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# rotation algorithms
#
# YR 3 April 2019 -- gradient projection algorithm
# YR 21 April 2019 -- pairwise rotation algorithm
# YR 11 May 2020 -- order.idx is done in rotation matrix
# (suggested by Florian Scharf)
# main function to rotate a single matrix 'A'
lav_matrix_rotate <- function(A = NULL, # original matrix
orthogonal = FALSE, # default is oblique
method = "geomin", # default rot method
method.args = list( geomin.epsilon = 0.01,
orthomax.gamma = 1,
cf.gamma = 0,
oblimin.gamma = 0,
promax.kappa = 4,
target = matrix(0,0,0),
target.mask = matrix(0,0,0) ),
init.ROT = NULL, # initial rotation matrix
init.ROT.check = TRUE, # check if init ROT is ok
rstarts = 100L, # number of random starts
row.weights = "default", # row weighting
std.ov = FALSE, # rescale ov
ov.var = NULL, # ov variances
warn = TRUE, # show warnings?
verbose = FALSE, # show iterations
algorithm = "gpa", # rotation algorithm
reflect = TRUE, # refect sign
order.lv.by = "index", # how to order the lv's
gpa.tol = 0.00001, # stopping tol gpa
tol = 1e-07, # stopping tol others
keep.rep = FALSE, # store replications
max.iter = 10000L) { # max gpa iterations
# check A
if(!inherits(A, "matrix")) {
stop("lavaan ERROR: A does not seem to a matrix")
}
P <- nrow(A); M <- ncol(A)
if(M < 2L) { # single dimension
res <- list(LAMBDA = A, PHI = matrix(1, 1, 1), ROT = matrix(1, 1, 1),
orthogonal = orthogonal, method = "none",
method.args = list(), row.weights = "none",
algorithm = "none", iter = 0L, converged = TRUE,
method.value = 0)
return(res)
}
# method
method <- tolower(method)
# if promax, skip everything, then call promax() later
if(method == "promax") {
#orig.algorithm <- algorithm
#orig.rstarts <- rstarts
algorithm <- "none"
rstarts <- 0L
init.ROT <- NULL
ROT <- diag(M)
}
# check init.ROT
if(!is.null(init.ROT) && init.ROT.check) {
if(!inherits(init.ROT, "matrix")) {
stop("lavaan ERROR: init.ROT does not seem to a matrix")
}
if(nrow(init.ROT) != M) {
stop("lavaan ERROR: nrow(init.ROT) = ", nrow(init.ROT),
" does not equal ncol(A) = ", M)
}
if(nrow(init.ROT) != ncol(init.ROT)) {
stop("lavaan ERROR: nrow(init.ROT) = ", nrow(init.ROT),
" does not equal ncol(init.ROT) = ", ncol(init.ROT))
}
# rotation matrix? init.ROT^T %*% init.ROT = I
RR <- crossprod(init.ROT)
if(!lav_matrix_rotate_check(init.ROT, orthogonal = orthogonal)) {
stop("lavaan ERROR: init.ROT does not look like a rotation matrix")
}
}
# determine method function name
if(method %in% c("cf-quartimax", "cf-varimax", "cf-equamax",
"cf-parsimax", "cf-facparsim")) {
method.fname <- "lav_matrix_rotate_cf"
method.args$cf.gamma <- switch(method,
"cf-quartimax" = 0,
