Adjustments + bugs fixing

[morpheus.git] / pkg / R / computeMu.R

diff --git a/pkg/R/computeMu.R b/pkg/R/computeMu.R
index f961fde..c1a9c51 100644 (file)
--- a/pkg/R/computeMu.R
+++ b/pkg/R/computeMu.R
@@ -3,6 +3,8 @@
 #' Estimate the normalized columns μ of the β matrix parameter in a mixture of
 #' logistic regressions models, with a spectral method described in the package vignette.
 #'
+#' @name computeMu
+#'
 #' @param X Matrix of input data (size nxd)
 #' @param Y Vector of binary outputs (size n)
 #' @param optargs List of optional argument:
@@ -21,28 +23,28 @@
 #'   and \code{generateSampleIO} for I/O random generation.
 #'
 #' @examples
-#' io = generateSampleIO(10000, 1/2, matrix(c(1,0,0,1),ncol=2), c(0,0), "probit")
-#' μ = computeMu(io$X, io$Y, list(K=2)) #or just X and Y for estimated K
+#' io <- generateSampleIO(10000, 1/2, matrix(c(1,0,0,1),ncol=2), c(0,0), "probit")
+#' μ <- computeMu(io$X, io$Y, list(K=2)) #or just X and Y for estimated K
 #'
 #' @export
-computeMu = function(X, Y, optargs=list())
+computeMu <- function(X, Y, optargs=list())
 {
   if (!is.matrix(X) || !is.numeric(X) || any(is.na(X)))
     stop("X: real matrix, no NA")
-  n = nrow(X)
-  d = ncol(X)
+  n <- nrow(X)
+  d <- ncol(X)
   if (!is.numeric(Y) || length(Y)!=n || any(Y!=0 & Y!=1))
     stop("Y: vector of 0 and 1, size nrow(X), no NA")
   if (!is.list(optargs))
     stop("optargs: list")
 
   # Step 0: Obtain the empirically estimated moments tensor, estimate also K
-  M = if (is.null(optargs$M)) computeMoments(X,Y) else optargs$M
-  K = optargs$K
+  M <- if (is.null(optargs$M)) computeMoments(X,Y) else optargs$M
+  K <- optargs$K
   if (is.null(K))
   {
     # TODO: improve this basic heuristic
-    Σ = svd(M[[2]])$d
+    Σ <- svd(M[[2]])$d
     large_ratio <- ( abs(Σ[-d] / Σ[-1]) > 3 )
     K <- if (any(large_ratio)) max(2, which.min(large_ratio)) else d
   }
@@ -50,24 +52,24 @@ computeMu = function(X, Y, optargs=list())
     stop("K: integer >= 2, <= d")
 
   # Step 1: generate a family of d matrices to joint-diagonalize to increase robustness
-  d = ncol(X)
-  fixed_design = FALSE
-  jd_nvects = ifelse(!is.null(optargs$jd_nvects), optargs$jd_nvects, 0)
+  d <- ncol(X)
+  fixed_design <- FALSE
+  jd_nvects <- ifelse(!is.null(optargs$jd_nvects), optargs$jd_nvects, 0)
   if (jd_nvects == 0)
   {
-    jd_nvects = d
-    fixed_design = TRUE
+    jd_nvects <- d
+    fixed_design <- TRUE
   }
-  M2_t = array(dim=c(d,d,jd_nvects))
+  M2_t <- array(dim=c(d,d,jd_nvects))
   for (i in seq_len(jd_nvects))
   {
-    rho = if (fixed_design) c(rep(0,i-1),1,rep(0,d-i)) else normalize( rnorm(d) )
-    M2_t[,,i] = .T_I_I_w(M[[3]],rho)
+    rho <- if (fixed_design) c(rep(0,i-1),1,rep(0,d-i)) else normalize( rnorm(d) )
+    M2_t[,,i] <- .T_I_I_w(M[[3]],rho)
   }
 
   # Step 2: obtain factors u_i (and their inverse) from the joint diagonalisation of M2_t
-  jd_method = ifelse(!is.null(optargs$jd_method), optargs$jd_method, "uwedge")
-  V =
+  jd_method <- ifelse(!is.null(optargs$jd_method), optargs$jd_method, "uwedge")
+  V <-
     if (jd_nvects > 1) {
       # NOTE: increasing itermax does not help to converge, thus we suppress warnings
       suppressWarnings({jd = jointDiag::ajd(M2_t, method=jd_method)})
@@ -77,17 +79,17 @@ computeMu = function(X, Y, optargs=list())
       eigen(M2_t[,,1])$vectors
 
   # Step 3: obtain final factors from joint diagonalisation of T(I,I,u_i)
-  M2_t = array(dim=c(d,d,K))
+  M2_t <- array(dim=c(d,d,K))
   for (i in seq_len(K))
-    M2_t[,,i] = .T_I_I_w(M[[3]],V[,i])
+    M2_t[,,i] <- .T_I_I_w(M[[3]],V[,i])
   suppressWarnings({jd = jointDiag::ajd(M2_t, method=jd_method)})
-  U = if (jd_method=="uwedge") MASS::ginv(jd$B) else jd$A
-  μ = normalize(U[,1:K])
+  U <- if (jd_method=="uwedge") MASS::ginv(jd$B) else jd$A
+  μ <- normalize(U[,1:K])
 
   # M1 also writes M1 = sum_k coeff_k * μ_k, where coeff_k >= 0
   # ==> search decomposition of vector M1 onto the (truncated) basis μ (of size dxK)
   # This is a linear system μ %*% C = M1 with C of size K ==> C = psinv(μ) %*% M1
-  C = MASS::ginv(μ) %*% M[[1]]
-  μ[,C < 0] = - μ[,C < 0]
+  C <- MASS::ginv(μ) %*% M[[1]]
+  μ[,C < 0] <- - μ[,C < 0]
   μ
 }