z.warning/z.delete small fix

Japal · Mar 13, 2024 · cf11ec6 · cf11ec6
1 parent 4724a83
commit cf11ec6
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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: 1.5.0-2
-Date: 2024-03-09
+Version: 1.5.0-3
+Date: 2024-03-13
 Authors@R: 
     c(person(given = "Javier",
              family = "Palarea-Albaladejo",
@@ -26,7 +26,7 @@ Description: Principled methods for the imputation of zeros, left-censored and m
     compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
 License: GPL (>= 2)
 Repository: CRAN, Github
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 URL: https://github.com/Japal/zCompositions
 BugReports: https://github.com/Japal/zCompositions/issues
diff --git a/NEWS b/NEWS
@@ -1,7 +1,7 @@
 RELEASE HISTORY OF THE "zCompositions" PACKAGE
 ==============================================
 
-CHANGES IN zCompositions VERSION 1.5.0-2 [2024-03]:
+CHANGES IN zCompositions VERSION 1.5.0-3 [2024-03]:
 ----------------------------------------------------
 
 MODIFICATIONS

diff --git a/R/lrDA.R b/R/lrDA.R
@@ -225,12 +225,13 @@ lrDA <-
       M <- matrix(colMeans(X_alr,na.rm=T),ncol=1)
       C <- cov(X_alr,use=ini.cov)}
     if (ini.cov == "multRepl"){
-      X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,imp.missing=imp.missing,closure=closure)
+      X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,imp.missing=imp.missing,closure=closure,z.warning=z.warning,z.delete=z.delete)
       X.mr_alr <- t(apply(X.mr,1,function(x) log(x)-log(x[pos])))[,-pos]
       M <- matrix(colMeans(X.mr_alr,na.rm=T),ncol=1)
       C <- cov(X.mr_alr)}
     if (ini.cov == "lrEM"){
-      X.em <- lrEM(X,label=NA,dl=dl,ini.cov="multRepl",frac=frac,imp.missing=imp.missing,closure=closure,suppress.print=TRUE)
+      X.em <- lrEM(X,label=NA,dl=dl,ini.cov="multRepl",frac=frac,imp.missing=imp.missing,closure=closure,suppress.print=TRUE,
+                   z.warning=z.warning,z.delete=z.delete)
       X.em_alr <- t(apply(X.em,1,function(x) log(x)-log(x[pos])))[,-pos]
       M <- matrix(colMeans(X.em_alr,na.rm=T),ncol=1)
       C <- cov(X.em_alr)}
@@ -265,7 +266,7 @@ lrDA <-
         varobs <- which(!is.na(X_alr[i[1],]))
         if (length(varobs) == 0){
           alt.in <- TRUE
-          temp <- multRepl(X[i,,drop=FALSE],label=NA,dl=dl[i,,drop=FALSE],frac=frac,imp.missing=imp.missing,closure=closure)
+          temp <- multRepl(X[i,,drop=FALSE],label=NA,dl=dl[i,,drop=FALSE],frac=frac,imp.missing=imp.missing,closure=closure,z.warning=z.warning,z.delete=z.delete)
           Y[i,] <- t(apply(temp,1,function(x) log(x)-log(x[pos])))[,-pos]
           if (runs == 1){
             alt.pat <- c(alt.pat,npat)

diff --git a/R/lrEM.R b/R/lrEM.R
@@ -224,7 +224,7 @@ lrEM <- function(X,label=NULL,dl=NULL,rob=FALSE,ini.cov=c("complete.obs","multRe
       M <- matrix(colMeans(X_alr,na.rm=T),ncol=1)
       C <- cov(X_alr,use=ini.cov)}
     else {
-        X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,imp.missing=imp.missing,closure=closure)
+        X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,imp.missing=imp.missing,closure=closure,z.warning=z.warning,z.delete=z.delete)
         if (any(X.mr < 0)) {stop("ini.cov: negative values produced using multRepl (please check out closure argument and multRepl help for advice)")}
         X.mr_alr <- t(apply(X.mr,1,function(x) log(x)-log(x[pos])))[,-pos]
         M <- matrix(colMeans(X.mr_alr,na.rm=T),ncol=1)
@@ -252,7 +252,7 @@ lrEM <- function(X,label=NULL,dl=NULL,rob=FALSE,ini.cov=c("complete.obs","multRe
         varobs <- which(!is.na(X_alr[i[1],]))
         if (length(varobs) == 0){
           alt.in <- TRUE
-          temp <- multRepl(X[i,,drop=FALSE],label=NA,dl=dl[i,,drop=FALSE],frac=frac,imp.missing=imp.missing,closure=closure)
+          temp <- multRepl(X[i,,drop=FALSE],label=NA,dl=dl[i,,drop=FALSE],frac=frac,imp.missing=imp.missing,closure=closure,z.warning=z.warning,z.delete=z.delete)
           Y[i,] <- t(apply(temp,1,function(x) log(x)-log(x[pos])))[,-pos]
           if (niters == 1){
             alt.pat <- c(alt.pat,npat)
@@ -303,10 +303,10 @@ lrEM <- function(X,label=NULL,dl=NULL,rob=FALSE,ini.cov=c("complete.obs","multRe
 