"cf-varimax" = 1 / P,
"cf-equamax" = M / (2 * P),
"cf-parsimax" = (M - 1) / (P + M - 2),
"cf-facparsim" = 1)
} else if(method %in% c("bi-quartimin", "biquartimin")) {
method.fname <- "lav_matrix_rotate_biquartimin"
} else if(method %in% c("bi-geomin", "bigeomin")) {
method.fname <- "lav_matrix_rotate_bigeomin"
} else {
method.fname <- paste("lav_matrix_rotate_", method, sep = "")
}
# check if rotation method exists
check <- try(get(method.fname), silent = TRUE)
if(inherits(check, "try-error")) {
stop("lavaan ERROR: unknown rotation method: ", method.fname)
}
# if target, check target matrix
if(method == "target" || method == "pst") {
target <- method.args$target
# check dimension of target/A
if(nrow(target) != nrow(A)) {
stop("lavaan ERROR: nrow(target) != nrow(A)")
}
if(ncol(target) != ncol(A)) {
stop("lavaan ERROR: ncol(target) != ncol(A)")
}
}
if(method == "pst") {
target.mask <- method.args$target.mask
# check dimension of target.mask/A
if(nrow(target.mask) != nrow(A)) {
stop("lavaan ERROR: nrow(target.mask) != nrow(A)")
}
if(ncol(target.mask) != ncol(A)) {
stop("lavaan ERROR: ncol(target.mask) != ncol(A)")
}
}
# we keep this here, so lav_matrix_rotate() can be used independently
if(method == "target" && anyNA(target)) {
method <- "pst"
method.fname <- "lav_matrix_rotate_pst"
target.mask <- matrix(1, nrow = nrow(target), ncol = ncol(target))
target.mask[ is.na(target) ] <- 0
method.args$target.mask <- target.mask
}
# set orthogonal option
if(missing(orthogonal)) {
# the default is oblique, except for varimax, entropy and a few others
if(method %in% c("varimax", "entropy", "mccammon",
"tandem1", "tandem2") ) {
orthogonal <- TRUE
} else {
orthogonal <- FALSE
}
} else {
if(!orthogonal && method %in% c("varimax", "entropy", "mccammon",
"tandem1", "tandem2")) {
warning("lavaan WARNING: rotation method ", dQuote(method),
" may not work with oblique rotation.")
}
}
# set row.weights
row.weights <- tolower(row.weights)
if(row.weights == "default") {
# the default is "none", except for varimax
if(method %in% c("varimax", "promax")) {
row.weights <- "kaiser"
} else {
row.weights <- "none"
}
}
# check algorithm
algorithm <- tolower(algorithm)
if(algorithm %in% c("gpa", "pairwise", "none")) {
# nothing to do
} else {
stop("lavaan ERROR: algorithm must be gpa or pairwise")
}
# 1. compute row weigths
# 1.a cov -> cor?
if(std.ov) {
A <- A * 1/sqrt(ov.var)
}
if(row.weights == "none") {
weights <- rep(1.0, P)
} else if(row.weights == "kaiser") {
weights <- lav_matrix_rotate_kaiser_weights(A)
} else if(row.weights == "cureton-mulaik") {
weights <- lav_matrix_rotate_cm_weights(A)
} else {
stop("lavaan ERROR: row.weights can be none, kaiser or cureton-mulaik")
