Implement Bioconductor requirements (#95)

microbiome · Nov 4, 2024 · 9fa4669 · 9fa4669
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,28 +1,28 @@
 Package: miaTime
 Type: Package
 Title: Microbiome Time Series Analysis
-Version: 0.1.23
+Version: 0.99.0
 Authors@R:
      c(person(given = "Leo", family = "Lahti", role = c("aut"),
               email = "[email protected]",
               comment = c(ORCID = "0000-0001-5537-637X")),
-       person(given = "Yagmur", family = "Simsek", role = c("aut", "cre"),
+       person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
+              email = "[email protected]",
+              comment = c(ORCID = "0000-0002-8563-8884")),
+       person(given = "Yagmur", family = "Simsek", role = c("aut"),
               email = "[email protected]"),
        person(given = "Sudarshan", family = "Shetty", role = c("ctb"),
               email = "[email protected]"),
-       person(given = "Chouaib", family = "Benchraka", role=c("ctb")),
-       person(given = "Tuomas", family = "Borman", role = c("ctb"),
-              email = "[email protected]",
-              comment = c(ORCID = "0000-0002-8563-8884")),
-      person(given = "Muluh", family = "Muluh", role=c("ctb"))
+       person(given = "Chouaib", family = "Benchraka", role = c("ctb")),
+      person(given = "Muluh", family = "Muluh", role = c("ctb"))
         )
-Description: 
+Description:
     The `miaTime` package provides tools for microbiome time series analysis
     based on (Tree)SummarizedExperiment infrastructure.
-biocViews: Microbiome, Software, Sequencing, Coverage
+biocViews: Microbiome, Software, Sequencing
 License: Artistic-2.0 | file LICENSE
 Depends:
-    R (>= 4.0),
+    R (>= 4.4.0),
     mia
 Imports:
     dplyr,
@@ -31,7 +31,7 @@ Imports:
     SingleCellExperiment,
     SummarizedExperiment,
     TreeSummarizedExperiment
-Suggests: 
+Suggests:
     BiocStyle,
     devtools,
     ggplot2,
@@ -41,17 +41,10 @@ Suggests:
     rmarkdown,
     scater,
     testthat,
-    tidySingleCellExperiment,
-    tidySummarizedExperiment,
-    TreeSummarizedExperiment,
-    vegan,
-    zoo
-Remotes:
-    github::microbiome/mia
-Encoding: UTF-8
+    vegan
 URL: https://github.com/microbiome/miaTime
+BugReports: https://github.com/microbiome/miaTime/issues
+Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr
-LazyData: false
-Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,8 @@ exportMethods(addBaselineDivergence)
 exportMethods(addStepwiseDivergence)
 exportMethods(getBaselineDivergence)
 exportMethods(getStepwiseDivergence)
+import(TreeSummarizedExperiment)
+import(mia)
 importFrom(dplyr,arrange)
 importFrom(dplyr,group_by)
 importFrom(dplyr,lag)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+Changes in version 0.99.0
++ Take into account Bioconductor requirements
+
+Changes in 0.1.23
++ Restructure *BaselineDivergence and *StepwiseDivergence
 
 Changes in version 0.1.19
 + changed assay_name to assay.type

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -0,0 +1,22 @@
+# All generic methods are listed here
+
+#' @rdname addBaselineDivergence
+#' @export
+setGeneric("getBaselineDivergence", signature = "x", function(x, ...)
+    standardGeneric("getBaselineDivergence"))
+
+#' @rdname addBaselineDivergence
+#' @export
+setGeneric("addBaselineDivergence", signature = "x", function(x, ...)
+    standardGeneric("addBaselineDivergence"))
+
+#' @rdname addStepwiseDivergence
+#' @export
+#'
+setGeneric("getStepwiseDivergence", signature = c("x"), function(x, ...)
+    standardGeneric("getStepwiseDivergence"))
+
+#' @rdname addStepwiseDivergence
+#' @export
+setGeneric("addStepwiseDivergence", signature = "x", function(x, ...)
+    standardGeneric("addStepwiseDivergence"))
diff --git a/R/getBaselineDivergence.R b/R/getBaselineDivergence.R
@@ -96,11 +96,6 @@
 #' 
 NULL
 
-#' @rdname addBaselineDivergence
-#' @export
-setGeneric("getBaselineDivergence", signature = "x", function(x, ...)
-    standardGeneric("getBaselineDivergence"))
-
 #' @rdname addBaselineDivergence
 #' @export
 setMethod("getBaselineDivergence", signature = c(x = "SummarizedExperiment"),
@@ -163,11 +158,6 @@ setMethod("getBaselineDivergence", signature = c(x = "SummarizedExperiment"),
     }
 )
 
-#' @rdname addBaselineDivergence
-#' @export
-setGeneric("addBaselineDivergence", signature = "x", function(x, ...)
-    standardGeneric("addBaselineDivergence"))
-
 #' @rdname addBaselineDivergence
 #' @export
 setMethod("addBaselineDivergence", signature = c(x = "SummarizedExperiment"),

diff --git a/R/getStepwiseDivergence.R b/R/getStepwiseDivergence.R
@@ -50,12 +50,6 @@
 #' 
 NULL
 
