diff --git a/NAMESPACE b/NAMESPACE
index f558daa..586f7a8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,9 +6,9 @@ export(Comparator)
 export(DifferentialAbundanceResult)
 export(alphaDiv)
 export(betaDiv)
-export(differentialAbundance)
 export(getAbundances)
 export(getGroupLabels)
+export(internalDiffAbund)
 export(rankedAbundance)
 export(removeIncompleteSamples)
 exportClasses(AbsoluteAbundanceData)
diff --git a/R/method-differentialAbundance.R b/R/method-differentialAbundance.R
index 929ef16..b0a0a0c 100644
--- a/R/method-differentialAbundance.R
+++ b/R/method-differentialAbundance.R
@@ -246,16 +246,16 @@ setMethod("maaslin", signature("AbundanceData", "Comparator"), function(data, co
 #' @importFrom purrr discard
 #' @useDynLib microbiomeComputations
 #' @export
-#' @rdname differentialAbundance-methods
-setGeneric("differentialAbundance",
-  function(data, comparator, method = c('DESeq2', 'Maaslin2'), pValueFloor = P_VALUE_FLOOR, verbose = c(TRUE, FALSE)) standardGeneric("differentialAbundance"),
+#' @rdname internalDiffAbund-methods
+setGeneric("internalDiffAbund",
+  function(data, comparator, method = c('DESeq2', 'Maaslin2'), pValueFloor = P_VALUE_FLOOR, verbose = c(TRUE, FALSE)) standardGeneric("internalDiffAbund"),
   signature = c("data", "comparator")
 )
 
 # this is consistent regardless of rel vs abs abund. the statistical methods will differ depending on that. 
-#' @rdname differentialAbundance-methods
-#' @aliases differentialAbundance,AbundanceData,Comparator-method
-setMethod("differentialAbundance", signature("AbundanceData", "Comparator"), function(data, comparator, method = c('DESeq2', 'Maaslin2'), pValueFloor = P_VALUE_FLOOR, verbose = c(TRUE, FALSE)) {
+#' @rdname internalDiffAbund-methods
+#' @aliases internalDiffAbund,AbundanceData,Comparator-method
+setMethod("internalDiffAbund", signature("AbundanceData", "Comparator"), function(data, comparator, method = c('DESeq2', 'Maaslin2'), pValueFloor = P_VALUE_FLOOR, verbose = c(TRUE, FALSE)) {
     data <- cleanComparatorVariable(data, comparator, verbose)
     recordIdColumn <- data@recordIdColumn
     ancestorIdColumns <- data@ancestorIdColumns
diff --git a/man/differentialAbundance-methods.Rd b/man/internalDiffAbund-methods.Rd
similarity index 86%
rename from man/differentialAbundance-methods.Rd
rename to man/internalDiffAbund-methods.Rd
index 5f78989..d2c7824 100644
--- a/man/differentialAbundance-methods.Rd
+++ b/man/internalDiffAbund-methods.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/method-differentialAbundance.R
-\name{differentialAbundance}
-\alias{differentialAbundance}
-\alias{differentialAbundance,AbundanceData,Comparator-method}
+\name{internalDiffAbund}
+\alias{internalDiffAbund}
+\alias{internalDiffAbund,AbundanceData,Comparator-method}
 \title{Differential abundance}
 \usage{
-differentialAbundance(
+internalDiffAbund(
   data,
   comparator,
   method = c("DESeq2", "Maaslin2"),
@@ -13,7 +13,7 @@ differentialAbundance(
   verbose = c(TRUE, FALSE)
 )
 
-\S4method{differentialAbundance}{AbundanceData,Comparator}(
+\S4method{internalDiffAbund}{AbundanceData,Comparator}(
   data,
   comparator,
   method = c("DESeq2", "Maaslin2"),
diff --git a/tests/testthat/test-differentialAbundance.R b/tests/testthat/test-differentialAbundance.R
index d12beab..bf3eb26 100644
--- a/tests/testthat/test-differentialAbundance.R
+++ b/tests/testthat/test-differentialAbundance.R
@@ -1,6 +1,6 @@
 # Tests for differential abundance methods
 