}
A <- A * weights
# 2. rotate
# multiple random starts?
if(rstarts > 0L) {
REP <- sapply(seq_len(rstarts), function(rep) {
# random start (always orthogonal)
init.ROT <- lav_matrix_rotate_gen(M = M, orthogonal = TRUE)
if(verbose) {
cat("\n")
cat("rstart = ", sprintf("%4d", rep), " start:\n")
}
# choose rotation algorithm
if(algorithm == "gpa") {
ROT <- lav_matrix_rotate_gpa(A = A, orthogonal = orthogonal,
init.ROT = init.ROT,
method.fname = method.fname,
method.args = method.args,
warn = warn,
verbose = verbose,
gpa.tol = gpa.tol,
max.iter = max.iter)
info <- attr(ROT, "info"); attr(ROT, "info") <- NULL
res <- c(info$method.value, lav_matrix_vec(ROT))
} else if(algorithm == "pairwise") {
ROT <- lav_matrix_rotate_pairwise(A = A,
orthogonal = orthogonal,
init.ROT = init.ROT,
method.fname = method.fname,
method.args = method.args,
warn = warn,
verbose = verbose,
tol = tol,
max.iter = max.iter)
info <- attr(ROT, "info"); attr(ROT, "info") <- NULL
res <- c(info$method.value, lav_matrix_vec(ROT))
}
if(verbose) {
cat("rstart = ", sprintf("%4d", rep),
" end; current crit = ", sprintf("%17.15f", res[1]), "\n")
}
res
})
best.idx <- which.min(REP[1,])
ROT <- matrix(REP[-1, best.idx], nrow = M, ncol = M)
if(keep.rep) {
info <- list(method.value = REP[1, best.idx], REP = REP)
} else {
info <- list(method.value = REP[1, best.idx])
}
} else if(algorithm != "none") {
# initial rotation matrix
if(is.null(init.ROT)) {
init.ROT <- diag(M)
}
# Gradient Projection Algorithm
if(algorithm == "gpa") {
ROT <- lav_matrix_rotate_gpa(A = A, orthogonal = orthogonal,
init.ROT = init.ROT,
method.fname = method.fname,
method.args = method.args,
warn = warn,
verbose = verbose,
gpa.tol = gpa.tol,
max.iter = max.iter)
} else if(algorithm == "pairwise") {
ROT <- lav_matrix_rotate_pairwise(A = A,
orthogonal = orthogonal,
init.ROT = init.ROT,
method.fname = method.fname,
method.args = method.args,
warn = warn,
verbose = verbose,
tol = tol,
max.iter = max.iter)
}
info <- attr(ROT, "info"); attr(ROT, "info") <- NULL
}
# final rotation
if(orthogonal) {
LAMBDA <- A %*% ROT
PHI <- diag(ncol(LAMBDA)) # correlation matrix == I
} else {
LAMBDA <- t(solve(ROT, t(A)))
PHI <- crossprod(ROT) # correlation matrix
}
# 3. undo row weighting
LAMBDA <- LAMBDA / weights
# here, after re-weighted, we run promax if needed
if(method == "promax") {
LAMBDA.orig <- LAMBDA
# first, run 'classic' varimax using varimax() from the stats package
# we split varimax from promax, so we can control the normalize flag
normalize.flag <- row.weights == "kaiser"
xx <- stats::varimax(x = LAMBDA, normalize = normalize.flag)
# promax
kappa <- method.args$promax.kappa
out <- lav_matrix_rotate_promax(x = xx$loadings, m = kappa,
varimax.ROT = xx$rotmat)
LAMBDA <- out$loadings
PHI <- solve(crossprod(out$rotmat))
# compute 'ROT' to be compatible with GPa
ROTt.inv <- solve(crossprod(LAMBDA.orig),
crossprod(LAMBDA.orig, LAMBDA))
ROT <- solve(t(ROTt.inv))
info <- list(algorithm = "promax", iter = 0L, converged = TRUE,
method.value = as.numeric(NA))
}
# 3.b undo cov -> cor
if(std.ov) {
LAMBDA <- LAMBDA * sqrt(ov.var)
}
# 4.a reflect so that column sum is always positive
if(reflect) {
SUM <- colSums(LAMBDA)
neg.idx <- which(SUM < 0)
if(length(neg.idx) > 0L) {
LAMBDA[, neg.idx] <- -1 * LAMBDA[, neg.idx, drop = FALSE]
ROT[, neg.idx] <- -1 * ROT[, neg.idx, drop = FALSE]
if(!orthogonal) {
# recompute PHI
PHI <- crossprod(ROT)
}
}
}
# 4.b reorder the columns
if(order.lv.by == "sumofsquares") {
