidy=TRUE----------------------------------------------------
# # Estimate Sx and Sy and true S matrix
# Sjx = out$Ux[1:joint_rank, ] %*% xDataA
# Six = out$Ux[(joint_rank+1):n.comp.X, ] %*% xDataA
# Sjy = out$Uy[1:joint_rank, ] %*% yDataA
# Siy = out$Uy[(joint_rank+1):n.comp.Y, ] %*% yDataA
#
# # Estimate Mj and true Mj
# Mxjoint = tcrossprod(invLx, out$Ux[1:joint_rank, ])
# Mxindiv = tcrossprod(invLx, out$Ux[(joint_rank+1):n.comp.X, ])
# Myjoint = tcrossprod(invLy, out$Uy[1:joint_rank, ])
# Myindiv = tcrossprod(invLy, out$Uy[(joint_rank+1):n.comp.Y, ])
#
# # signchange to keep all the S and M skewness positive
# Sjx_sign = signchange(Sjx,Mxjoint)
# Sjy_sign = signchange(Sjy,Myjoint)
# Six_sign = signchange(Six,Mxindiv)
# Siy_sign = signchange(Siy,Myindiv)
#
# Sjx = Sjx_sign$S
# Sjy = Sjy_sign$S
# Six = Six_sign$S
# Siy = Siy_sign$S
#
# Mxjoint = Sjx_sign$M
# Myjoint = Sjy_sign$M
# Mxindiv = Six_sign$M
# Myindiv = Siy_sign$M
#
# est.Mj=aveM(Mxjoint,Myjoint)
#
# trueMj <- data.frame(mj1=data$mj[,1],mj2=data$mj[,2],number=1:48)
# SINGMj <- data.frame(mj1=est.Mj[,1],mj2=est.Mj[,2],number=1:48)
#
#
## ----eval=FALSE,echo=FALSE, tidy=TRUE-----------------------------------------
#
# lgrid = 33
# par(mfrow = c(2,4))
#
# image(matrix(Sjx[1,], lgrid, lgrid), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Jx"]*", 1"))
# image(matrix(Sjx[2,], lgrid, lgrid), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Jx"]*", 2"))
# image(matrix(Six[1,], lgrid, lgrid), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Ix"]*", 1"))
# image(matrix(Six[2,], lgrid, lgrid), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Ix"]*", 2"))
#
# image(vec2net(Sjy[1,]), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Jy"]*", 1"))
# image(vec2net(Sjy[2,]), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Jy"]*", 2"))
# image(vec2net(Siy[1,]), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Iy"]*", 1"))
# image(vec2net(Siy[2,]), col = heat.colors(12), xaxt = "n", yaxt = "n",main=expression("Estimate S"["Iy"]*", 2"))
#
#
## ----estiexample1,echo=FALSE,out.width = "100%",fig.cap="Estimated joint loadings in example 1."----
knitr::include_graphics("figs/Esti_example1.png",dpi = NA)
## ----eval=FALSE,echo=TRUE,tidy=TRUE-------------------------------------------
# library(tidyverse)
# library(ggpubr)
#
# t1 <- ggplot(data = trueMj)+
# geom_point(mapping = aes(y=mj1,x=number))+
# ggtitle(expression("True M"["J"]*", 1"))+
# theme_bw()+
# theme(panel.grid = element_blank())
#
# t2 <- ggplot(data = trueMj)+
# geom_point(mapping = aes(y=mj2,x=number))+
# ggtitle(expression("True M"["J"]*", 2"))+
# theme_bw()+
# theme(panel.grid = element_blank())
#
# #SING mj
#
# S1 <- ggplot(data = SINGMj)+
# geom_point(mapping = aes(y=mj1,x=number))+
# ggtitle(expression("Estimated M"["J"]*", 1"))+
# theme_bw()+
# theme(panel.grid = element_blank())
#
# S2 <- ggplot(data = SINGMj)+
# geom_point(mapping = aes(y=mj2,x=number))+
# ggtitle(expression("Estimated M"["J"]*", 2"))+
# theme_bw()+
# theme(panel.grid = element_blank())
#
# ggarrange(t1,t2,S1,S2,ncol = 2,nrow = 2)
## ----mjex1,echo=FALSE,out.width = "100%",fig.cap="Estimated joint subject scores in example 1."----
knitr::include_graphics("figs/MJ.png",dpi = NA)
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