-test_that('differentialAbundance returns a correctly formatted data.table', {
+test_that('internalDiffAbund returns a correctly formatted data.table', {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -56,7 +56,7 @@ test_that('differentialAbundance returns a correctly formatted data.table', {
                           )
   )
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
   expect_equal(length(result@droppedColumns), 182)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
@@ -93,7 +93,7 @@ test_that('differentialAbundance returns a correctly formatted data.table', {
                             )
                           )
   )
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
   expect_equal(length(result@droppedColumns), 407)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
@@ -128,7 +128,7 @@ test_that('differentialAbundance returns a correctly formatted data.table', {
                           groupB = groupBBins
   )
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
   expect_s3_class(dt, 'data.table')
@@ -159,7 +159,7 @@ test_that('differentialAbundance returns a correctly formatted data.table', {
                           groupB = groupBBins
   )
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
   expect_s3_class(dt, 'data.table')
@@ -172,7 +172,7 @@ test_that('differentialAbundance returns a correctly formatted data.table', {
 
 })
 
-test_that("differentialAbundance can handle messy inputs", {
+test_that("internalDiffAbund can handle messy inputs", {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -233,7 +233,7 @@ test_that("differentialAbundance can handle messy inputs", {
                           )
   )
 
-  result <- differentialAbundance(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=F)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
   expect_s3_class(dt, 'data.table')
@@ -267,7 +267,7 @@ test_that("differentialAbundance can handle messy inputs", {
                           groupB = groupBBins
   )
 
-  result <- differentialAbundance(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=F)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
   expect_s3_class(dt, 'data.table')
@@ -298,7 +298,7 @@ test_that("differentialAbundance can handle messy inputs", {
                           groupA = groupABins,
                           groupB = groupBBins
   )
-  result <- differentialAbundance(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=T)
+  result <- internalDiffAbund(testDataMessy, comparator=comparatorVariable, method='DESeq2', verbose=T)
   dt <- result@data
   expect_equal(names(dt), c('SampleID'))
   expect_s3_class(dt, 'data.table')
@@ -313,7 +313,7 @@ test_that("differentialAbundance can handle messy inputs", {
 })
 
 
-test_that("differentialAbundance returns a ComputeResult with the correct slots" , {
+test_that("internalDiffAbund returns a ComputeResult with the correct slots" , {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -365,13 +365,13 @@ test_that("differentialAbundance returns a ComputeResult with the correct slots"
                           )
   )
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F)
   expect_equal(result@parameters, 'recordIdColumn = entity.SampleID, comparatorColName = entity.binA, method = DESeq2, groupA =binA_a, groupB = binA_b')
   expect_equal(result@recordIdColumn, 'entity.SampleID')
   expect_equal(class(result@droppedColumns), 'character')
 })
 
-test_that("differentialAbundance fails with improper inputs", {
+test_that("internalDiffAbund fails with improper inputs", {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -421,11 +421,11 @@ test_that("differentialAbundance fails with improper inputs", {
                           groupB = groupBBins
   )
 
-  expect_error(differentialAbundance(testData, comparator=comparisonVariable, method='DESeq2', verbose=F))
+  expect_error(internalDiffAbund(testData, comparator=comparisonVariable, method='DESeq2', verbose=F))
 
 })
 
-test_that("differentialAbundance catches DESeq2 errors", {
+test_that("internalDiffAbund catches DESeq2 errors", {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -474,12 +474,12 @@ test_that("differentialAbundance catches DESeq2 errors", {
               sampleMetadata = sampleMetadata,
               recordIdColumn = 'entity.SampleID')
 
-  expect_error(differentialAbundance(testData, comparator=comparisonVariable, method='DESeq2', verbose=T))
+  expect_error(internalDiffAbund(testData, comparator=comparisonVariable, method='DESeq2', verbose=T))
 
 
 })
 