L2 <- LAMBDA * LAMBDA
order.idx <- base::order(colSums(L2), decreasing = TRUE)
} else if(order.lv.by == "index") {
# reorder using Asparouhov & Muthen 2009 criterion (see Appendix D)
max.loading <- apply(abs(LAMBDA), 2, max)
# 1: per factor, number of the loadings that are at least 0.8 of the
# highest loading of the factor
# 2: mean of the index numbers
average.index <- sapply(seq_len(ncol(LAMBDA)), function(i)
mean(which(abs(LAMBDA[,i]) >= 0.8 * max.loading[i])))
# order of the factors
order.idx <- base::order(average.index)
} else if(order.lv.by == "none") {
order.idx <- seq_len(ncol(LAMBDA))
} else {
stop("lavaan ERROR: order must be index, sumofsquares or none")
}
# do the same in PHI
LAMBDA <- LAMBDA[, order.idx, drop = FALSE]
PHI <- PHI[order.idx, order.idx, drop = FALSE]
# new in 0.6-6, also do this in ROT, so we won't have to do this
# again upstream
ROT <- ROT[, order.idx, drop = FALSE]
# 6. return results as a list
res <- list(LAMBDA = LAMBDA, PHI = PHI, ROT = ROT, order.idx = order.idx,
orthogonal = orthogonal, method = method,
method.args = method.args, row.weights = row.weights)
# add method info
res <- c(res, info)
res
}
# Gradient Projection Algorithm (Jennrich 2001, 2002)
#
# - this is a translation of the SAS PROC IML code presented in the Appendix
# of Bernaards & Jennrich (2005)
# - as the orthogonal and oblique algorithm are so similar, they are
# combined in a single function
# - the default is oblique rotation
#
lav_matrix_rotate_gpa <- function(A = NULL, # original matrix
orthogonal = FALSE, # default is oblique
init.ROT = NULL, # initial rotation
method.fname = NULL, # criterion function
method.args = list(), # optional method args
warn = TRUE,
verbose = FALSE,
gpa.tol = 0.00001,
max.iter = 10000L) {
# number of columns
M <- ncol(A)
# transpose of A (not needed for orthogonal)
At <- t(A)
# check init.ROT
if(is.null(init.ROT)) {
ROT <- diag(M)
} else {
ROT <- init.ROT
}
# set initial value of alpha to 1
alpha <- 1
# initial rotation
if(orthogonal) {
LAMBDA <- A %*% ROT
} else {
LAMBDA <- t(solve(ROT, At))
}
# using the current LAMBDA, evaluate the user-specified
# rotation criteron; return Q (the criterion) and its gradient Gq
Q <- do.call(method.fname,
c(list(LAMBDA = LAMBDA), method.args, list(grad = TRUE)))
Gq <- attr(Q, "grad"); attr(Q, "grad") <- NULL
Q.current <- Q
# compute gradient GRAD of f() at ROT from the gradient Gq of Q at LAMBDA
# in a manner appropiate for orthogonal or oblique rotation
if(orthogonal) {
GRAD <- crossprod(A, Gq)
} else {
GRAD <- -1 * solve(t(init.ROT), crossprod(Gq, LAMBDA))
}
# start iterations
converged <- FALSE
for(iter in seq_len(max.iter + 1L)) {
# compute projection Gp of GRAD onto the linear manifold tangent at
# ROT to the manifold of orthogonal or normal (for oblique) matrices
#
# this projection is zero if and only if ROT is a stationary point of
# f() restricted to the orthogonal/normal matrices
if(orthogonal) {
MM <- crossprod(ROT, GRAD)
SYMM <- (MM + t(MM))/2
Gp <- GRAD - (ROT %*% SYMM)
} else {
Gp <- GRAD - t( t(ROT) * colSums(ROT * GRAD) )
}
# check Frobenius norm of Gp
frob <- sqrt( sum(Gp * Gp) )
# if verbose, print
if(verbose) {
cat("iter = ", sprintf("%4d", iter-1),
" Q = ", sprintf("%9.7f", Q.current),
" frob.log10 = ", sprintf("%10.7f", log10(frob)),
" alpha = ", sprintf("%9.7f", alpha), "\n")
}
if(frob < gpa.tol) {
converged <- TRUE
break
}
# update
alpha <- 2*alpha
for(i in seq_len(1000)) { # make option?
