Add getAlpha (#669)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.15.15
+Version: 1.15.16
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",

NAMESPACE

@@ -55,6 +55,7 @@ export(estimateRichness)
 export(full_join)
 export(getAbundanceClass)
 export(getAbundant)
+export(getAlpha)
 export(getBestDMNFit)
 export(getCCA)
 export(getConditionallyLowAbundant)
@@ -210,6 +211,7 @@ exportMethods(estimateRichness)
 exportMethods(full_join)
 exportMethods(getAbundanceClass)
 exportMethods(getAbundant)
+exportMethods(getAlpha)
 exportMethods(getBestDMNFit)
 exportMethods(getCCA)
 exportMethods(getConditionallyLowAbundant)
@@ -319,7 +321,6 @@ importFrom(DelayedArray,rowSums)
 importFrom(DelayedArray,rowsum)
 importFrom(DelayedArray,setAutoBPPARAM)
 importFrom(DelayedArray,type)
-importFrom(DelayedMatrixStats,colMeans2)
 importFrom(DelayedMatrixStats,colQuantiles)
 importFrom(DelayedMatrixStats,colSums2)
 importFrom(DelayedMatrixStats,rowMaxs)

R/AllGenerics.R

@@ -3,23 +3,15 @@
 #' @rdname addAlpha
 #' @export
 setGeneric(
-    "addAlpha", signature = c("x"),
-    function(
-        x, assay.type = "counts",
-        index = c(
-            "coverage_diversity", "fisher_diversity", "faith_diversity",
-            "gini_simpson_diversity", "inverse_simpson_diversity",
-            "log_modulo_skewness_diversity", "shannon_diversity",
-            "absolute_dominance", "dbp_dominance",
-            "core_abundance_dominance", "gini_dominance",
-            "dmn_dominance", "relative_dominance",
-            "simpson_lambda_dominance", "camargo_evenness",
-            "pielou_evenness", "simpson_evenness",
-            "evar_evenness", "bulla_evenness", "ace_richness",
-            "chao1_richness", "hill_richness", "observed_richness"),
-        name = index, niter = NULL, ...)
+    "addAlpha", signature = c("x"), function(x, ...)
     standardGeneric("addAlpha"))
 
+#' @rdname addAlpha
+#' @export
+setGeneric(
+    "getAlpha", signature = c("x"), function(x, ...)
+    standardGeneric("getAlpha"))
+
 #' @rdname getDissimilarity
 #' @export
 setGeneric(