#' EMGLLF #' #' Description de EMGLLF #' #' @param phiInit an initialization for phi #' @param rhoInit an initialization for rho #' @param piInit an initialization for pi #' @param gamInit initialization for the a posteriori probabilities #' @param mini integer, minimum number of iterations in the EM algorithm, by default = 10 #' @param maxi integer, maximum number of iterations in the EM algorithm, by default = 100 #' @param gamma integer for the power in the penaly, by default = 1 #' @param lambda regularization parameter in the Lasso estimation #' @param X matrix of covariates (of size n*p) #' @param Y matrix of responses (of size n*m) #' @param eps real, threshold to say the EM algorithm converges, by default = 1e-4 #' #' @return A list ... phi,rho,pi,LLF,S,affec: #' phi : parametre de moyenne renormalisé, calculé par l'EM #' rho : parametre de variance renormalisé, calculé par l'EM #' pi : parametre des proportions renormalisé, calculé par l'EM #' LLF : log vraisemblance associée à cet échantillon, pour les valeurs estimées des paramètres #' S : ... affec : ... #' #' @export EMGLLF <- function(phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma, lambda, X, Y, eps, fast) { if (!fast) { # Function in R return(.EMGLLF_R(phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma, lambda, X, Y, eps)) } # Function in C n <- nrow(X) #nombre d'echantillons p <- ncol(X) #nombre de covariables m <- ncol(Y) #taille de Y (multivarié) k <- length(piInit) #nombre de composantes dans le mélange .Call("EMGLLF", phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma, lambda, X, Y, eps, phi = double(p * m * k), rho = double(m * m * k), pi = double(k), LLF = double(maxi), S = double(p * m * k), affec = integer(n), n, p, m, k, PACKAGE = "valse") } # R version - slow but easy to read .EMGLLF_R <- function(phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma, lambda, X, Y, eps) { # Matrix dimensions: NOTE: phiInit *must* be an array (even if p==1) n <- dim(Y)[1] p <- dim(phiInit)[1] m <- dim(phiInit)[2] k <- dim(phiInit)[3] # Outputs phi <- array(NA, dim = c(p, m, k)) phi[1:p, , ] <- phiInit rho <- rhoInit pi <- piInit llh <- -Inf S <- array(0, dim = c(p, m, k)) # Algorithm variables gam <- gamInit Gram2 <- array(0, dim = c(p, p, k)) ps2 <- array(0, dim = c(p, m, k)) X2 <- array(0, dim = c(n, p, k)) Y2 <- array(0, dim = c(n, m, k)) EPS <- 1e-15 for (ite in 1:maxi) { # Remember last pi,rho,phi values for exit condition in the end of loop Phi <- phi Rho <- rho Pi <- pi # Computations associated to X and Y for (r in 1:k) { for (mm in 1:m) Y2[, mm, r] <- sqrt(gam[, r]) * Y[, mm] for (i in 1:n) X2[i, , r] <- sqrt(gam[i, r]) * X[i, ] for (mm in 1:m) ps2[, mm, r] <- crossprod(X2[, , r], Y2[, mm, r]) for (j in 1:p) { for (s in 1:p) Gram2[j, s, r] <- crossprod(X2[, j, r], X2[, s, r]) } } ## M step # For pi b <- sapply(1:k, function(r) sum(abs(phi[, , r]))) gam2 <- colSums(gam) a <- sum(gam %*% log(pi)) # While the proportions are nonpositive kk <- 0 pi2AllPositive <- FALSE while (!pi2AllPositive) { pi2 <- pi + 0.1^kk * ((1/n) * gam2 - pi) pi2AllPositive <- all(pi2 >= 0) kk <- kk + 1 } # t(m) is the largest value in the grid O.1^k such that it is nonincreasing while (kk < 1000 && -a/n + lambda * sum(pi^gamma * b) < # na.rm=TRUE to handle 0*log(0) -sum(gam2 * log(pi2), na.rm=TRUE)/n + lambda * sum(pi2^gamma * b)) { pi2 <- pi + 0.1^kk * (1/n * gam2 - pi) kk <- kk + 1 } t <- 0.1^kk pi <- (pi + t * (pi2 - pi))/sum(pi + t * (pi2 - pi)) # For phi and rho for (r in 1:k) { for (mm in 1:m) { ps <- 0 for (i in 1:n) ps <- ps + Y2[i, mm, r] * sum(X2[i, , r] * phi[, mm, r]) nY2 <- sum(Y2[, mm, r]^2) rho[mm, mm, r] <- (ps + sqrt(ps^2 + 4 * nY2 * gam2[r]))/(2 * nY2) } } for (r in 1:k) { for (j in 1:p) { for (mm in 1:m) { S[j, mm, r] <- -rho[mm, mm, r] * ps2[j, mm, r] + sum(phi[-j, mm, r] * Gram2[j, -j, r]) if (abs(S[j, mm, r]) <= n * lambda * (pi[r]^gamma)) { phi[j, mm, r] <- 0 } else if (S[j, mm, r] > n * lambda * (pi[r]^gamma)) { phi[j, mm, r] <- (n * lambda * (pi[r]^gamma) - S[j, mm, r])/Gram2[j, j, r] } else { phi[j, mm, r] <- -(n * lambda * (pi[r]^gamma) + S[j, mm, r])/Gram2[j, j, r] } } } } ## E step # Precompute det(rho[,,r]) for r in 1...k detRho <- sapply(1:k, function(r) det(rho[, , r])) sumLogLLH <- 0 for (i in 1:n) { # Update gam[,]; use log to avoid numerical problems logGam <- sapply(1:k, function(r) { log(pi[r]) + log(detRho[r]) - 0.5 * sum((Y[i, ] %*% rho[, , r] - X[i, ] %*% phi[, , r])^2) }) logGam <- logGam - max(logGam) #adjust without changing proportions gam[i, ] <- exp(logGam) norm_fact <- sum(gam[i, ]) gam[i, ] <- gam[i, ] / norm_fact sumLogLLH <- sumLogLLH + log(norm_fact) - log((2 * base::pi)^(m/2)) } sumPen <- sum(pi^gamma * b) last_llh <- llh llh <- -sumLogLLH/n #+ lambda * sumPen dist <- ifelse(ite == 1, llh, (llh - last_llh)/(1 + abs(llh))) Dist1 <- max((abs(phi - Phi))/(1 + abs(phi))) Dist2 <- max((abs(rho - Rho))/(1 + abs(rho))) Dist3 <- max((abs(pi - Pi))/(1 + abs(Pi))) dist2 <- max(Dist1, Dist2, Dist3) if (ite >= mini && (dist >= eps || dist2 >= sqrt(eps))) break } list(phi = phi, rho = rho, pi = pi, llh = llh, S = S) }