# step in the negative projected gradient direction
# (note, the original algorithm in Jennrich 2001 used G, not Gp)
X <- ROT - alpha * Gp
if(orthogonal) {
# use SVD to compute the projection ROTt of X onto the manifold
# of orthogonal matrices
svd.out <- svd(X)
U <- svd.out$u
V <- svd.out$v
ROTt <- U %*% t(V)
} else {
# compute the projection ROTt of X onto the manifold
# of normal matrices
v <- 1/sqrt(apply(X^2, 2, sum))
ROTt <- X %*% diag(v)
}
# rotate again
if(orthogonal) {
LAMBDA <- A %*% ROTt
} else {
LAMBDA <- t(solve(ROTt, At))
}
# evaluate criterion
Q.new <- do.call(method.fname, c(list(LAMBDA = LAMBDA),
method.args, list(grad = TRUE)))
Gq <- attr(Q.new, "grad"); attr(Q.new, "grad") <- NULL
# check stopping criterion
if(Q.new < Q.current - 0.5*frob*frob*alpha) {
break
} else {
alpha <- alpha/2
}
if(warn && i == 1000) {
warning("lavaan WARNING: half-stepping failed in GPA\n")
}
}
# update
ROT <- ROTt
Q.current <- Q.new
if(orthogonal) {
GRAD <- crossprod(A, Gq)
} else {
GRAD <- -1 * solve(t(ROT), crossprod(Gq, LAMBDA))
}
} # iter
# warn if no convergence
if(!converged && warn) {
warning("lavaan WARNING: ",
"GP rotation algorithm did not converge after ",
max.iter, " iterations")
}
# algorithm information
info <- list(algorithm = "gpa",
iter = iter - 1L,
converged = converged,
method.value = Q.current)
attr(ROT, "info") <- info
ROT
}
# pairwise rotation algorithm with direct line search
#
# based on Kaiser's (1959) algorithm and Jennrich and Sampson (1966) algorithm
# but to make it generic, a line search is used; inspired by Browne 2001
#
# - orthogonal: rotate one pair of columns (=plane) at a time
# - oblique: rotate 1 factor in one pair of columns (=plane) at a time
# note: in the oblique case, (1,2) is not the same as (2,1)
# - BUT use optimize() to find the optimal angle (for each plane)
# (see Browne, 2001, page 130)
# - repeat until the changes in the f() criterion are below tol
#
lav_matrix_rotate_pairwise <- function(A = NULL, # original matrix
orthogonal = FALSE,
init.ROT = NULL,
method.fname = NULL, # crit function
method.args = list(), # method args
warn = TRUE,
verbose = FALSE,
tol = 1e-8,
max.iter = 1000L) {
# number of columns
M <- ncol(A)
# initial LAMBDA + PHI
if(is.null(init.ROT)) {
LAMBDA <- A
if(!orthogonal) {
PHI <- diag(M)
}
} else {
if(orthogonal) {
LAMBDA <- A %*% init.ROT
} else {
LAMBDA <- t(solve(init.ROT, t(A)))
PHI <- crossprod(init.ROT)
}
}
# using the current LAMBDA, evaluate the user-specified
# rotation criteron; return Q (the criterion) only
Q.current <- do.call(method.fname, c(list(LAMBDA = LAMBDA),
method.args, list(grad = FALSE)))
# if verbose, print
if(verbose) {
cat("iter = ", sprintf("%4d", 0),
" Q = ", sprintf("%13.11f", Q.current), "\n")
}
# plane combinations
if(orthogonal) {
PLANE <- utils::combn(M, 2)
} else {
tmp <- utils::combn(M, 2)
PLANE <- cbind(tmp, tmp[c(2,1),,drop = FALSE])
}
# define objective function -- orthogonal
objf_orth <- function(theta = 0, A = NULL, col1 = 0L, col2 = 0L) {
# construct ROT
ROT <- diag(M)
