Add stability calculation

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: miaTime
 Type: Package
 Title: Microbiome Time Series Analysis
-Version: 0.99.4
+Version: 0.99.5
 Authors@R:
      c(person(given = "Leo", family = "Lahti", role = c("aut"),
               email = "[email protected]",
@@ -29,6 +29,7 @@ Imports:
     methods,
     S4Vectors,
     SingleCellExperiment,
+    stats,
     SummarizedExperiment,
     tidyr,
     TreeSummarizedExperiment

NAMESPACE

@@ -3,18 +3,22 @@
 export(addBaselineDivergence)
 export(addBimodality)
 export(addShortTermChange)
+export(addStability)
 export(addStepwiseDivergence)
 export(getBaselineDivergence)
 export(getBimodality)
 export(getShortTermChange)
+export(getStability)
 export(getStepwiseDivergence)
 exportMethods(addBaselineDivergence)
 exportMethods(addBimodality)
 exportMethods(addShortTermChange)
+exportMethods(addStability)
 exportMethods(addStepwiseDivergence)
 exportMethods(getBaselineDivergence)
 exportMethods(getBimodality)
 exportMethods(getShortTermChange)
+exportMethods(getStability)
 exportMethods(getStepwiseDivergence)
 import(S4Vectors)
 import(SingleCellExperiment)
@@ -24,14 +28,25 @@ import(methods)
 import(mia)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
+importFrom(dplyr,all_vars)
+importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter_at)
 importFrom(dplyr,group_by)
+importFrom(dplyr,if_else)
 importFrom(dplyr,lag)
 importFrom(dplyr,mutate)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,sym)
 importFrom(dplyr,ungroup)
+importFrom(dplyr,vars)
+importFrom(stats,coef)
+importFrom(stats,lm)
+importFrom(stats,median)
+importFrom(stats,setNames)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,unnest)

NEWS

@@ -1,3 +1,6 @@
+Changes in version 0.99.5
++ Added functions for estimating stability
+
 Changes in version 0.99.4
 + Added functions for calculating short term change metrics
 

R/AllGenerics.R

@@ -40,3 +40,13 @@ setGeneric("addShortTermChange", signature = "x", function(x, ...)
 #' @export
 setGeneric("getShortTermChange", signature = "x", function(x, ...)
     standardGeneric("getShortTermChange"))
+
+#' @rdname getStability
+#' @export
+setGeneric("getStability", signature = "x", function(x, ...)
+    standardGeneric("getStability"))
+
+#' @rdname getStability
+#' @export
+setGeneric("addStability", signature = "x", function(x, ...)
+    standardGeneric("addStability"))

R/getBaselineDivergence.R

@@ -375,7 +375,6 @@ setMethod("addBaselineDivergence", signature = c(x = "SummarizedExperiment"),
 }
 
 # This function converts time divergence results to DF object
-#' @importFrom dplyr summarize
 .convert_divergence_to_df <- function(
         x, res, time_res, reference,
         name = c("divergence", "time_diff", "ref_samples"), ...){

R/getBimodality.R

@@ -92,7 +92,10 @@ setMethod("addBimodality", signature = c(x = "SummarizedExperiment"),
     function(x, name = "bimodality", ...){
         .check_input(name, "character scalar")
         x <- .check_and_get_altExp(x, ...)
-        res <- getBimodality(x, name = name, ...) |> as.list()
+        args <- c(
+            list(x = x, name = name),
+            list(...)[!names(list(...)) %in% c("altexp")])
+        res <- do.call(getBimodality, args) |> as.list()
         x <- .add_values_to_colData(x, unname(res), names(res), MARGIN = 1L)
         return(x)
     }