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Small update
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Small update of z.warning and z.delete behaviour to warn of data set containing < 2 columns/rows meeting the threshold
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@Japal
Japal committed Dec 22, 2023
1 parent 5bec33b commit 62376ea
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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,8 +1,8 @@
Package: zCompositions
Type: Package
Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
Version: 1.5
Date: 2023-12-07
Version: 1.5.0-1
Date: 2023-12-22
Authors@R:
c(person(given = "Javier",
family = "Palarea-Albaladejo",
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9 changes: 8 additions & 1 deletion NEWS
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@@ -1,7 +1,14 @@
RELEASE HISTORY OF THE "zCompositions" PACKAGE
==============================================

CHANGES IN zCompositions VERSION 1.5 [2023-12]:
CHANGES IN zCompositions VERSION 1.5.0-1 [2023-12]:
----------------------------------------------------

MODIFICATIONS

* Error when all columns contain more zeros/unobs values than threshold set by z.warning controlled.

CHANGES IN zCompositions VERSION 1.5.0 [2023-12]:
----------------------------------------------------

MODIFICATIONS
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10 changes: 6 additions & 4 deletions R/cmultRepl.R
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Expand Up @@ -27,27 +27,29 @@ cmultRepl <- function(X,label=0,method=c("GBM","SQ","BL","CZM","user"),output=c(
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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10 changes: 6 additions & 4 deletions R/lrDA.R
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Expand Up @@ -158,27 +158,29 @@ lrDA <-
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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10 changes: 6 additions & 4 deletions R/lrEM.R
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Expand Up @@ -149,27 +149,29 @@ lrEM <- function(X,label=NULL,dl=NULL,rob=FALSE,ini.cov=c("complete.obs","multRe
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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10 changes: 6 additions & 4 deletions R/lrEMplus.R
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Expand Up @@ -40,27 +40,29 @@ lrEMplus <- function(X, dl = NULL, rob = FALSE, ini.cov = c("complete.obs", "mul
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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10 changes: 6 additions & 4 deletions R/lrSVD.R
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Expand Up @@ -329,27 +329,29 @@ lrSVD <- function(X, label = NULL, dl = NULL, frac = 0.65, ncp = 2,
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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11 changes: 6 additions & 5 deletions R/lrSVDplus.R
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Original file line number Diff line number Diff line change
Expand Up @@ -353,31 +353,32 @@ lrSVDplus <- function(X, dl = NULL, frac = 0.65, ncp = 2, beta = 0.5, method = c
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}


# Balance matrix for olr
Smat <- diag(rep(1, D))
Smat[upper.tri(Smat)] <- -1
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10 changes: 6 additions & 4 deletions R/multKM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -58,27 +58,29 @@ multKM <-
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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10 changes: 6 additions & 4 deletions R/multLN.R
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Expand Up @@ -31,27 +31,29 @@ multLN <-
if (any(checkNumZerosCol/nrow(X) >= z.warning)) {
cases <- which(checkNumZerosCol/nrow(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (ncol(X)-2)) {stop(paste("More than 2 columns contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

checkNumZerosRow <- apply(X,1,function(x) sum(is.na(x)))
if (any(checkNumZerosRow/ncol(X) >= z.warning)) {
cases <- which(checkNumZerosRow/ncol(X) >= z.warning)
if (z.delete == TRUE){
if (length(cases) > (nrow(X)-2)) {stop(paste("More than 2 rows contain >",z.warning*100,"% zeros/unobserved values (see arguments z.warning and z.delete).",sep=""))}
X <- X[,-cases]
action <- "deleted"
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning).\n",sep=""))
warning(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete).\n",sep=""))
}
else{
action <- "found"
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (can modify threshold using argument z.warning. Check out with zPatterns()).\n",sep=""))
stop(paste("Column no. ",cases," containing >",z.warning*100,"% zeros/unobserved values ",action," (see arguments z.warning and z.delete. Check out with zPatterns()).\n",sep=""))
}
}

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