     if (ini.cov == "multRepl"){
      if (imp.missing == TRUE){
-          X.mr <- multRepl(X,label=NA,imp.missing=T,closure=closure)
+          X.mr <- multRepl(X,label=NA,imp.missing=T,closure=closure,z.warning=z.warning,z.delete=z.delete)
           if (any(X.mr < 0)) {stop("ini.cov: negative values produced using multRepl (please check out closure argument and multRepl help for advice)")}
           }
-     else {X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,closure=closure)
+     else {X.mr <- multRepl(X,label=NA,dl=dl,frac=frac,closure=closure,z.warning=z.warning,z.delete=z.delete)
            if (any(X.mr < 0)) {stop("ini.cov: negative values produced using multRepl (please check out closure argument and multRepl help for advice)")}
           }
     }
@@ -335,7 +335,7 @@ lrEM <- function(X,label=NULL,dl=NULL,rob=FALSE,ini.cov=c("complete.obs","multRe
           if (imp.missing==FALSE){
             X[misspat==npat,] <- multRepl(X.old[misspat==npat,,drop=FALSE],
                                           label=NA,dl=dl[misspat==npat,,drop=FALSE],
-                                          frac=frac,closure=closure)    
+                                          frac=frac,closure=closure,z.warning=z.warning,z.delete=z.delete)    
           }
           if (imp.missing==TRUE){
             stop("Please remove samples with only one observed component (check it out using zPatterns).")

diff --git a/R/lrEMplus.R b/R/lrEMplus.R
@@ -102,7 +102,8 @@ lrEMplus <- function(X, dl = NULL, rob = FALSE, ini.cov = c("complete.obs", "mul
     # Initial lrEM imputation of missing data
     X.old <- lrEM(X.old, label = NA, imp.missing = TRUE, ini.cov = ini.cov, rob = rob,
                   tolerance = tolerance, max.iter = max.iter, rlm.maxit = rlm.maxit,
-                  suppress.print = TRUE, closure = closure)
+                  suppress.print = TRUE, closure = closure, z.warning = z.warning,
+                  z.delete = z.delete)
   }
 
   if (sum(is.na(X)) <= sum(X==0,na.rm=T)){
@@ -118,7 +119,8 @@ lrEMplus <- function(X, dl = NULL, rob = FALSE, ini.cov = c("complete.obs", "mul
     # Initial lrEM imputation of zeros
     X.old <- lrEM(X.old, label = 0, dl = dl, ini.cov = ini.cov, rob = rob,
                   tolerance = tolerance, max.iter = max.iter, rlm.maxit = rlm.maxit,
-                  suppress.print = TRUE, closure = closure)
+                  suppress.print = TRUE, closure = closure, z.warning = z.warning,
+                  z.delete = z.delete)
   }
 
   # Initial parameter estimates
@@ -139,11 +141,11 @@ lrEMplus <- function(X, dl = NULL, rob = FALSE, ini.cov = c("complete.obs", "mul
     X.old[which(X==0)] <- 0
     X.new <- lrEM(X.old, label = 0, dl = dl, ini.cov =  ini.cov, rob = rob,
                   tolerance = tolerance, max.iter = max.iter, rlm.maxit = rlm.maxit, suppress.print = TRUE,
-                  closure = closure)
+                  closure = closure, z.warning = z.warning, z.delete = z.delete)
     X.new[is.na(X)] <- NA
     X.new <- lrEM(X.new, label = NA, imp.missing = TRUE, ini.cov =  ini.cov, rob = rob,
                   tolerance = tolerance, max.iter = max.iter, rlm.maxit = rlm.maxit, suppress.print = TRUE,
-                  closure = closure)
+                  closure = closure, z.warning = z.warning, z.delete = z.delete)
 
     X.new_alr <- log(X.new)-log(X.new[,D])
     X.new_alr <- as.matrix(X.new_alr[,-D])

diff --git a/R/multReplus.R b/R/multReplus.R
@@ -127,7 +127,7 @@ multReplus <- function(X, dl = NULL, frac = 0.65, closure = NULL, z.warning = 0.
 
   ## Imputation of zeros ----
 
-  X <- multRepl(X,label=0,dl=dl,frac=frac,closure=closure)
+  X <- multRepl(X,label=0,dl=dl,frac=frac,closure=closure,z.warning=z.warning,z.delete=z.delete)
 
   ## Final section ----
 

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 1.5.0-2\cr
-Date: \tab 2024-03-09\cr
+Version: \tab 1.5.0-3\cr
+Date: \tab 2024-03-13\cr
 License: \tab GPL (>= 2)\cr
 }
 }