Fix issue labelled rows in mult- functions

Fix small bug with mult- function and labelled rows
Japal · Jun 18, 2024 · fdf344d · fdf344d
1 parent cf11ec6
commit fdf344d
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Showing 7 changed files with 19 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: zCompositions
 Type: Package
 Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
-Version: 1.5.0-3
-Date: 2024-03-13
+Version: 1.5.0-4
+Date: 2024-06-18
 Authors@R: 
     c(person(given = "Javier",
              family = "Palarea-Albaladejo",

diff --git a/NEWS b/NEWS
@@ -1,6 +1,13 @@
 RELEASE HISTORY OF THE "zCompositions" PACKAGE
 ==============================================
 
+CHANGES IN zCompositions VERSION 1.5.0-4 [2024-06]:
+----------------------------------------------------
+
+MODIFICATIONS
+
+* Fix small bug in mult- functions when using labelled rows.
+
 CHANGES IN zCompositions VERSION 1.5.0-3 [2024-03]:
 ----------------------------------------------------
 

diff --git a/R/lrDA.R b/R/lrDA.R
@@ -150,8 +150,10 @@ lrDA <-
     nn <- nrow(X); p <- ncol(X)
     if (nn <= p) stop("The lrDA algorithm works on regular data sets (no. rows > no. columns). You can consider lrSVD for wide dat sets.")
 
+    rnames <- rownames(X)
     X[X==label] <- NA
     X <- apply(X,2,as.numeric)
+    rownames(X) <- rnames
     c <- apply(X,1,sum,na.rm=TRUE)
 
     checkNumZerosCol <- apply(X, 2, function(x) sum(is.na(x)))

diff --git a/R/multKM.R b/R/multKM.R
@@ -51,8 +51,10 @@ multKM <-
       return(as.numeric(x))
     }
 
+    rnames <- rownames(X)
     X[X==label] <- NA
     X <- apply(X,2,as.numeric)
+    rownames(X) <- rnames
 
     checkNumZerosCol <- apply(X, 2, function(x) sum(is.na(x)))
 

diff --git a/R/multLN.R b/R/multLN.R
@@ -24,8 +24,10 @@ multLN <-
     if (ncol(dl)!=ncol(X)) stop("The number of columns in X and dl do not agree")
     if ((nrow(dl)>1) & (nrow(dl)!=nrow(X))) stop("The number of rows in X and dl do not agree")
 
+    rnames <- rownames(X)
     X[X==label] <- NA
     X <- apply(X,2,as.numeric)
+    rownames(X) <- rnames
 
     checkNumZerosCol <- apply(X, 2, function(x) sum(is.na(x)))
 

diff --git a/R/multRepl.R b/R/multRepl.R
@@ -47,8 +47,10 @@ multRepl <-
     if (!is.null(names(X))) nam <- names(X)
     if (is.vector(X)) X <- as.data.frame(matrix(X,ncol=length(X)),stringsAsFactors=TRUE)
 
+    rnames <- rownames(X)
     X[X==label] <- NA
     X <- apply(X,2,as.numeric)
+    if (!is.null(rownames(X))) {rownames(X) <- rnames} # Needed for the vector case
     if (is.vector(X)) X <- as.data.frame(matrix(X,ncol=length(X)),stringsAsFactors=TRUE)
 
     if (nrow(X) > 1){

diff --git a/man/zCompositions-package.Rd b/man/zCompositions-package.Rd
@@ -11,8 +11,8 @@ Following compositional data analysis principles, this package provides simple a
 \tabular{ll}{
 Package: \tab zCompositions\cr
 Type: \tab Package\cr
-Version: \tab 1.5.0-3\cr
-Date: \tab 2024-03-13\cr
+Version: \tab 1.5.0-4\cr
+Date: \tab 2024-06-18\cr
 License: \tab GPL (>= 2)\cr
 }
 }