ROT[col1, col1] <- base::cos(theta)
ROT[col1, col2] <- base::sin(theta)
ROT[col2, col1] <- -1 * base::sin(theta)
ROT[col2, col2] <- base::cos(theta)
# rotate
LAMBDA <- A %*% ROT
# evaluate criterion
Q <- do.call(method.fname, c(list(LAMBDA = LAMBDA),
method.args, list(grad = FALSE)))
Q
}
# define objective function -- oblique
objf_obliq <- function(delta = 0, A = NULL, col1 = 0L, col2 = 0L,
phi12 = 0) {
# construct ROT
ROT <- diag(M)
# gamma
gamma2 <- 1 + (2 * delta * phi12) + (delta * delta)
ROT[col1, col1] <- sqrt(abs(gamma2))
ROT[col1, col2] <- -1 * delta
ROT[col2, col1] <- 0
ROT[col2, col2] <- 1
# rotate
LAMBDA <- A %*% ROT
# evaluate criterion
Q <- do.call(method.fname, c(list(LAMBDA = LAMBDA),
method.args, list(grad = FALSE)))
Q
}
# start iterations
converged <- FALSE
Q.old <- Q.current
for(iter in seq_len(max.iter)) {
# rotate - one cycle
for(pl in seq_len(ncol(PLANE))) {
# choose plane
col1 <- PLANE[1, pl]
col2 <- PLANE[2, pl]
# optimize
if(orthogonal) {
out <- optimize(f = objf_orth, interval = c(-pi/4, +pi/4),
A = LAMBDA, col1 = col1, col2 = col2,
maximum = FALSE, tol = .Machine$double.eps^0.25)
# best rotation - for this plane
theta <- out$minimum
# construct ROT
ROT <- diag(M)
ROT[col1, col1] <- base::cos(theta)
ROT[col1, col2] <- base::sin(theta)
ROT[col2, col1] <- -1 * base::sin(theta)
ROT[col2, col2] <- base::cos(theta)
} else {
phi12 <- PHI[col1, col2]
out <- optimize(f = objf_obliq, interval = c(-1, +1),
A = LAMBDA, col1 = col1, col2 = col2,
phi12 = phi12,
maximum = FALSE, tol = .Machine$double.eps^0.25)
# best rotation - for this plane
delta <- out$minimum
# construct ROT
ROT <- diag(M)
# gamma
gamma2 <- 1 + (2 * delta * phi12) + (delta * delta)
gamma <- sqrt(abs(gamma2))
ROT[col1, col1] <- gamma
ROT[col1, col2] <- -1 * delta
ROT[col2, col1] <- 0
ROT[col2, col2] <- 1
}
# rotate
LAMBDA <- LAMBDA %*% ROT
if(!orthogonal) {
# rotate PHI
PHI[col1, ] <- (1/gamma)*PHI[col1,] + (delta/gamma)*PHI[col2,]
PHI[, col1] <- PHI[col1, ]
PHI[col1, col1] <- 1
}
} # all planes
# check for convergence
Q.current <- do.call(method.fname, c(list(LAMBDA = LAMBDA),
method.args, list(grad = FALSE)))
# absolute change in Q
diff <- abs(Q.old - Q.current)
# if verbose, print
if(verbose) {
cat("iter = ", sprintf("%4d", iter),
" Q = ", sprintf("%13.11f", Q.current),
" change = ", sprintf("%13.11f", diff), "\n")
}
if(diff < tol) {
converged <- TRUE
break
} else {
Q.old <- Q.current
}
} # iter
# warn if no convergence
if(!converged && warn) {
warning("lavaan WARNING: ",
"pairwise rotation algorithm did not converge after ",
max.iter, " iterations")
}
# compute final rotation matrix
if(orthogonal) {
ROT <- solve(crossprod(A), crossprod(A, LAMBDA))
} else {
# to be compatible with GPa
ROTt.inv <- solve(crossprod(A), crossprod(A, LAMBDA))
ROT <- solve(t(ROTt.inv))
}
# algorithm information
info <- list(algorithm = "pairwise",
iter = iter,
converged = converged,
method.value = Q.current)
attr(ROT, "info") <- info
ROT
}
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