From 89bd6446928a149747d9ecec7d6f1778ee029a31 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 09:52:31 -0500
Subject: [PATCH 1/7] veupathutils -> mbioutils

---
 R/class-AbundanceData.R            |  4 +--
 R/method-alphaDiv.R                | 34 ++++++++++-----------
 R/method-betaDiv.R                 | 38 +++++++++++------------
 R/method-correlation.R             | 26 ++++++++--------
 R/method-differentialAbundance.R   | 48 +++++++++++++++---------------
 R/method-rankedAbundance.R         | 36 +++++++++++-----------
 R/methods-AbundanceData.R          | 12 ++++----
 R/methods-Comparator.R             |  2 +-
 R/methods-json.R                   |  2 +-
 R/microbiomeComputations-package.R |  2 +-
 R/utils.R                          |  4 +--
 11 files changed, 104 insertions(+), 104 deletions(-)

diff --git a/R/class-AbundanceData.R b/R/class-AbundanceData.R
index 789fbe3..132e1b0 100644
--- a/R/class-AbundanceData.R
+++ b/R/class-AbundanceData.R
@@ -37,7 +37,7 @@ check_abundance_data <- function(object) {
 #' @slot removeEmptyRecords A logical indicating whether empty (all NA/ zero) samples should be removed.
 #' @name AbundanceData-class
 #' @rdname AbundanceData-class
-#' @importFrom veupathUtils SampleMetadata
-#' @importFrom veupathUtils CollectionWithMetadata
+#' @importFrom mbioUtils SampleMetadata
+#' @importFrom mbioUtils CollectionWithMetadata
 #' @export 
 AbundanceData <- setClass("AbundanceData", contains = "CollectionWithMetadata", validity = check_abundance_data)
\ No newline at end of file
diff --git a/R/method-alphaDiv.R b/R/method-alphaDiv.R
index abd26e3..ad9d49f 100644
--- a/R/method-alphaDiv.R
+++ b/R/method-alphaDiv.R
@@ -8,7 +8,7 @@
 #' @return ComputeResult object
 #' @importFrom vegan diversity
 #' @importFrom stringi stri_trans_totitle
-#' @import veupathUtils
+#' @import mbioUtils
 #' @import data.table
 #' @importFrom methods new slot validObject
 #' @importFrom stats as.dist as.formula median quantile var
@@ -29,8 +29,8 @@ setMethod("alphaDiv", signature("AbundanceData"), function(data, method = c('sha
     naToZero <- data@imputeZero
 
     # Initialize and check inputs
-    method <- veupathUtils::matchArg(method)
-    verbose <- veupathUtils::matchArg(verbose)
+    method <- mbioUtils::matchArg(method)
+    verbose <- mbioUtils::matchArg(verbose)
 
     # Check that incoming df meets requirements
     if (!'data.table' %in% class(df)) {
@@ -38,7 +38,7 @@ setMethod("alphaDiv", signature("AbundanceData"), function(data, method = c('sha
     }
     
     computeMessage <- ''
-    veupathUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
+    mbioUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
     
     # Compute alpha diversity
     if (identical(method, 'shannon') | identical(method, 'simpson')){
@@ -58,41 +58,41 @@ setMethod("alphaDiv", signature("AbundanceData"), function(data, method = c('sha
     result@ancestorIdColumns <- ancestorIdColumns
 
     # Handle errors or return positive computeMessage
-    if (veupathUtils::is.error(alphaDivDT)) {
-      veupathUtils::logWithTime(paste('Alpha diversity computation FAILED with parameters, method =', method), verbose)
+    if (mbioUtils::is.error(alphaDivDT)) {
+      mbioUtils::logWithTime(paste('Alpha diversity computation FAILED with parameters, method =', method), verbose)
       stop() 
     } else {
       computeMessage <- paste('Computed', method, 'alpha diversity.')
-      veupathUtils::logWithTime(paste(method, 'alpha diversity computation complete.'), verbose)
+      mbioUtils::logWithTime(paste(method, 'alpha diversity computation complete.'), verbose)
     }
 
     # Assemble data table
     dt <- data.table::as.data.table(df[, ..allIdColumns])
     dt$alphaDiversity <- alphaDivDT
 
-    entity <- veupathUtils::strSplit(recordIdColumn, ".", 4, 1)
+    entity <- mbioUtils::strSplit(recordIdColumn, ".", 4, 1)
     result@computationDetails <- computeMessage
     result@parameters <- paste('method =', method)
     result@recordIdColumn <- recordIdColumn
     result@ancestorIdColumns <- ancestorIdColumns
 
-    computedVariableMetadata <- veupathUtils::VariableMetadata(
-                 variableClass = veupathUtils::VariableClass(value = "computed"),
-                 variableSpec = veupathUtils::VariableSpec(variableId = names(dt[, -..allIdColumns]), entityId = entity),
-                 plotReference = veupathUtils::PlotReference(value = "yAxis"),
+    computedVariableMetadata <- mbioUtils::VariableMetadata(
+                 variableClass = mbioUtils::VariableClass(value = "computed"),
+                 variableSpec = mbioUtils::VariableSpec(variableId = names(dt[, -..allIdColumns]), entityId = entity),
+                 plotReference = mbioUtils::PlotReference(value = "yAxis"),
                  displayName = computedVarLabel,
                  displayRangeMin = 0,
                  displayRangeMax = max(max(dt$alphaDiversity, na.rm = TRUE),1),
-                 dataType = veupathUtils::DataType(value = "NUMBER"),
-                 dataShape = veupathUtils::DataShape(value = "CONTINUOUS")
+                 dataType = mbioUtils::DataType(value = "NUMBER"),
+                 dataShape = mbioUtils::DataShape(value = "CONTINUOUS")
       )
       
-    result@computedVariableMetadata <- veupathUtils::VariableMetadataList(S4Vectors::SimpleList(computedVariableMetadata))
-    names(dt) <- veupathUtils::stripEntityIdFromColumnHeader(names(dt))
+    result@computedVariableMetadata <- mbioUtils::VariableMetadataList(S4Vectors::SimpleList(computedVariableMetadata))
+    names(dt) <- mbioUtils::stripEntityIdFromColumnHeader(names(dt))
     result@data <- dt 
     
     validObject(result)
-    veupathUtils::logWithTime(paste('Alpha diversity computation completed with parameters method=', method), verbose)
+    mbioUtils::logWithTime(paste('Alpha diversity computation completed with parameters method=', method), verbose)
     
     return(result)
 })
diff --git a/R/method-betaDiv.R b/R/method-betaDiv.R
index 3629fa4..b2a8790 100644
--- a/R/method-betaDiv.R
+++ b/R/method-betaDiv.R
@@ -11,7 +11,7 @@
 #' @importFrom vegan vegdist
 #' @importFrom ape pcoa
 #' @importFrom stringi stri_replace_all_fixed
-#' @import veupathUtils
+#' @import mbioUtils
 #' @import data.table
 #' @useDynLib microbiomeComputations
 #' @rdname betaDiv-methods
@@ -31,8 +31,8 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     allIdColumns <- c(recordIdColumn, ancestorIdColumns)
 
