Upadate on the taxonomy

.Rbuildignore

 ^.*\.Rproj$
 ^\.Rproj\.user$
+^external_data_pkg$
+^LICENCE-CECILL-2.1.txt$
+^data-raw$

.gitignore

@@ -7,3 +7,5 @@ B100000.fasta
 B3500.fasta
 B5.fasta
 Bison-gh.uniq.fasta
+*.o
+*.so

DESCRIPTION

 Package: ROBITools2
 Type: Package
-Title: What the Package Does (Title Case)
+Title: Provides tools to help in the analysing of DNA metabarcoding data.
 Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <yourself@somewhere.net>
+Author: Eric Coissac
+Maintainer: Eric Coissac <eric.coissac@metabarcoding.org>
 Description: More about what it does (maybe more than one line)
     Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+License: CeCILL-2
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.0
@@ -45,6 +45,7 @@ Collate:
     'robitag.R'
     'robitaxid.R'
     'tags_categories.R'
+    'taxonomy_default.R'
     'taxonomy_methods.R'
     'taxonomy_robi.R'
     'taxonomy_ncbi.R'

NAMESPACE

@@ -94,6 +94,7 @@ S3method(pillar_shaft,robitaxid)
 S3method(pillar_shaft,robiuniqueid)
 S3method(print,robicategory)
 S3method(reference_taxonomy,robilca)
+S3method(reference_taxonomy,robitaxid)
 S3method(reference_taxonomy,robitaxonomy)
 S3method(rep,robicategory)
 S3method(rep,robitag)
@@ -159,6 +160,7 @@ export(filter_tag_homopolymere)
 export(filter_tag_homopolymere_min)
 export(full_taxonomy)
 export(genus)
+export(get_default_taxonomy)
 export(gradient_tol1)
 export(gradient_tol2)
 export(ids)
@@ -206,6 +208,7 @@ export(read_fasta)
 export(read_ncbi_taxdump)
 export(read_obitab)
 export(read_obitools_taxonomy)
+export(read_robitaxonomy)
 export(reference_taxonomy)
 export(resets_category_tags)
 export(rkmer)
@@ -227,6 +230,7 @@ export(rseq)
 export(sample_ids_name)
 export(samples)
 export(scientific_name)
+export(set_default_taxonomy)
 export(species)
 export(superkingdom)
 export(tags_positive_ctrls)
@@ -238,6 +242,7 @@ export(unclass_robiobject)
 export(validate_robisample)
 export(validate_robitaxonomy)
 export(write.xlsx)
+export(write_robitaxonomy)
 import(R6)
 import(doParallel)
 import(dplyr)

R/ROBITools2.R

@@ -3,13 +3,10 @@
 #' @description Provides tools to help in the analysing of DNA metabarcoding data.
 #'
 #' @details
-#' The functions in the ProcMod package aims to estimate and to test correlation
-#' between matrices, correcting for the spurious correlations because of the
-#' over-fitting effect.
+#'  More about what it does (maybe more than one line)
+#' Use four spaces when indenting paragraphs within the Description.
 #'
-#' over-fitting effect.
-#'
-#' The ProcMod package is developed on the metabarcoding.org gitlab
+#' The ROBITools2 package is developed on the metabarcoding.org gitlab
 #' (https://git.metabarcoding.org/obitools/ROBITools2.git).
 #' The gitlab of metabarcoding.org provides up-to-date information and
 #' forums for bug reports.

R/robitaxid.R

@@ -111,8 +111,8 @@ robitaxid <- function(x, check_against=NULL, verbose = TRUE) {
 #' @return a \code{robitaxid} instance
 #'
 #' @examples
-#'   x <- robitaxid(c("A","B","C"))
-#'   as_robitaxid(x)
+#'   x <- robitaxid(c(1,2,2759))
+#'   is_robitaxid(x)
 #'
 #' @author Eric Coissac <eric.coissac@metabarcoding.org>
 #' @export
@@ -171,9 +171,28 @@ pillar_shaft.robitaxid <- function(x, ...) {
   pillar::new_pillar_shaft_simple(out, align = "right")
 }
 
+#' @details For \code{\link[ROBITools2]{robitaxid}}, is no reference taxonomy
+#'          are attached to an instance, then the ROBITools2 default taxonomy
+#'          is returned.
+#'
+#' @seealso \code{\link[ROBITools2]{get_default_taxonomy}},
+#'          \code{\link[ROBITools2]{set_default_taxonomy}}.
+#'
+#' @rdname reference_taxonomy
+#' @export
+#'
+#' @examples
+#'
+#'   x <- robitaxid(c(1,2,2759))
+#'   reference_taxonomy(x)
+#'
+reference_taxonomy.robitaxid = function(object) {
+  ref <- attr(object,"reference_taxonomy")
+  if (is.null(ref)) get_default_taxonomy() else ref
+}
 #########################
 #
-# robitaxid_forward
+# robitaxid_master
 #
 #########################
 
@@ -331,3 +350,5 @@ as_robitaxonomy.robilca <- function(object) {
 }
 
 
+
+

R/taxonomy_default.R

+.The_default_taxonomy = new.env(parent = emptyenv())
+
+#' @export
+set_default_taxonomy <- function(taxonomy) {
+  .The_default_taxonomy$taxonomy <- taxonomy
+  invisible(taxonomy)
+}
+
+#' @export
+get_default_taxonomy <- function() {
+  .The_default_taxonomy$taxonomy
+}
\ No newline at end of file

