fixed gen3 library

selbouhaddani · Oct 15, 2024 · 650e46b · 650e46b
1 parent 249f22b
commit 650e46b
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Showing 4 changed files with 20 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,7 +12,7 @@ LazyData: TRUE
 LinkingTo: Rcpp, RcppArmadillo
 Imports:
     stats, utils, MASS, OmicsPLS, Rcpp, RcppArmadillo, dplyr, tibble, magrittr, parallel
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
diff --git a/R/PO2PLS_functions.R b/R/PO2PLS_functions.R
@@ -10,7 +10,6 @@
 #'
 #' Maintainer: Said el Bouhaddani (\email{s.el_bouhaddani@@outlook.com}).
 #'
-#' @docType package
 #' @name PO2PLS-package
 #' @keywords Probabilistic-O2PLS
 #' @import OmicsPLS Rcpp RcppArmadillo magrittr dplyr tibble parallel
@@ -19,7 +18,7 @@
 #' @importFrom stats pchisq rnorm runif sd
 #' @importFrom MASS ginv
 #' @useDynLib PO2PLS, .registration=TRUE
-NULL
+"_PACKAGE"
 
 #' Construct a block-diagonal matrix
 #'

diff --git a/R/PO2PLS_gen3.R b/R/PO2PLS_gen3.R
@@ -1,5 +1,5 @@
-library(OmicsPLS)
-library(PO2PLS)
+# library(OmicsPLS)
+# library(PO2PLS)
 
 # p <- 10
 # q <- 11
@@ -9,15 +9,15 @@ library(PO2PLS)
 # ry <- 1
 # prm <- generate_params(p, q, r, rx, ry)
 # prm3 <- generate_params(p, p3, r, rx, ry)
-# 
+#
 # prm
 # prm3
 
 
 gen_par3 <- function(p1, p2, p3, r, rx1, rx2, rx3, alpha = 0.1){
   prm <- generate_params(p1, p2, r, rx1, rx2, alpha)
   prm3 <- generate_params(p3, p2, r, rx3, rx2, alpha)
-  list(W1 = prm$W, 
+  list(W1 = prm$W,
        W2 = prm$C,
        W3 = prm3$W,
        Wo1 = prm$Wo,
@@ -41,61 +41,61 @@ gen_dat3 <- function(N, params, alpha_out = 0.1, sparse = FALSE){
   Wo1 <- params$Wo1
   Wo2 <- params$Wo2
   Wo3 <- params$Wo3
-  
+
   r <- ncol(W1)
   rx1 <- ncol(Wo1)
   rx2 <- ncol(Wo2)
   rx3 <- ncol(Wo3)
   p1 <- nrow(W1)
   p2 <- nrow(W2)
   p3 <- nrow(W3)
-  
+
   if(sparse){
     W1[-(1:(p1/4)),] <- 0
     W2[-(1:(p2/4)),] <- 0
     W3[-(1:(p3/4)),] <- 0
   }
   # print(W1)
-  
+
   SigT = params$SigT
   SigTo1 = params$SigTo1 + 1e-06 * SigT[1] * (params$SigTo1[1] == 0)
   SigTo2 = params$SigTo2 + 1e-06 * SigT[1] * (params$SigTo2[1] == 0)
   SigTo3 = params$SigTo3 + 1e-06 * SigT[1] * (params$SigTo3[1] == 0)
-  
+
   N <- 3/2 * N
-  
+
   Tt <- matrix(rnorm(N * r), N, r) %*% chol(SigT)
   To1 <- matrix(rnorm(N * rx1), N, rx1) %*% chol(SigTo1)
   To2 <- matrix(rnorm(N * rx2), N, rx2) %*% chol(SigTo2)
   To3 <- matrix(rnorm(N * rx3), N, rx3) %*% chol(SigTo3)
-  
+
   E1 <- matrix(rnorm(N * p1), N, p1) * sqrt(params$sig2E1)
   E2 <- matrix(rnorm(N * p2), N, p2) * sqrt(params$sig2E2)
   E3 <- matrix(rnorm(N * p3), N, p3) * sqrt(params$sig2E3)
-  
+
   X1 <- Tt %*% t(W1) + To1 %*% t(Wo1) + E1
   X2 <- Tt %*% t(W2) + To2 %*% t(Wo2) + E2
   X3 <- Tt %*% t(W3) + To3 %*% t(Wo3) + E3
-  
+
   outc <- Tt %*% params$beta_T
   outc <- outc + rnorm(N, 0, sd = sqrt( alpha_out/(1-alpha_out)*var(outc) ))
-  
+
   indx1 <- order(outc)[1:(N/3)]
   indx2 <- order(-outc)[1:(N/3)]
   indxN <- c(indx1, indx2)
-  
+
   outc_bin <- 1*(outc > 0)
   outc_bin <- outc_bin[indxN]
-  
+
   #print((indxN))
   #print(str(X1))
-  
+
   X1 <- X1[indxN,]
   X2 <- X2[indxN,]
   X3 <- X3[indxN,]
-  
+
   return(list(X1 = X1, X2 = X2, X3 = X3, outc = outc_bin))
-  
+
 }
 
 

diff --git a/R/PO2PLS_output.R b/R/PO2PLS_output.R
@@ -173,8 +173,6 @@ print.loglik.po2m <- function(x, digits=3, ...){
 #' @export
 LRT <- function(fit, fit0, digits=3, ...) UseMethod("LRT")
 
-#' @inherit LRT
-#'
 #' @rdname LRT
 #' @export
 LRT.po2m <- function(fit, fit0, digits=3, ...){