     # Initialize and check inputs
-    method <- veupathUtils::matchArg(method)
-    verbose <- veupathUtils::matchArg(verbose)
+    method <- mbioUtils::matchArg(method)
+    verbose <- mbioUtils::matchArg(verbose)
 
     # Check that incoming df meets requirements - consider moving to a validateOTU function or similar
     if (!'data.table' %in% class(df)) {
@@ -40,7 +40,7 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     }
 
     computeMessage <- ''
-    veupathUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
+    mbioUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
 
     # Compute beta diversity using given dissimilarity method
     if (identical(method, 'bray') | identical(method, 'jaccard')) {
@@ -62,11 +62,11 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     result@ancestorIdColumns <- ancestorIdColumns
 
     # Handle errors or return positive computeMessage
-    if (veupathUtils::is.error(dist)) {
-      veupathUtils::logWithTime(paste('Beta diversity computation FAILED with parameters method=', method, ', k=', k), verbose)
+    if (mbioUtils::is.error(dist)) {
+      mbioUtils::logWithTime(paste('Beta diversity computation FAILED with parameters method=', method, ', k=', k), verbose)
       stop() 
     } else {
-      veupathUtils::logWithTime("Computed dissimilarity matrix.", verbose)
+      mbioUtils::logWithTime("Computed dissimilarity matrix.", verbose)
       computeMessage <- paste(method, "dissimilarity matrix computation successful.")
     }
 
@@ -80,7 +80,7 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
 
     dt <- cbind(dt, df[, ..allIdColumns])
     data.table::setcolorder(dt, allIdColumns)
-    veupathUtils::logWithTime("Finished ordination step.", verbose)
+    mbioUtils::logWithTime("Finished ordination step.", verbose)
 
     # Extract percent variance
     eigenvecs <- pcoa$values$Relative_eig
@@ -91,7 +91,7 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     # For now returning data and percentVar for how much is in the plot.
     percentVar <- percentVar[1:k]
     
-    entity <- veupathUtils::strSplit(recordIdColumn,".", 4, 1)
+    entity <- mbioUtils::strSplit(recordIdColumn,".", 4, 1)
     result@computationDetails <- paste(computeMessage, ', pcoaVariance =', percentVar)
     result@parameters <- paste('method =', method)   
     
@@ -99,30 +99,30 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     displayNames <- paste0(axesNames, " ", sprintf(percentVar,fmt = '%#.1f'), "%")
 
     makeVariableMetadataObject <- function(displayName) {
-      axisName <- veupathUtils::strSplit(displayName, " ")
+      axisName <- mbioUtils::strSplit(displayName, " ")
       #bit hacky, see if you can think of something better
       plotRef <- ifelse(grepl('Axis1', displayName, fixed=T), 'xAxis', 'yAxis')
 
-      veupathUtils::VariableMetadata(
-                 variableClass = veupathUtils::VariableClass(value = "computed"),
-                 variableSpec = veupathUtils::VariableSpec(variableId = axisName, entityId = entity),
-                 plotReference = veupathUtils::PlotReference(value = plotRef),
+      mbioUtils::VariableMetadata(
+                 variableClass = mbioUtils::VariableClass(value = "computed"),
+                 variableSpec = mbioUtils::VariableSpec(variableId = axisName, entityId = entity),
+                 plotReference = mbioUtils::PlotReference(value = plotRef),
                  displayName = displayName,
                  displayRangeMin = min(dt[[axisName]]),
                  displayRangeMax = max(dt[[axisName]]),
-                 dataType = veupathUtils::DataType(value = "NUMBER"),
-                 dataShape = veupathUtils::DataShape(value = "CONTINUOUS")
+                 dataType = mbioUtils::DataType(value = "NUMBER"),
+                 dataShape = mbioUtils::DataShape(value = "CONTINUOUS")
       )
     }
           
-    computedVariableMetadata <- veupathUtils::VariableMetadataList(lapply(displayNames, makeVariableMetadataObject))
+    computedVariableMetadata <- mbioUtils::VariableMetadataList(lapply(displayNames, makeVariableMetadataObject))
 
     result@computedVariableMetadata <- computedVariableMetadata
-    names(dt) <- veupathUtils::stripEntityIdFromColumnHeader(names(dt))
+    names(dt) <- mbioUtils::stripEntityIdFromColumnHeader(names(dt))
     result@data <- dt
 
     validObject(result)
-    veupathUtils::logWithTime(paste('Beta diversity computation completed with parameters recordIdColumn=', recordIdColumn, ', method =', method, ', k =', k, ', verbose =', verbose), verbose)
+    mbioUtils::logWithTime(paste('Beta diversity computation completed with parameters recordIdColumn=', recordIdColumn, ', method =', method, ', k =', k, ', verbose =', verbose), verbose)
     
     return(result)
 })
\ No newline at end of file
diff --git a/R/method-correlation.R b/R/method-correlation.R
index 3fb91be..a221baf 100644
--- a/R/method-correlation.R
+++ b/R/method-correlation.R
@@ -1,12 +1,12 @@
-correlationGeneric <- getGeneric("correlation", package = "veupathUtils")
-selfCorrelationGeneric <- getGeneric("selfCorrelation", package = "veupathUtils")
+correlationGeneric <- getGeneric("correlation", package = "mbioUtils")
+selfCorrelationGeneric <- getGeneric("selfCorrelation", package = "mbioUtils")
 
 setClassUnion("missingOrNULL", c("missing", "NULL"))
 
 #' Self Correlation
 #'
 #' This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a 
-#' convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc.
+#' convenience wrapper around mbioUtils::correlation, with the exception that it additionally supports sparcc.
 #' 
 #' @param data An AbundanceData object
 #' @param method string defining the type of correlation to run. The currently supported values are 'spearman','pearson' and 'sparcc'
@@ -16,31 +16,31 @@ setClassUnion("missingOrNULL", c("missing", "NULL"))
 #' @param varianceThreshold numeric threshold to filter features by variance across samples
 #' @param stdDevThreshold numeric threshold to filter features by standard deviation across samples
 #' @return ComputeResult object
-#' @import veupathUtils
+#' @import mbioUtils
 #' @export
 #' @rdname selfCorrelation-methods
 #' @aliases selfCorrelation,AbundanceData-method
 setMethod(selfCorrelationGeneric, signature("AbundanceData"), 
 function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), proportionNonZeroThreshold = 0.5, varianceThreshold = 0, stdDevThreshold = 0) {
   