-test_that("differentialAbundance method Maaslin2 does stuff",{
+test_that("internalDiffAbund method Maaslin2 does stuff",{
   
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -538,7 +538,7 @@ test_that("differentialAbundance method Maaslin2 does stuff",{
                           )
   )
 
-  result <- differentialAbundance(testData,
+  result <- internalDiffAbund(testData,
               comparator = comparatorVariable,
               method='Maaslin2',
               verbose=F)
@@ -546,7 +546,7 @@ test_that("differentialAbundance method Maaslin2 does stuff",{
   stats <- result@statistics@statistics
 
 
-  resultCounts <- differentialAbundance(testCountsData,
+  resultCounts <- internalDiffAbund(testCountsData,
               comparator = comparatorVariable,
               method='Maaslin2',
               verbose=F)
@@ -560,7 +560,7 @@ test_that("differentialAbundance method Maaslin2 does stuff",{
   expect_equal(stats, statsCounts)
 })
 
-test_that("toJSON for DifferentialAbundanceResult works",{
+test_that("toJSON for internalDiffAbundResult works",{
   
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -609,7 +609,7 @@ test_that("toJSON for DifferentialAbundanceResult works",{
                           )
   )
 
-  result <- differentialAbundance(testData,
+  result <- internalDiffAbund(testData,
               comparator = comparatorVariable,
               method='Maaslin2',
               verbose=F)
@@ -678,29 +678,29 @@ test_that("The smallest pvalue we can get is our p value floor", {
   )
 
   # Try with different p value floors
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', pValueFloor = 0, verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', pValueFloor = 0, verbose=F)
   expect_equal(min(result@statistics@statistics$pValue), 0)
   expect_equal(min(result@statistics@statistics$adjustedPValue, na.rm=T), 0) # Confirmed NAs are for pvalue=1
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', pValueFloor = P_VALUE_FLOOR, verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', pValueFloor = P_VALUE_FLOOR, verbose=F)
   expect_equal(min(result@statistics@statistics$pValue), P_VALUE_FLOOR)
   expect_equal(min(result@statistics@statistics$adjustedPValue, na.rm=T), result@statistics@adjustedPValueFloor) # Confirmed NAs are for pvalue=1
 
 
 
   # Repeat with Maaslin2
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='Maaslin2', pValueFloor = 0, verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='Maaslin2', pValueFloor = 0, verbose=F)
   expect_equal(min(result@statistics@statistics$pValue), 0)
   expect_equal(min(result@statistics@statistics$adjustedPValue), 0)
 
-  result <- differentialAbundance(testData, comparator=comparatorVariable, method='Maaslin2', pValueFloor = P_VALUE_FLOOR, verbose=F)
+  result <- internalDiffAbund(testData, comparator=comparatorVariable, method='Maaslin2', pValueFloor = P_VALUE_FLOOR, verbose=F)
   expect_equal(min(result@statistics@statistics$pValue), P_VALUE_FLOOR)
   expect_equal(min(result@statistics@statistics$adjustedPValue), result@statistics@adjustedPValueFloor)
 
 
 })
 
-test_that("differentialAbundance fails if comparator has one value", {
+test_that("internalDiffAbund fails if comparator has one value", {
 
   testOTU_path <- testthat::test_path('testdata','testOTU.rda')
   load(testOTU_path)
@@ -734,6 +734,6 @@ test_that("differentialAbundance fails if comparator has one value", {
     groupB = veupathUtils::BinList(S4Vectors::SimpleList(c(veupathUtils::Bin(binLabel="binB"))))
   )
 
-  expect_error(differentialAbundance(testData, comparator=comparatorVariable, method='DESeq2', verbose=F))
-  expect_error(differentialAbundance(testData, comparator=comparatorVariable, method='Maaslin2', verbose=F))
+  expect_error(internalDiffAbund(testData, comparator=comparatorVariable, method='DESeq2', verbose=F))
+  expect_error(internalDiffAbund(testData, comparator=comparatorVariable, method='Maaslin2', verbose=F))
 })
\ No newline at end of file