estimateAlpha

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.25
+Version: 1.13.26
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

NAMESPACE

@@ -3,6 +3,7 @@
 export(IdTaxaToDataFrame)
 export(TAXONOMY_RANKS)
 export(ZTransform)
+export(addAlpha)
 export(addCluster)
 export(addContaminantQC)
 export(addDPCoA)
@@ -138,6 +139,7 @@ export(unsplitByRanks)
 export(unsplitOn)
 exportMethods("relabundance<-")
 exportMethods(ZTransform)
+exportMethods(addAlpha)
 exportMethods(addCCA)
 exportMethods(addCluster)
 exportMethods(addContaminantQC)
@@ -270,6 +272,7 @@ importFrom(DelayedArray,colSums)
 importFrom(DelayedArray,getAutoBPPARAM)
 importFrom(DelayedArray,rowSums)
 importFrom(DelayedArray,setAutoBPPARAM)
+importFrom(DelayedMatrixStats,colMeans2)
 importFrom(DelayedMatrixStats,colSums2)
 importFrom(DelayedMatrixStats,rowMaxs)
 importFrom(DelayedMatrixStats,rowMeans2)

NEWS

@@ -143,3 +143,4 @@ calculateCCA to getCCA
 convertToPhyloseq
 + add rowTree agglomeration and RefSeq agglomeration in agglomerateByPrevalence
 + Fix tree merging in unsplit and mergeSEs functions
++ Added addAlpha; a wrapper for calculating all alpha diversity indices

R/deprecate.R

@@ -513,7 +513,7 @@ setMethod("left_join", signature = c(x = "ANY"),
 )
 
 #' @rdname deprecate
-#' @export            
+#' @export
 setGeneric("right_join", signature = c("x"),
            function(x, ...)
                standardGeneric("right_join"))
@@ -1018,3 +1018,85 @@ makeTreeSEFromPhyloseq <- function(x) {
     " Use 'convertFromPhyloseq' instead."))
   convertFromPhyloseq(...)
 }
+
+#' @rdname deprecate
+#' @export
+setGeneric(
+    "estimateEvenness", signature = c("x"), function(x, ...)
+        standardGeneric("estimateEvenness"))
+
+#' @rdname deprecate
+#' @export
+setMethod(
+    "estimateEvenness", signature = c(x = "ANY"), function(x, ...){
+        .Deprecated(msg = paste0(
+            "'estimateEvenness' is deprecated. Use 'addAlpha' instead."))
+        .estimate_evenness(x, ...)
+    }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric(
+    "estimateRichness", signature = c("x"),
+    function(x, ...) standardGeneric("estimateRichness"))
+
+#' @rdname deprecate
+#' @export
+setMethod(
+    "estimateRichness", signature = c(x="ANY"),
+    function(x, ...){
+        .Deprecated(msg = paste0(
+          "'estimateRichness' is deprecated. Use 'addAlpha' instead."))
+        .estimate_richness(x, ...)
+    }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric(
+    "estimateDiversity", signature = c("x"),
+    function(x, ...) standardGeneric("estimateDiversity"))
+
+#' @rdname deprecate
+#' @export
+setMethod(
+    "estimateDiversity", signature = c(x = "ANY"), function(x, ...){
+        .Deprecated(msg = paste0(
+            "'estimateDiversity' is deprecated. Use 'addAlpha' instead."))
+        .estimate_diversity(x, ...)
+    }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric(
+    "estimateFaith", signature = c("x"), function(x, ...)
+        standardGeneric("estimateFaith"))
+
+#' @rdname deprecate
+#' @export
+setMethod(
+    "estimateFaith", signature = c(x="ANY"),
+    function(x, ...){
+        .Deprecated(msg = paste0(
+          "'estimateFaith' is deprecated. Use 'addAlpha' instead."))
+        .estimate_faith(x, ...)
+    }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric(
+    "estimateDominance", signature = c("x"),
+    function(x, ...) standardGeneric("estimateDominance"))
+
+#' @rdname deprecate
+#' @export
+setMethod(
+    "estimateDominance", signature = c(x="ANY"),
+    function(x, ...){
+        .Deprecated(msg = paste0(
+          "'estimateDominance' is deprecated. Use 'addAlpha' instead."))
+        .estimate_dominance(x, ...)
+    })