-  format <- veupathUtils::matchArg(format)
-  method <- veupathUtils::matchArg(method)
-  verbose <- veupathUtils::matchArg(verbose)
+  format <- mbioUtils::matchArg(format)
+  method <- mbioUtils::matchArg(method)
+  verbose <- mbioUtils::matchArg(verbose)
 
   #prefilters applied
-  data <- veupathUtils::pruneFeatures(data, predicateFactory('proportionNonZero', proportionNonZeroThreshold), verbose)
-  data <- veupathUtils::pruneFeatures(data, predicateFactory('variance', varianceThreshold), verbose)
-  data <- veupathUtils::pruneFeatures(data, predicateFactory('sd', stdDevThreshold), verbose)
+  data <- mbioUtils::pruneFeatures(data, predicateFactory('proportionNonZero', proportionNonZeroThreshold), verbose)
+  data <- mbioUtils::pruneFeatures(data, predicateFactory('variance', varianceThreshold), verbose)
+  data <- mbioUtils::pruneFeatures(data, predicateFactory('sd', stdDevThreshold), verbose)
 
   abundances <- getAbundances(data, FALSE, FALSE, verbose)
-  corrResult <- veupathUtils::correlation(abundances, NULL, method = method, format = 'data.table', verbose = verbose)
+  corrResult <- mbioUtils::correlation(abundances, NULL, method = method, format = 'data.table', verbose = verbose)
 
-  veupathUtils::logWithTime(paste("Received df table with", nrow(abundances), "samples and", (ncol(abundances)-1), "features with abundances."), verbose)
+  mbioUtils::logWithTime(paste("Received df table with", nrow(abundances), "samples and", (ncol(abundances)-1), "features with abundances."), verbose)
 
   if (format == 'data.table') {
     return(corrResult)
   } else {
-    result <- veupathUtils::buildCorrelationComputeResult(corrResult, data, NULL, method, verbose)
+    result <- mbioUtils::buildCorrelationComputeResult(corrResult, data, NULL, method, verbose)
     result@computationDetails <- 'selfCorrelation'
     return(result)
   }  
diff --git a/R/method-differentialAbundance.R b/R/method-differentialAbundance.R
index b0a0a0c..89b35fd 100644
--- a/R/method-differentialAbundance.R
+++ b/R/method-differentialAbundance.R
@@ -1,17 +1,17 @@
 # a helper, to reuse and separate some logic
 cleanComparatorVariable <- function(data, comparator, verbose = c(TRUE, FALSE)) {
-  verbose <- veupathUtils::matchArg(verbose)
+  verbose <- mbioUtils::matchArg(verbose)
   
   if (!inherits(data, 'AbundanceData')) stop("data must be of the AbundanceData class.")
   if (!inherits(comparator, 'Comparator')) stop("comparator must be of the Comparator class.")
 
-  comparatorColName <- veupathUtils::getColName(comparator@variable@variableSpec)
+  comparatorColName <- mbioUtils::getColName(comparator@variable@variableSpec)
   data <- removeIncompleteSamples(data, comparatorColName, verbose)
   abundances <- getAbundances(data, verbose = verbose)
-  sampleMetadata <- veupathUtils::getSampleMetadata(data)
+  sampleMetadata <- mbioUtils::getSampleMetadata(data)
   recordIdColumn <- data@recordIdColumn
 
-  veupathUtils::logWithTime(paste("Received abundance table with", nrow(abundances), "samples and", (ncol(abundances)-1), "taxa."), verbose)
+  mbioUtils::logWithTime(paste("Received abundance table with", nrow(abundances), "samples and", (ncol(abundances)-1), "taxa."), verbose)
 
   # Subset to only include samples with metadata defined in groupA and groupB
     if (identical(comparator@variable@dataShape@value, "CONTINUOUS")) {
@@ -26,8 +26,8 @@ cleanComparatorVariable <- function(data, comparator, verbose = c(TRUE, FALSE))
 
       # Collect all instances where the comparatorColName has values in the bins from each group.
       # So inGroupA is a vector with 0 if the value in comparatorColName is not within any of the group A bins and >0 otherwise.
-      inGroupA <- veupathUtils::whichValuesInBinList(sampleMetadata[[comparatorColName]], comparator@groupA)
-      inGroupB <- veupathUtils::whichValuesInBinList(sampleMetadata[[comparatorColName]], comparator@groupB)
+      inGroupA <- mbioUtils::whichValuesInBinList(sampleMetadata[[comparatorColName]], comparator@groupA)
+      inGroupB <- mbioUtils::whichValuesInBinList(sampleMetadata[[comparatorColName]], comparator@groupB)
 
       # Eventually move this check to Comparator validation. See #47
       if ((any(inGroupA * inGroupB) > 0)) {
@@ -70,13 +70,13 @@ cleanComparatorVariable <- function(data, comparator, verbose = c(TRUE, FALSE))
     if (length(unique(sampleMetadata[[comparatorColName]])) < 2) {
       stop("The comparator variable must have at least two values/ groups within the subset.")
     }
-    veupathUtils::logWithTime(paste0("Found ",length(keepSamples)," samples with a value for ", comparatorColName, " in either groupA or groupB. The calculation will continue with only these samples."), verbose)
+    mbioUtils::logWithTime(paste0("Found ",length(keepSamples)," samples with a value for ", comparatorColName, " in either groupA or groupB. The calculation will continue with only these samples."), verbose)
 
     # Subset the abundance data based on the kept samples
     abundances <- abundances[get(recordIdColumn) %in% keepSamples, ]
 
     data@data <- abundances
-    data@sampleMetadata <- veupathUtils::SampleMetadata(
+    data@sampleMetadata <- mbioUtils::SampleMetadata(
       data = sampleMetadata,
       recordIdColumn = data@sampleMetadata@recordIdColumn
     )
@@ -115,13 +115,13 @@ setGeneric("deseq",
 )
 
 setMethod("deseq", signature("AbsoluteAbundanceData", "Comparator"), function(data, comparator, verbose = c(TRUE, FALSE)) {
-  verbose <- veupathUtils::matchArg(verbose)
+  verbose <- mbioUtils::matchArg(verbose)
 
   recordIdColumn <- data@recordIdColumn
   ancestorIdColumns <- data@ancestorIdColumns
   allIdColumns <- c(recordIdColumn, ancestorIdColumns)
-  sampleMetadata <- veupathUtils::getSampleMetadata(data)
-  comparatorColName <- veupathUtils::getColName(comparator@variable@variableSpec)
+  sampleMetadata <- mbioUtils::getSampleMetadata(data)
+  comparatorColName <- mbioUtils::getColName(comparator@variable@variableSpec)
 
