Merge pull request #112 from adrientaudiere/dev

v 0.13

.github/workflows/test-coverage.yaml

@@ -1,8 +1,7 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  release:
-    types: [published]
+  workflow_dispatch:
 
 name: test-coverage
 

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.12.1
+Version: 0.13.0
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
 License: AGPL-3
 Encoding: UTF-8
 LazyData: true
 Depends:
-    R (>= 3.5.0),
+    R (>= 4.1.0),
     phyloseq,
     ggplot2 (>= 3.5.0),
     dada2,

NAMESPACE

@@ -19,6 +19,7 @@ export(all_object_size)
 export(ancombc_pq)
 export(are_modality_even_depth)
 export(as_binary_otu_table)
+export(assign_blastn)
 export(assign_idtaxa)
 export(assign_sintax)
 export(assign_vsearch_lca)
@@ -115,6 +116,7 @@ export(read_pq)
 export(rename_samples)
 export(rename_samples_otu_table)
 export(reorder_taxa_pq)
+export(resolve_vector_ranks)
 export(ridges_pq)
 export(rotl_pq)
 export(sam_data_matching_names)

NEWS.md

@@ -1,3 +1,8 @@
+# MiscMetabar 0.13.0 (in development) 
+
+- Add function [assign_blastn()] and add a method `blast` in the function [add_new_taxonomy_pq()].
+- Add function [resolve_vector_ranks()] to resolve conflict in a vector of taxonomy values
+
 # MiscMetabar 0.12.1 (in development) 
 
 - Add parameter name `min_bootstrap` in [add_new_taxonomy_pq()]

R/MiscMetabar-package.R

@@ -28,7 +28,7 @@ if (getRversion() >= "2.15.1") {
     "na_remove", "stratum", "to_lodes_form", "clean_fastq", "clean_sam",
     "samples_names_common", "seq_id", "alpha_hill", "Modality", "Type", "complexity",
     "value_bootstrap", "LearnTaxa", "OrientNucleotides", "RemoveGaps",
-    "method", "readDNAStringSet"
+    "method", "readDNAStringSet", "Taxa name"
   ))
 }