update namespace for some imported functions which moved

microbiomeDB · Mar 27, 2024 · c6e4ec1 · c6e4ec1
1 parent 9a362a1
commit c6e4ec1
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -41,7 +41,6 @@ importFrom(igraph,graph_from_data_frame)
 importFrom(microbiomeComputations,DifferentialAbundanceResult)
 importFrom(microbiomeComputations,alphaDiv)
 importFrom(microbiomeComputations,betaDiv)
-importFrom(microbiomeComputations,correlation)
 importFrom(microbiomeComputations,differentialAbundance)
 importFrom(microbiomeComputations,rankedAbundance)
 importFrom(microbiomeComputations,selfCorrelation)
@@ -69,10 +68,11 @@ importFrom(microbiomeData,getCollection)
 importFrom(microbiomeData,getCollectionNames)
 importFrom(microbiomeData,getMetadataVariableNames)
 importFrom(microbiomeData,getSampleMetadata)
-importFrom(microbiomeData,getSampleMetadataIdColumns)
 importFrom(microbiomeData,updateCollectionName)
 importFrom(veupathUtils,ComputeResult)
 importFrom(veupathUtils,CorrelationResult)
 importFrom(veupathUtils,correlation)
+importFrom(veupathUtils,getSampleMetadata)
+importFrom(veupathUtils,getSampleMetadataIdColumns)
 importFrom(veupathUtils,matchArg)
 importFrom(veupathUtils,selfCorrelation)
diff --git a/R/computes.R b/R/computes.R
@@ -15,7 +15,6 @@ microbiomeComputations::betaDiv
 microbiomeComputations::differentialAbundance
 
 #' @importFrom veupathUtils correlation
-#' @importFrom microbiomeComputations correlation
 #' @export
 veupathUtils::correlation
 

diff --git a/R/methods.R b/R/methods.R
@@ -59,13 +59,13 @@ setMethod("getComputeResult", "DifferentialAbundanceResult", function(object, fo
     return(data.table::setDT(object@statistics))
 })
 
-#' @importFrom microbiomeData getSampleMetadata
-#' @importFrom microbiomeData getSampleMetadataIdColumns
+#' @importFrom veupathUtils getSampleMetadata
+#' @importFrom veupathUtils getSampleMetadataIdColumns
 mergeComputeResultAndMetadata <- function(computeResult, dataset, metadataVariables) {
     dt <- getComputeResult(computeResult, "data.table")
-    metadata <- microbiomeData::getSampleMetadata(dataset, includeIds = TRUE, metadataVariables = metadataVariables)
+    metadata <- veupathUtils::getSampleMetadata(dataset, includeIds = TRUE, metadataVariables = metadataVariables)
 
-    metadataIdColumns <- microbiomeData::getSampleMetadataIdColumns(dataset)
+    metadataIdColumns <- veupathUtils::getSampleMetadataIdColumns(dataset)
     dt <- merge(dt, metadata, by = metadataIdColumns, all.x = TRUE)
 
     return(dt)