   # First, remove id columns and any columns that are all 0s.
   cleanedData <- purrr::discard(data@data[, -..allIdColumns], function(col) {identical(union(unique(col), c(0, NA)), c(0, NA))})
@@ -137,7 +137,7 @@ setMethod("deseq", signature("AbsoluteAbundanceData", "Comparator"), function(da
   # and ANCOMBC expect the order to match, and will not perform this check.
   if (!identical(rownames(sampleMetadata), colnames(counts))){
     # Reorder sampleMetadata to match counts
-    veupathUtils::logWithTime("Sample order differs between data and metadata. Reordering data based on the metadata sample order.", verbose)
+    mbioUtils::logWithTime("Sample order differs between data and metadata. Reordering data based on the metadata sample order.", verbose)
     data.table::setcolorder(counts, rownames(sampleMetadata))
   }
 
@@ -157,8 +157,8 @@ setMethod("deseq", signature("AbsoluteAbundanceData", "Comparator"), function(da
     deseq_output <- DESeq2::DESeq(dds)
   })
 
-  if (veupathUtils::is.error(deseq_output)) {
-    veupathUtils::logWithTime(paste0('Differential abundance FAILED with parameters recordIdColumn=', recordIdColumn, ', method = DESeq2', ', verbose =', verbose), verbose)
+  if (mbioUtils::is.error(deseq_output)) {
+    mbioUtils::logWithTime(paste0('Differential abundance FAILED with parameters recordIdColumn=', recordIdColumn, ', method = DESeq2', ', verbose =', verbose), verbose)
     stop()
   }
 
@@ -187,13 +187,13 @@ setGeneric("maaslin",
 
 # this leaves room for us to grow into dedicated params (normalization and analysis method etc) for counts if desired
 setMethod("maaslin", signature("AbundanceData", "Comparator"), function(data, comparator, verbose = c(TRUE, FALSE)) {
-  verbose <- veupathUtils::matchArg(verbose)
+  verbose <- mbioUtils::matchArg(verbose)
 
   recordIdColumn <- data@recordIdColumn
   ancestorIdColumns <- data@ancestorIdColumns
   allIdColumns <- c(recordIdColumn, ancestorIdColumns)
-  sampleMetadata <- veupathUtils::getSampleMetadata(data)
-  comparatorColName <- veupathUtils::getColName(comparator@variable@variableSpec)
+  sampleMetadata <- mbioUtils::getSampleMetadata(data)
+  comparatorColName <- mbioUtils::getColName(comparator@variable@variableSpec)
   abundances <- data@data
 
   # First, remove id columns and any columns that are all 0s.
@@ -238,7 +238,7 @@ setMethod("maaslin", signature("AbundanceData", "Comparator"), function(data, co
 #' The default value uses the P_VALUE_FLOOR=1e-200 constant defined in this package.
 #' @param verbose boolean indicating if timed logging is desired
 #' @return ComputeResult object
-#' @import veupathUtils
+#' @import mbioUtils
 #' @import data.table
 #' @import DESeq2
 #' @importFrom Maaslin2 Maaslin2
@@ -260,11 +260,11 @@ setMethod("internalDiffAbund", signature("AbundanceData", "Comparator"), functio
     recordIdColumn <- data@recordIdColumn
     ancestorIdColumns <- data@ancestorIdColumns
     allIdColumns <- c(recordIdColumn, ancestorIdColumns)
-    comparatorColName <- veupathUtils::getColName(comparator@variable@variableSpec)
+    comparatorColName <- mbioUtils::getColName(comparator@variable@variableSpec)
 
     ## Initialize and check inputs
-    method <- veupathUtils::matchArg(method)
-    verbose <- veupathUtils::matchArg(verbose)
+    method <- mbioUtils::matchArg(method)
+    verbose <- mbioUtils::matchArg(verbose)
 
     
     ## Compute differential abundance
@@ -286,7 +286,7 @@ setMethod("internalDiffAbund", signature("AbundanceData", "Comparator"), functio
     } else {
       stop('Unaccepted differential abundance method. Accepted methods are "DESeq2" and "Maaslin2".')
     }
-    veupathUtils::logWithTime(paste0('Completed method=',method,'. Formatting results.'), verbose)
+    mbioUtils::logWithTime(paste0('Completed method=',method,'. Formatting results.'), verbose)
 
     # Sometimes p-values can be very small, even smaller than the smallest representable number (gives p-value=0). The smallest
     # representable number changes based on env, so to avoid inconsistency set a p-value floor so that any
@@ -326,11 +326,11 @@ setMethod("internalDiffAbund", signature("AbundanceData", "Comparator"), functio
 
     # The resulting data should contain only the samples actually used.
     result@data <- data@data[, ..allIdColumns]
-    names(result@data) <- veupathUtils::stripEntityIdFromColumnHeader(names(result@data))
+    names(result@data) <- mbioUtils::stripEntityIdFromColumnHeader(names(result@data))
 
 
     validObject(result)
-    veupathUtils::logWithTime(paste('Differential abundance computation completed with parameters recordIdColumn = ', recordIdColumn,", comparatorColName = ", comparatorColName, ', method = ', method, ', groupA =', getGroupLabels(comparator, "groupA"), ', groupB = ', getGroupLabels(comparator, "groupB")), verbose)
+    mbioUtils::logWithTime(paste('Differential abundance computation completed with parameters recordIdColumn = ', recordIdColumn,", comparatorColName = ", comparatorColName, ', method = ', method, ', groupA =', getGroupLabels(comparator, "groupA"), ', groupB = ', getGroupLabels(comparator, "groupB")), verbose)
     
     return(result)
 })
diff --git a/R/method-rankedAbundance.R b/R/method-rankedAbundance.R
index eeee7c5..2a3c60c 100644
--- a/R/method-rankedAbundance.R
+++ b/R/method-rankedAbundance.R
@@ -7,7 +7,7 @@
 #' @param cutoff integer indicating the maximium number of taxa to be kept after ranking.
 #' @param verbose boolean indicating if timed logging is desired
 #' @return ComputeResult object
-#' @import veupathUtils
+#' @import mbioUtils
 #' @import data.table
 #' @importFrom S4Vectors SimpleList
 #' @export
@@ -27,8 +27,8 @@ setMethod("rankedAbundance", signature("AbundanceData"), function(data, method =
     allIdColumns <- c(recordIdColumn, ancestorIdColumns)
 