-#' @rdname addStepwiseDivergence
-#' @export
-#'
-setGeneric("getStepwiseDivergence", signature = c("x"), function(x, ...)
-    standardGeneric("getStepwiseDivergence"))
-
 #' @rdname addStepwiseDivergence
 #' @export
 setMethod("getStepwiseDivergence", signature = c(x = "ANY"),
@@ -113,11 +107,6 @@ setMethod("getStepwiseDivergence", signature = c(x = "ANY"),
     }
 )
 
-#' @rdname addStepwiseDivergence
-#' @export
-setGeneric("addStepwiseDivergence", signature = "x", function(x, ...)
-    standardGeneric("addStepwiseDivergence"))
-
 #' @rdname addStepwiseDivergence
 #' @export
 setMethod("addStepwiseDivergence", signature = c(x = "SummarizedExperiment"),

diff --git a/R/data.R → R/miaTime.R b/R/data.R → R/miaTime.R
@@ -1,3 +1,16 @@
+#' \code{miaTime} Package.
+#'
+#' \code{miaTime} implements time series methods in \link[mia]{mia} ecosystem.
+#' @name miaTime-package
+#' @aliases miaTime
+#' @seealso \link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment} class
+"_PACKAGE"
+NULL
+
+#' @import mia
+#' @import TreeSummarizedExperiment
+NULL
+
 #' @title HITChip Atlas with 1006 Western Adults
 #' @description This data set contains genus-level microbiota profiling with
 #' HITChip for 1006 western adults with no reported health complications,

diff --git a/README.md b/README.md
@@ -2,14 +2,17 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check-bioc-devel](https://github.com/microbiome/miaTime/workflows/R-CMD-check-bioc-devel/badge.svg)](https://github.com/microbiome/miaTime/actions)
-<!--[![R-CMD-check-bioc](https://github.com/microbiome/mia/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/microbiome/mia/actions/workflows/check-bioc.yml)-->
-[![Codecov test
-coverage](https://codecov.io/gh/microbiome/miaTime/branch/master/graph/badge.svg)](https://codecov.io/gh/microbiome/miaTime?branch=master)
+[![Platforms](http://bioconductor.org/shields/availability/release/miaTime.svg)](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
+[![rworkflows](https://github.com/microbiome/miaTime/actions/workflows/rworkflows.yml/badge.svg?branch=devel)](https://github.com/microbiome/miaTime/actions)
+[![Bioc-release](http://bioconductor.org/shields/build/release/bioc/miaTime.svg)](http://bioconductor.org/packages/release/bioc/html/miaTime.html)
+[![Bioc-age](http://bioconductor.org/shields/years-in-bioc/miaTime.svg)](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
+[![Codecov test coverage](https://codecov.io/gh/microbiome/miaTime/branch/devel/graph/badge.svg)](https://codecov.io/gh/microbiome/miaTime?branch=devel)
+[![Dependencies](http://bioconductor.org//shields/dependencies/release/miaTime.svg)](https://bioconductor.org/packages/release/bioc/html/miaTime.html)
 
 <!-- badges: end -->
 
-# miaTime
+## Using the package
+
 This R package can be used to analyse time series data for microbial
 communities. The package is part of [miaverse](https://microbiome.github.io/), 
 and is based on the `TreeSummarizedExperiment` data container.
@@ -18,16 +21,35 @@ See the [package homepage](https://microbiome.github.io/miaTime) for
 example workflows.
 
 ## Installation
-
-The package can be directly installed from R command line.
 
+### Bioc-release
 
-```r
-devtools::install_github("microbiome/miaTime")
-library(miaTime)
 ```
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("miaTime")
+```
+
+### Bioc-devel
 
-### Contributions and acknowledgments
+```
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+# The following initializes usage of Bioc devel
+BiocManager::install(version='devel')
+
+BiocManager::install("miaTime")
+```
+
+### GitHub
+
+```
+remotes::install_github("microbiome/miaTime")
+```
+
+## Contributions and acknowledgments
 
 You can find us online from [Gitter](https://gitter.im/microbiome/miaverse).
 
@@ -43,22 +65,8 @@ flow kind of approach. Development version should be done against the
 citation("miaTime")  
 ```
 
-```
-## Kindly cite the miaTime R package as follows:
-## 
-##   (C) Yagmur Simsek and Leo Lahti. miaTime R package Version 0.1.21
-##   Package URL: microbiome.github.io/miaTime
-## 
-## A BibTeX entry for LaTeX users is
-## 
-##   @Misc{,
-##     title = {miaTime R package},
-##     author = {Yagmur Simsek and Leo Lahti},
-##     url = {microbiome.github.io/miaTime},
-##     note = {Version 0.1.21},
-##   }
-```
-
-# Code of conduct
+## Code of conduct
 
-The project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+The project is released with a
+[Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+By contributing to this project, you agree to abide by its terms.
diff --git a/man/SilvermanAGutData.Rd b/man/SilvermanAGutData.Rd
diff --git a/man/addBaselineDivergence.Rd b/man/addBaselineDivergence.Rd
diff --git a/man/addStepwiseDivergence.Rd b/man/addStepwiseDivergence.Rd
diff --git a/man/hitchip1006.Rd b/man/hitchip1006.Rd
diff --git a/man/miaTime-package.Rd b/man/miaTime-package.Rd
diff --git a/man/minimalgut.Rd b/man/minimalgut.Rd
diff --git a/man/temporalMicrobiome20.Rd b/man/temporalMicrobiome20.Rd