get tests passing again

DESCRIPTION

@@ -25,4 +25,7 @@ Description: This package is intended to be used to explore the curated datasets
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.1
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -14,6 +14,7 @@ export(getComputeResult)
 export(getComputeResultWithMetadata)
 export(getCuratedDatasetNames)
 export(rankedAbundance)
+export(selfCorrelation)
 exportMethods(getComputeResult)
 exportMethods(getComputeResultWithMetadata)
 importFrom(microbiomeComputations,DifferentialAbundanceResult)
@@ -22,6 +23,7 @@ importFrom(microbiomeComputations,betaDiv)
 importFrom(microbiomeComputations,correlation)
 importFrom(microbiomeComputations,differentialAbundance)
 importFrom(microbiomeComputations,rankedAbundance)
+importFrom(microbiomeComputations,selfCorrelation)
 importFrom(microbiomeData,BONUS)
 importFrom(microbiomeData,Bangladesh)
 importFrom(microbiomeData,DiabImmune)

R/computes.R

@@ -17,3 +17,7 @@ microbiomeComputations::differentialAbundance
 #' @importFrom microbiomeComputations correlation
 #' @export
 microbiomeComputations::correlation
+
+#' @importFrom microbiomeComputations selfCorrelation
+#' @export
+microbiomeComputations::selfCorrelation

tests/testthat/test-GetComputeResult.R

@@ -1,5 +1,5 @@
 test_that("we can get compute results in different formats", {
-    mbioDataset <- microbiomeData::DiabImmune
+    mbioDataset <- MicrobiomeDB::DiabImmune
     genus <- getCollection(mbioDataset, "16S Genus", continuousMetadataOnly = TRUE)
 
     # make sure metadata dont contain IRIs
@@ -28,23 +28,23 @@ test_that("we can get compute results in different formats", {
                             )
                         )
     )
-    diffAbundOutput <- microbiomeComputations::differentialAbundance(getCollection(mbioDataset, "16S Genus"), comparatorVariable, method='Maaslin', verbose=FALSE)
+    diffAbundOutput <- MicrobiomeDB::differentialAbundance(getCollection(mbioDataset, "16S Genus"), comparatorVariable, method='Maaslin', verbose=FALSE)
     expect_equal(inherits(diffAbundOutput, "ComputeResult"), TRUE)
 
-    correlationOutput <- microbiomeComputations::selfCorrelation(getCollection(mbioDataset, "16S Genus"), method='spearman', verbose=FALSE)
+    correlationOutput <- MicrobiomeDB::selfCorrelation(getCollection(mbioDataset, "16S Genus"), method='spearman', verbose=FALSE)
     correlationDT <- getComputeResult(correlationOutput, "data.table")
     expect_equal(inherits(correlationDT, "data.table"), TRUE)
     expect_equal(all(c('data1', 'data2', 'correlationCoef', 'pValue') %in% names(correlationDT)), TRUE)
 
     # make sure continuousMetadataOnly flag works so we can do taxa X metadata correlations   
-    correlationOutput <- microbiomeComputations::correlation(genus, method='spearman', verbose=FALSE)
+    correlationOutput <- MicrobiomeDB::correlation(genus, method='spearman', verbose=FALSE)
     expect_equal(inherits(correlationOutput, "ComputeResult"), TRUE)
 
     correlationIGraph <- getComputeResult(correlationOutput, "igraph")
     expect_equal(inherits(correlationIGraph, "igraph"), TRUE)
 
     # make sure getComputeResultWithMetadata works
-    alphaDivOutput <- microbiomeComputations::alphaDiv(getCollection(mbioDataset, "16S Genus"), method='shannon', verbose=FALSE)
+    alphaDivOutput <- MicrobiomeDB::alphaDiv(getCollection(mbioDataset, "16S Genus"), method='shannon', verbose=FALSE)
     expect_equal(inherits(alphaDivOutput, "ComputeResult"), TRUE)
     alphaDivDT <- getComputeResultWithMetadata(alphaDivOutput, mbioDataset, metadataVariables = c('country', 'delivery_mode'))
     expect_equal(inherits(alphaDivDT, "data.table"), TRUE)