     # Initialize and check inputs
-    method <- veupathUtils::matchArg(method)
-    verbose <- veupathUtils::matchArg(verbose)
+    method <- mbioUtils::matchArg(method)
+    verbose <- mbioUtils::matchArg(verbose)
 
     # Check that incoming df meets requirements
     if (!'data.table' %in% class(df)) {
@@ -36,7 +36,7 @@ setMethod("rankedAbundance", signature("AbundanceData"), function(data, method =
     }
 
     computeMessage <- ''
-    veupathUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
+    mbioUtils::logWithTime(paste("Received df table with", nrow(df), "samples and", (ncol(df)-1), "taxa."), verbose)
 
     # Reshape back to sample, taxonomicLevel, abundance
     formattedDT <- data.table::melt(df, measure.vars=colnames(df[, -..allIdColumns]), variable.factor=F, variable.name='TaxonomicLevel', value.name="Abundance")
@@ -55,42 +55,42 @@ setMethod("rankedAbundance", signature("AbundanceData"), function(data, method =
     keepCols <- c(allIdColumns, topN)
     dt = df[, ..keepCols]
 
-    veupathUtils::logWithTime("Finished ranking taxa", verbose)
+    mbioUtils::logWithTime("Finished ranking taxa", verbose)
     
     result <- new("ComputeResult")
     result@name <- 'rankedAbundance'
     result@recordIdColumn <- recordIdColumn
     result@ancestorIdColumns <- ancestorIdColumns
 
-    entity <- veupathUtils::strSplit(recordIdColumn,".", 4, 1)
+    entity <- mbioUtils::strSplit(recordIdColumn,".", 4, 1)
     result@computationDetails <- computeMessage
     result@parameters <- paste0('method = ',method, ', isCutoff = ', isCutoff)
 
-    collectionMemberVariableIds <- unlist(lapply(names(dt[, -..allIdColumns]), veupathUtils::strSplit, ".", 4, 2))
+    collectionMemberVariableIds <- unlist(lapply(names(dt[, -..allIdColumns]), mbioUtils::strSplit, ".", 4, 2))
 
     makeVariableSpecs <- function(variableId) {
-	    veupathUtils::VariableSpec(variableId = variableId, entityId = entity)
+	    mbioUtils::VariableSpec(variableId = variableId, entityId = entity)
     }
 
-    computedVariableMetadata <- veupathUtils::VariableMetadata(
-                 variableClass = veupathUtils::VariableClass(value = "computed"),
-                 variableSpec = veupathUtils::VariableSpec(variableId = "rankedAbundance", entityId = entity),
-                 plotReference = veupathUtils::PlotReference(value = "xAxis"),
+    computedVariableMetadata <- mbioUtils::VariableMetadata(
+                 variableClass = mbioUtils::VariableClass(value = "computed"),
+                 variableSpec = mbioUtils::VariableSpec(variableId = "rankedAbundance", entityId = entity),
+                 plotReference = mbioUtils::PlotReference(value = "xAxis"),
                  displayName = "To be determined by client",
                  displayRangeMin = 0,
                  displayRangeMax = 1,
-                 dataType = veupathUtils::DataType(value = "NUMBER"),
-                 dataShape = veupathUtils::DataShape(value = "CONTINUOUS"),
+                 dataType = mbioUtils::DataType(value = "NUMBER"),
+                 dataShape = mbioUtils::DataShape(value = "CONTINUOUS"),
                  isCollection = TRUE,
-                 members = veupathUtils::VariableSpecList(S4Vectors::SimpleList(lapply(collectionMemberVariableIds, makeVariableSpecs)))
+                 members = mbioUtils::VariableSpecList(S4Vectors::SimpleList(lapply(collectionMemberVariableIds, makeVariableSpecs)))
       )
     
-    result@computedVariableMetadata <- veupathUtils::VariableMetadataList(S4Vectors::SimpleList(computedVariableMetadata))
-    names(dt) <- veupathUtils::stripEntityIdFromColumnHeader(names(dt))
+    result@computedVariableMetadata <- mbioUtils::VariableMetadataList(S4Vectors::SimpleList(computedVariableMetadata))
+    names(dt) <- mbioUtils::stripEntityIdFromColumnHeader(names(dt))
     result@data <- dt
 
     validObject(result)
-    veupathUtils::logWithTime(paste('Ranked abundance computation completed with parameters recordIdColumn=', recordIdColumn, ', method =', method, ', cutoff =', cutoff, ', naToZero = ', naToZero, ', verbose =', verbose), verbose)
+    mbioUtils::logWithTime(paste('Ranked abundance computation completed with parameters recordIdColumn=', recordIdColumn, ', method =', method, ', cutoff =', cutoff, ', naToZero = ', naToZero, ', verbose =', verbose), verbose)
 
     return(result)
   })
diff --git a/R/methods-AbundanceData.R b/R/methods-AbundanceData.R
index 65fa2e0..13f6664 100644
--- a/R/methods-AbundanceData.R
+++ b/R/methods-AbundanceData.R
@@ -18,11 +18,11 @@ setGeneric("getAbundances",
 #' @rdname getAbundances
 #' @aliases getAbundances,AbundanceData-method
 setMethod("getAbundances", signature("AbundanceData"), function(object, ignoreImputeZero = c(FALSE, TRUE), includeIds = c(TRUE, FALSE), verbose = c(TRUE, FALSE)) {
-  ignoreImputeZero <- veupathUtils::matchArg(ignoreImputeZero)
-  includeIds <- veupathUtils::matchArg(includeIds)
-  verbose <- veupathUtils::matchArg(verbose)
+  ignoreImputeZero <- mbioUtils::matchArg(ignoreImputeZero)
+  includeIds <- mbioUtils::matchArg(includeIds)
+  verbose <- mbioUtils::matchArg(verbose)
 
-  dt <- veupathUtils::getCollectionData(object, variableNames = NULL, ignoreImputeZero = ignoreImputeZero, includeIds = includeIds, verbose = verbose)
+  dt <- mbioUtils::getCollectionData(object, variableNames = NULL, ignoreImputeZero = ignoreImputeZero, includeIds = includeIds, verbose = verbose)
 
   return(dt)
 })
@@ -47,9 +47,9 @@ setGeneric("removeIncompleteSamples",
 #' @rdname removeIncompleteSamples
 #' @aliases removeIncompleteSamples,AbundanceData-method
 setMethod("removeIncompleteSamples", signature("AbundanceData"), function(object, colName = character(), verbose = c(TRUE, FALSE)) {
-  verbose <- veupathUtils::matchArg(verbose)
+  verbose <- mbioUtils::matchArg(verbose)
 
