From ce7f42bbb338fcd4093a31932701274572a6406c Mon Sep 17 00:00:00 2001
From: Ted Enamorado <tedenamorado@1064-al-05006.lan>
Date: Thu, 16 Nov 2023 23:08:06 -0600
Subject: [PATCH] fixing issues with Matrix class

---
 R/gammaCK2par.R    |  8 +++++++-
 R/gammaCKpar.R     | 10 ++++++++--
 R/gammaNUMCK2par.R |  8 +++++++-
 R/gammaNUMCKpar.R  | 10 +++++++---
 4 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/R/gammaCK2par.R b/R/gammaCK2par.R
index 7148bbc..f0a0423 100644
--- a/R/gammaCK2par.R
+++ b/R/gammaCK2par.R
@@ -126,7 +126,13 @@ gammaCK2par <- function(matAp, matBp, n.cores = NULL, cut.a = 0.92, method = "jw
           t <- Matrix(t, sparse = T)
         }
         
-        t@x[t@x >= cut] <- 2; gc()       	
+        if(is(t, "ddiMatrix")) {
+          t <- t * 2
+        } else {
+          t@x[t@x >= cut] <- 2
+        }
+        gc()
+        
         slice.1 <- m[[2]]
         slice.2 <- y[[2]]
         indexes.2 <- which(t == 2, arr.ind = T)
diff --git a/R/gammaCKpar.R b/R/gammaCKpar.R
index fb01afc..7c380c8 100644
--- a/R/gammaCKpar.R
+++ b/R/gammaCKpar.R
@@ -128,8 +128,14 @@ gammaCKpar <- function(matAp, matBp, n.cores = NULL, cut.a = 0.92, cut.p = 0.88,
         		t <- Matrix(t, sparse = T)
         	}
         
-        t@x[t@x >= cut[1]] <- 2
-        t@x[t@x >= cut[2] & t@x < cut[1]] <- 1; gc()
+        if(is(t, "ddiMatrix")) {
+          t <- t * 2
+        } else {
+          t@x[t@x >= cut[1]] <- 2
+          t@x[t@x >= cut[2] & t@x < cut[1]] <- 1
+        }
+        gc()
+
         slice.1 <- m[[2]]
         slice.2 <- y[[2]]
         indexes.2 <- which(t == 2, arr.ind = T)
diff --git a/R/gammaNUMCK2par.R b/R/gammaNUMCK2par.R
index 4b0a96c..fd1e374 100644
--- a/R/gammaNUMCK2par.R
+++ b/R/gammaNUMCK2par.R
@@ -89,7 +89,13 @@ gammaNUMCK2par <- function(matAp, matBp, n.cores = NULL, cut.a = 1) {
         t[ t > cut ] <- 0
         t <- Matrix(t, sparse = T)
         
-        t@x[t@x <= cut] <- 2; gc()       	
+        if(is(t, "ddiMatrix")) {
+          t <- t * 2
+        } else {
+          t@x[t@x <= cut] <- 2
+        }
+        gc()
+        
         slice.1 <- m[[2]]
         slice.2 <- y[[2]]
         indexes.2 <- which(t == 2, arr.ind = T)
diff --git a/R/gammaNUMCKpar.R b/R/gammaNUMCKpar.R
index 51c67e2..d2046fe 100644
--- a/R/gammaNUMCKpar.R
+++ b/R/gammaNUMCKpar.R
@@ -83,9 +83,13 @@ gammaNUMCKpar <- function(matAp, matBp, n.cores = NULL, cut.a = 1, cut.p = 2) {
         t[ t > cut[2] ] <- 0
         t <- Matrix(t, sparse = T)
 
-        t@x[t@x <= cut[1]] <- cut[2] + 1; gc()       	                
-        t@x[t@x > cut[1] & t@x <= cut[2]] <- 1; gc()       	
-
+        if(is(t, "ddiMatrix")) {
+          t <- t * (cut[2] + 1)
+        } else {
+          t@x[t@x <= cut[1]] <- cut[2] + 1; gc()       	                
+          t@x[t@x > cut[1] & t@x <= cut[2]] <- 1; gc()       	
+        }
+        
         slice.1 <- m[[2]]
         slice.2 <- y[[2]]
         indexes.2 <- which(t == cut[2] + 1, arr.ind = T)