refactor getBaselineDivergence/getStepwiseDivergence

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: miaTime
 Type: Package
 Title: Microbiome Time Series Analysis
-Version: 0.1.22
+Version: 0.1.23
 Authors@R:
      c(person(given = "Leo", family = "Lahti", role = c("aut"),
               email = "[email protected]",
@@ -22,28 +22,29 @@ Description:
 biocViews: Microbiome, Software, Sequencing, Coverage
 License: Artistic-2.0 | file LICENSE
 Depends:
-    R (>= 4.0)
+    R (>= 4.0),
+    mia
 Imports:
     dplyr,
-    methods,    
-    mia,
+    methods,
     S4Vectors,
-    SummarizedExperiment,
     SingleCellExperiment,
-    vegan,
-    scater
+    SummarizedExperiment,
+    TreeSummarizedExperiment
 Suggests: 
-    TreeSummarizedExperiment,
-    tidySingleCellExperiment,
-    tidySummarizedExperiment,
+    BiocStyle,
+    devtools,
     ggplot2,
-    miaViz,
+    knitr,
     lubridate,
+    miaViz,
     rmarkdown,
-    knitr,
-    devtools,
-    BiocStyle,
+    scater,
     testthat,
+    tidySingleCellExperiment,
+    tidySummarizedExperiment,
+    TreeSummarizedExperiment,
+    vegan,
     zoo
 Remotes:
     github::microbiome/mia

NAMESPACE

@@ -1,20 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
+export(addBaselineDivergence)
+export(addStepwiseDivergence)
 export(getBaselineDivergence)
 export(getStepwiseDivergence)
-export(getTimeDivergence)
-exportMethods(getTimeDivergence)
-importFrom(S4Vectors,DataFrame)
-importFrom(SingleCellExperiment,altExp)
-importFrom(SummarizedExperiment,"colData<-")
-importFrom(SummarizedExperiment,assay)
-importFrom(SummarizedExperiment,colData)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,filter)
+exportMethods(addBaselineDivergence)
+exportMethods(addStepwiseDivergence)
+exportMethods(getBaselineDivergence)
+exportMethods(getStepwiseDivergence)
+importFrom(dplyr,arrange)
 importFrom(dplyr,group_by)
+importFrom(dplyr,lag)
 importFrom(dplyr,mutate)
-importFrom(dplyr,select)
-importFrom(methods,is)
-importFrom(mia,estimateDivergence)
-importFrom(mia,mergeSEs)
-importFrom(vegan,vegdist)
+importFrom(dplyr,ungroup)

R/data.R

@@ -84,7 +84,8 @@ NULL
 NULL
 
 #' @title SilvermanAGutData
-#' @description The SilvermanAGutData dataset contains 16S rRNA gene based high-throughput
+#' @description
+#' The SilvermanAGutData dataset contains 16S rRNA gene based high-throughput
 #' profiling of 4 in vitro artificial gut models. The sampling was done hourly
 #' and daily to capture sub-daily dynamics of microbial community originating
 #' from human feces. The data consists of 413 taxa from 639 samples.