R/taxonomy_methods.R

@@ -10,10 +10,14 @@ NULL
 #' robiobjects including taxonomy can be linked to a reference taxonomy.
 #' This method return this taxonomy.
 #'
+#' @param object the interrogated object.
+#'
+#' @return a robitaxonomy instance.
+#'
 #' @author Eric Coissac
 #' @export
-reference_taxonomy = function(taxonomy) {
-  UseMethod("reference_taxonomy", taxonomy)
+reference_taxonomy = function(object) {
+  UseMethod("reference_taxonomy", object)
 }
 
 #' @author Eric Coissac

R/taxonomy_robi.R

@@ -52,7 +52,7 @@ is_robitaxonomy = function(object) {
 
 
 
-.robitaxonomy <- R6Class("robitaxonomy",lock_objects = FALSE,
+.robitaxonomy <- R6Class("robitaxonomy",
 
                          public = list(
         nodes = NULL,
@@ -358,9 +358,9 @@ lowest_common_ancestor.robitaxonomy <- function(taxonomy,
 
 #' @rdname reference_taxonomy
 #' @export
-reference_taxonomy.robitaxonomy = function(taxonomy) {
-  ref <- taxonomy$reference_taxonomy
-  if (is.null(ref)) taxonomy else ref
+reference_taxonomy.robitaxonomy = function(object) {
+  ref <- object$reference_taxonomy
+  if (is.null(ref)) object else ref
 }
 
 #' @rdname alternative_names
@@ -415,4 +415,15 @@ full_taxonomy.robitaxonomy = function(taxonomy) {
                    reference_taxonomy = NULL)
 }
 
+#' @export
+write_robitaxonomy <- function(taxonomy, file) {
+  save(taxonomy,file = file)
+
+  invisible(taxonomy)
+}
+
+#' @export
+read_robitaxonomy <- function(file) {
+  get(load(file))
+}
 

ROBITools2.Rproj

@@ -17,4 +17,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace

man/ROBITools2.Rd

@@ -8,13 +8,10 @@
 Provides tools to help in the analysing of DNA metabarcoding data.
 }
 \details{
-The functions in the ProcMod package aims to estimate and to test correlation
-between matrices, correcting for the spurious correlations because of the
-over-fitting effect.
+More about what it does (maybe more than one line)
+Use four spaces when indenting paragraphs within the Description.
 
-over-fitting effect.
-
-The ProcMod package is developed on the metabarcoding.org gitlab
+The ROBITools2 package is developed on the metabarcoding.org gitlab
 (https://git.metabarcoding.org/obitools/ROBITools2.git).
 The gitlab of metabarcoding.org provides up-to-date information and
 forums for bug reports.

man/as_robitaxid.Rd

@@ -34,8 +34,8 @@ a \code{robitaxid} instance
 Converts an object to a \code{robitaxid} instance
 }
 \examples{
-  x <- robitaxid(c("A","B","C"))
-  as_robitaxid(x)
+  x <- robitaxid(c(1,2,2759))
+  is_robitaxid(x)
 
 }
 \author{

man/reference_taxonomy.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/robitaxid.R, R/taxonomy_methods.R,
 %   R/taxonomy_robi.R
-\name{reference_taxonomy.robilca}
+\name{reference_taxonomy.robitaxid}
+\alias{reference_taxonomy.robitaxid}
 \alias{reference_taxonomy.robilca}
 \alias{reference_taxonomy}
 \alias{reference_taxonomy.robitaxonomy}
 \title{Returns the reference taxonomy of an object}
 \usage{
+\method{reference_taxonomy}{robitaxid}(object)
+
 \method{reference_taxonomy}{robilca}(taxonomy)
 
-reference_taxonomy(taxonomy)
+reference_taxonomy(object)
 
-\method{reference_taxonomy}{robitaxonomy}(taxonomy)
+\method{reference_taxonomy}{robitaxonomy}(object)
+}
+\arguments{
+\item{object}{the interrogated object.}
+}
+\value{
+a robitaxonomy instance.
 }
 \description{
 robiobjects including taxonomy can be linked to a reference taxonomy.
 This method return this taxonomy.
 }
+\details{
+For \code{\link[ROBITools2]{robitaxid}}, is no reference taxonomy
+         are attached to an instance, then the ROBITools2 default taxonomy
+         is returned.
+}
+\examples{
+
+  x <- robitaxid(c(1,2,2759))
+  reference_taxonomy(x)
+
+}
+\seealso{
+\code{\link[ROBITools2]{get_default_taxonomy}},
+         \code{\link[ROBITools2]{set_default_taxonomy}}.
+}
 \author{
 Eric Coissac
 }

man/robiuniqueid.Rd

@@ -4,7 +4,7 @@
 \alias{robiuniqueid}
 \title{Build a \code{robiuniqueid} instance}
 \usage{
-robiuniqueid(x, make_unique = TRUE, sep = "_", verbose = TRUE)
+robiuniqueid(x, make_unique = TRUE, sep = "_", verbose = is_robi_verbose())
 }
 \arguments{
 \item{x}{an object coercible to a \code{charactere}}

src/.gitignore

+ROBITools2.so