-  object <- veupathUtils::removeIncompleteRecords(object, colName = colName, verbose = verbose)
+  object <- mbioUtils::removeIncompleteRecords(object, colName = colName, verbose = verbose)
 
   return(object)
 })
\ No newline at end of file
diff --git a/R/methods-Comparator.R b/R/methods-Comparator.R
index 5a78046..00aa734 100644
--- a/R/methods-Comparator.R
+++ b/R/methods-Comparator.R
@@ -15,7 +15,7 @@ setGeneric("getGroupLabels",
 #' @rdname Comparator-methods
 #' @aliases getGroupLabels,Comparator-method 
 setMethod("getGroupLabels", signature("Comparator"), function(object, group = c("groupA", "groupB")) {
-  group <- veupathUtils::matchArg(group)
+  group <- mbioUtils::matchArg(group)
 
   groupBinList <- slot(object, group)
 
diff --git a/R/methods-json.R b/R/methods-json.R
index 5e62e04..828eef9 100644
--- a/R/methods-json.R
+++ b/R/methods-json.R
@@ -1,4 +1,4 @@
-toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
+toJSONGeneric <- getGeneric("toJSON", package = "mbioUtils")
 
 setMethod(toJSONGeneric, signature("DifferentialAbundanceResult"), function(object, ...) {
   tmp <- character()
diff --git a/R/microbiomeComputations-package.R b/R/microbiomeComputations-package.R
index 62e3678..3c0b019 100644
--- a/R/microbiomeComputations-package.R
+++ b/R/microbiomeComputations-package.R
@@ -5,5 +5,5 @@
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start
 ## usethis namespace: end
-#' @import veupathUtils
+#' @import mbioUtils
 NULL
diff --git a/R/utils.R b/R/utils.R
index 43da403..6911325 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -26,10 +26,10 @@
 # }
 
 #' @import data.table
-#' @import veupathUtils
+#' @import mbioUtils
 rankTaxa <- function(df, method=c('median','max','q3','variance')) {
 
-    method <- veupathUtils::matchArg(method)
+    method <- mbioUtils::matchArg(method)
     #### Notes: Assume df has rows as samples and at least columns Abundance and TaxonomicLevel
 
     if (identical(method, 'median')) {

From 2213f87379fd6a8dbcf2ae53646825f92eeb28a1 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 09:53:57 -0500
Subject: [PATCH 2/7] update tests for renamed dep

---
 tests/testthat/test-Comparator.R            |  44 ++---
 tests/testthat/test-correlation.R           |   2 +-
 tests/testthat/test-differentialAbundance.R | 170 ++++++++++----------
 3 files changed, 108 insertions(+), 108 deletions(-)

diff --git a/tests/testthat/test-Comparator.R b/tests/testthat/test-Comparator.R
index 52cddff..72b57cc 100644
--- a/tests/testthat/test-Comparator.R
+++ b/tests/testthat/test-Comparator.R
@@ -1,15 +1,15 @@
 test_that('Comparator validation works', {
 
-  groupABinList <- veupathUtils::BinList(
+  groupABinList <- mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           )
-  groupBBinList <- veupathUtils::BinList(
+  groupBBinList <- mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -18,24 +18,24 @@ test_that('Comparator validation works', {
   
   # Ensure Comparator has a variableId
   expect_error(microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                          variable = mbioUtils::VariableMetadata(
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
                           groupA = groupABinList,
                           groupB = groupBBinList
   ))
 
   # Ensure Comparator has no overlap in groupA and groupB
-  groupBBinList <- veupathUtils::BinList(
+  groupBBinList <- mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           )
   expect_error(microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                          variable = mbioUtils::VariableMetadata(
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
                           groupA = groupABinList,
                           groupB = groupBBinList
@@ -43,8 +43,8 @@ test_that('Comparator validation works', {
 
   # Ensure Comparator requires bin starts and ends when variable is continuous
   expect_error(microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                          variable = mbioUtils::VariableMetadata(
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABinList,
                           groupB = groupBBinList
@@ -52,8 +52,8 @@ test_that('Comparator validation works', {
 
   # Ensure Comparator requires both groupA and groupB
   expect_error(microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                          variable = mbioUtils::VariableMetadata(
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABinList
   ))
@@ -63,21 +63,21 @@ test_that('Comparator validation works', {
 
 test_that("getGroupLabels returns bin labels", {
   # With a continuous variable
-  bin1 <- veupathUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
-  bin2 <- veupathUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
-  bin3 <- veupathUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
-  bin4 <- veupathUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
+  bin1 <- mbioUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
+  bin2 <- mbioUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
+  bin3 <- mbioUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
+  bin4 <- mbioUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
 
-  groupABins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
-  groupBBins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
+  groupABins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
+  groupBBins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'contA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
diff --git a/tests/testthat/test-correlation.R b/tests/testthat/test-correlation.R
index 76ca75a..4c31bcb 100644
--- a/tests/testthat/test-correlation.R
+++ b/tests/testthat/test-correlation.R
@@ -14,7 +14,7 @@ test_that("correlation returns an appropriately structured result for assay agai
   df <- df[, c("entity.SampleID", keepCols), with = FALSE]
 
   nSamples <- dim(df)[1]
-  sampleMetadata <- veupathUtils::SampleMetadata(
+  sampleMetadata <- mbioUtils::SampleMetadata(
     data = data.frame(list(
       "entity.SampleID" = df[["entity.SampleID"]],
       "entity.contA" = rnorm(nSamples),
diff --git a/tests/testthat/test-differentialAbundance.R b/tests/testthat/test-differentialAbundance.R
index bf3eb26..55c1c3c 100644
--- a/tests/testthat/test-differentialAbundance.R
+++ b/tests/testthat/test-differentialAbundance.R
@@ -33,23 +33,23 @@ test_that('internalDiffAbund returns a correctly formatted data.table', {
 
   # A Binary comparator variable
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'binA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -71,23 +71,23 @@ test_that('internalDiffAbund returns a correctly formatted data.table', {
 
   # When defined groups end up subsetting the incoming data
     comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'cat4',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CATEGORICAL")
+                            dataShape = mbioUtils::DataShape(value="CATEGORICAL")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_b"
                               ))
                             )
@@ -108,21 +108,21 @@ test_that('internalDiffAbund returns a correctly formatted data.table', {
 
 
   # With a continuous variable
-  bin1 <- veupathUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
-  bin2 <- veupathUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
-  bin3 <- veupathUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
-  bin4 <- veupathUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
+  bin1 <- mbioUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
+  bin2 <- mbioUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
+  bin3 <- mbioUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
+  bin4 <- mbioUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
 
-  groupABins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
-  groupBBins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
+  groupABins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
+  groupBBins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'contA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
@@ -148,12 +148,12 @@ test_that('internalDiffAbund returns a correctly formatted data.table', {
   groupBBins <- BinList(S4Vectors::SimpleList(c(bin3, bin4)))
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'dateA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
@@ -206,27 +206,27 @@ test_that("internalDiffAbund can handle messy inputs", {
 
   # With only some comparisonVariable values found in the metadata
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'cat4',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CATEGORICAL")
+                            dataShape = mbioUtils::DataShape(value="CATEGORICAL")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_a"
-                              ), veupathUtils::Bin(
+                              ), mbioUtils::Bin(
                                 binLabel="cat4_c"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_b"
-                              ), veupathUtils::Bin(
+                              ), mbioUtils::Bin(
                                 binLabel="test"
                               ))
                             )
@@ -247,21 +247,21 @@ test_that("internalDiffAbund can handle messy inputs", {
 
 
   # With a continuous variable that has NAs
-  bin1 <- veupathUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
-  bin2 <- veupathUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
-  bin3 <- veupathUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
-  bin4 <- veupathUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
+  bin1 <- mbioUtils::Bin(binStart='2', binEnd='3', binLabel="[2, 3)")
+  bin2 <- mbioUtils::Bin(binStart='3', binEnd='4', binLabel="[3, 4)")
+  bin3 <- mbioUtils::Bin(binStart='4', binEnd='5', binLabel="[4, 5)")
+  bin4 <- mbioUtils::Bin(binStart='5', binEnd='6', binLabel="[5, 6)")
 
-  groupABins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
-  groupBBins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
+  groupABins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
+  groupBBins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin3, bin4)))
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'contA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
@@ -280,20 +280,20 @@ test_that("internalDiffAbund can handle messy inputs", {
 
 
   # With a categorical variable that has NAs
-  bin1 <- veupathUtils::Bin(binLabel="cat4_a")
-  bin2 <- veupathUtils::Bin(binLabel="cat4_b")
-  bin3 <- veupathUtils::Bin(binLabel="cat4_c")
+  bin1 <- mbioUtils::Bin(binLabel="cat4_a")
+  bin2 <- mbioUtils::Bin(binLabel="cat4_b")
+  bin3 <- mbioUtils::Bin(binLabel="cat4_c")
 
-  groupABins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
-  groupBBins <- veupathUtils::BinList(S4Vectors::SimpleList(c(bin3)))
+  groupABins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin1, bin2)))
+  groupBBins <- mbioUtils::BinList(S4Vectors::SimpleList(c(bin3)))
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'cat4',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CATEGORICAL")
+                            dataShape = mbioUtils::DataShape(value="CATEGORICAL")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
@@ -342,23 +342,23 @@ test_that("internalDiffAbund returns a ComputeResult with the correct slots" , {
               recordIdColumn = 'entity.SampleID')
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'binA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -403,19 +403,19 @@ test_that("internalDiffAbund fails with improper inputs", {
 
   
   # Fail when bins in Group A and Group B overlap
-  bin1 <- veupathUtils::Bin(binStart=2, binEnd=3, binLabel="[2, 3)")
-  bin2 <- veupathUtils::Bin(binStart=3, binEnd=4, binLabel="[3, 4)")
-  bin3 <- veupathUtils::Bin(binStart=3, binEnd=5, binLabel="[3, 5)")
-  bin4 <- veupathUtils::Bin(binStart=5, binEnd=6, binLabel="[5, 6)")
+  bin1 <- mbioUtils::Bin(binStart=2, binEnd=3, binLabel="[2, 3)")
+  bin2 <- mbioUtils::Bin(binStart=3, binEnd=4, binLabel="[3, 4)")
+  bin3 <- mbioUtils::Bin(binStart=3, binEnd=5, binLabel="[3, 5)")
+  bin4 <- mbioUtils::Bin(binStart=5, binEnd=6, binLabel="[5, 6)")
   groupABins <- BinList(S4Vectors::SimpleList(c(bin1, bin2)))
   groupBBins <- BinList(S4Vectors::SimpleList(c(bin3, bin4)))
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'contA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CONTINUOUS")
+                            dataShape = mbioUtils::DataShape(value="CONTINUOUS")
                           ),
                           groupA = groupABins,
                           groupB = groupBBins
@@ -444,23 +444,23 @@ test_that("internalDiffAbund catches DESeq2 errors", {
   )
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'binA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -515,23 +515,23 @@ test_that("internalDiffAbund method Maaslin2 does stuff",{
   )
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'cat4',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CATEGORICAL")
+                            dataShape = mbioUtils::DataShape(value="CATEGORICAL")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="cat4_b"
                               ))
                             )
@@ -586,23 +586,23 @@ test_that("toJSON for internalDiffAbundResult works",{
   )
 
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'binA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="CATEGORICAL")
+                            dataShape = mbioUtils::DataShape(value="CATEGORICAL")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -654,23 +654,23 @@ test_that("The smallest pvalue we can get is our p value floor", {
 
   # A Binary comparator variable
   comparatorVariable <- microbiomeComputations::Comparator(
-                          variable = veupathUtils::VariableMetadata(
+                          variable = mbioUtils::VariableMetadata(
                             variableSpec = VariableSpec(
                               variableId = 'binA',
                               entityId = 'entity'
                             ),
-                            dataShape = veupathUtils::DataShape(value="BINARY")
+                            dataShape = mbioUtils::DataShape(value="BINARY")
                           ),
-                          groupA = veupathUtils::BinList(
+                          groupA = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_a"
                               ))
                             )
                           ),
-                          groupB = veupathUtils::BinList(
+                          groupB = mbioUtils::BinList(
                             S4Vectors::SimpleList(
-                              c(veupathUtils::Bin(
+                              c(mbioUtils::Bin(
                                 binLabel="binA_b"
                               ))
                             )
@@ -723,15 +723,15 @@ test_that("internalDiffAbund fails if comparator has one value", {
   )
 
   comparatorVariable <- microbiomeComputations::Comparator(
-    variable = veupathUtils::VariableMetadata(
+    variable = mbioUtils::VariableMetadata(
       variableSpec = VariableSpec(
         variableId = 'binA',
         entityId = 'entity'
       ),
-      dataShape = veupathUtils::DataShape(value="BINARY")
+      dataShape = mbioUtils::DataShape(value="BINARY")
     ),
-    groupA = veupathUtils::BinList(S4Vectors::SimpleList(c(veupathUtils::Bin(binLabel="binA")))),
-    groupB = veupathUtils::BinList(S4Vectors::SimpleList(c(veupathUtils::Bin(binLabel="binB"))))
+    groupA = mbioUtils::BinList(S4Vectors::SimpleList(c(mbioUtils::Bin(binLabel="binA")))),
+    groupB = mbioUtils::BinList(S4Vectors::SimpleList(c(mbioUtils::Bin(binLabel="binB"))))
   )
 
   expect_error(internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F))

From 02feddf1057c930ee88004c1671d38237d25c25d Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 09:54:07 -0500
Subject: [PATCH 3/7] update docs

---
 DESCRIPTION                    | 12 +++++++-----
 NAMESPACE                      |  6 +++---
 man/selfCorrelation-methods.Rd |  2 +-
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cd47385..28513ae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: microbiomeComputations
 Title: Compute Results for Microbiome Analyses
-Version: 5.1.6
+Version: 5.1.7
 Authors@R: 
     c(person(given = "Danielle",
            family = "Callan",
@@ -20,14 +20,16 @@ Imports:
     purrr,
     Rcpp (>= 0.11.0),
     S4Vectors,
-    SpiecEasi,
+    SpiecEasi (>= 1.0.7),
     stringi,
     vegan,
-    veupathUtils (>= 2.7.0)
+    mbioUtils (>= 0.1.0)
 Depends:
     R (>= 2.10)
 Remotes:
-    VEuPathDB/veupathUtils
+    microbiomeDB/mbioUtils,
+    zdk123/SpiecEasi@v1.0.7,
+    bioc::Maaslin2
 LinkingTo: Rcpp
 URL: https://github.com/microbiomeDB/microbiomeComputations, https://microbiomedb.github.io/microbiomeComputations/
 BugReports: https://github.com/microbiomeDB/microbiomeComputations/issues
@@ -36,7 +38,7 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index 586f7a8..67bd822 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,12 +18,14 @@ exportClasses(DifferentialAbundanceResult)
 exportMethods(selfCorrelation)
 import(DESeq2)
 import(data.table)
+import(mbioUtils)
 import(methods)
-import(veupathUtils)
 importFrom(Maaslin2,Maaslin2)
 importFrom(Rcpp,sourceCpp)
 importFrom(S4Vectors,SimpleList)
 importFrom(ape,pcoa)
+importFrom(mbioUtils,CollectionWithMetadata)
+importFrom(mbioUtils,SampleMetadata)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(methods,validObject)
@@ -38,6 +40,4 @@ importFrom(stringi,stri_replace_all_fixed)
 importFrom(stringi,stri_trans_totitle)
 importFrom(vegan,diversity)
 importFrom(vegan,vegdist)
-importFrom(veupathUtils,CollectionWithMetadata)
-importFrom(veupathUtils,SampleMetadata)
 useDynLib(microbiomeComputations)
diff --git a/man/selfCorrelation-methods.Rd b/man/selfCorrelation-methods.Rd
index 74408af..abc7fad 100644
--- a/man/selfCorrelation-methods.Rd
+++ b/man/selfCorrelation-methods.Rd
@@ -34,5 +34,5 @@ ComputeResult object
 }
 \description{
 This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a
-convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc.
+convenience wrapper around mbioUtils::correlation, with the exception that it additionally supports sparcc.
 }

From 980ef74da08761bb91d7f2d1a278fcea6ec1ae85 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 10:03:19 -0500
Subject: [PATCH 4/7] clarify deps

---
 DESCRIPTION | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 28513ae..992ca2a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,9 +27,7 @@ Imports:
 Depends:
     R (>= 2.10)
 Remotes:
-    microbiomeDB/mbioUtils,
-    zdk123/SpiecEasi@v1.0.7,
-    bioc::Maaslin2
+    microbiomeDB/mbioUtils
 LinkingTo: Rcpp
 URL: https://github.com/microbiomeDB/microbiomeComputations, https://microbiomedb.github.io/microbiomeComputations/
 BugReports: https://github.com/microbiomeDB/microbiomeComputations/issues

From cd9e5748e6350cc9c588d6cceb3e7fe724f5ebe3 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 10:19:11 -0500
Subject: [PATCH 5/7] clarify deps

---
 DESCRIPTION | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 992ca2a..55a2df6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,9 @@ Imports:
 Depends:
     R (>= 2.10)
 Remotes:
-    microbiomeDB/mbioUtils
+    microbiomeDB/mbioUtils,
+    zdk123/SpiecEasi@v1.0.7
+biocViews:
 LinkingTo: Rcpp
 URL: https://github.com/microbiomeDB/microbiomeComputations, https://microbiomedb.github.io/microbiomeComputations/
 BugReports: https://github.com/microbiomeDB/microbiomeComputations/issues

From c17fd40791b62cbd22b53c9616fb1557525a45bb Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 10:43:18 -0500
Subject: [PATCH 6/7] for now guarantee deps in gh actions manually

---
 .github/workflows/R-CMD-check.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 14159b7..bff08d8 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -39,6 +39,12 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - name: Install Bioconductor packages
+        run: |
+          if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+          BiocManager::install(c("Maaslin2", "DESeq2", "S4Vectors"), ask = FALSE, update = FALSE)
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

From 92532ba5104a40d47b7c3e022eda62b136505a89 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dmleake92@gmail.com>
Date: Fri, 21 Nov 2025 11:14:56 -0500
Subject: [PATCH 7/7] see if maaslin will install from gh

---
 .github/workflows/R-CMD-check.yaml |  6 +++---
 README.md                          | 15 +++++++++++++++
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index bff08d8..509c91d 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -39,10 +39,10 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - name: Install Bioconductor packages
+      - name: Install Maaslin2 from GitHub
         run: |
-          if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
-          BiocManager::install(c("Maaslin2", "DESeq2", "S4Vectors"), ask = FALSE, update = FALSE)
+          if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
+          remotes::install_github("biobakery/Maaslin2")
         shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
diff --git a/README.md b/README.md
index 9e9aeba..788d305 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,21 @@ Use the R package [remotes](https://cran.r-project.org/web/packages/remotes/inde
 remotes::install_github('microbiomeDB/microbiomeComputations')
 ```
 
+### Note on Maaslin2 Installation
+
+The `Maaslin2` package from Bioconductor may not have pre-compiled binaries available for all platforms (particularly ARM64 macOS). If you encounter installation issues, you can install it from source:
+
+```R
+if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+BiocManager::install("Maaslin2", type = "source")
+```
+
+Alternatively, you can install the development version directly from GitHub:
+
+```R
+remotes::install_github("biobakery/Maaslin2")
+```
+
 ## Usage
 ```
 # df is a data frame of abundance values with samples as rows. One column should hold the sample id, all other columns are assumed to be taxa