Merge pull request #77 from adrientaudiere/dev

Improve test coverage v0.7.2

.github/workflows/R-CMD-check.yaml

@@ -47,6 +47,6 @@ jobs:
         with:
           upload-snapshots: true
           #Character vector of arguments to pass to ⁠R CMD check⁠. 
-          args: 'c("--as-cran", "--no-tests", "--no-vignettes", "--no-manual", "--no-build-vignettes", "--ignore-vignettes")'
+          args: 'c("--as-cran", "--no-tests", "--no-vignettes", "--no-manual", "--no-build-vignettes", "--ignore-vignettes", "--no-examples")'
           #Character vector of arguments to pass to ⁠R CMD build.
           build_args: 'c("--no-build-vignettes", "--no-manual")'

.github/workflows/test-coverage.yaml

@@ -43,6 +43,7 @@ jobs:
           git clone https://github.com/torognes/swarm.git \
           && cd swarm/ \
           && make
+          sudo cp ../swarm /usr/bin/swarm
 
       - name: Install cutadapt
         run: |

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.1
+Version: 0.7.2
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatic pipeline in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerfull by integrating a large number of analysis, some of them from other R packages.  

NEWS.md

@@ -32,7 +32,7 @@
 - Add functions `get_funguild_db()` and `funguild_assign()` from the [FUNGuildR](https://github.com/brendanf/FUNGuildR/) package into MiscMetabar to decrease package dependencies 
 - Remove all dependencies from packages not available on CRAN or Bioconductor. Improve code using `goodpractice::gp`() and `devtools::check()` function
 - Add messages in various cases (NA in samples data, low number of sequences in samples, low number of sequences by taxa) when using `verify_pq()` with args `verbose=TRUE`
-- Fix a bug in `mutitax_bar_pq()` when using `nb_seq = FALSE`
+- Fix a bug in `multitax_bar_pq()` when using `nb_seq = FALSE`
 
 # MiscMetabar 0.52 
 

R/beta_div_test.R

@@ -589,6 +589,16 @@ multipatt_pq <- function(physeq,
 #'   ), color = "darkgrey") +
 #'   geom_point()
 #'
+#' res_time <- ancombc_pq(
+#'    subset_taxa_pq(
+#'      data_fungi_sp_known,
+#'      taxa_sums(data_fungi_sp_known) > 5000
+#'    ),
+#'    fact = "Time",
+#'    levels_fact = c("0", "15"),
+#'    tax_level = "Family",
+#'    verbose = TRUE
+#'  )
 #' @author Adrien Taudière
 #' @details
 #' This function is mainly a wrapper of the work of others.

R/blast.R

@@ -45,7 +45,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' # data(data_fungi)
+#' 
 #' blastpath <- "...YOUR_PATH_TO_BLAST..."
 #' blast_to_phyloseq(data_fungi,
 #'   seq2search = system.file("extdata", "ex.fasta",

R/controls.R

@@ -145,7 +145,7 @@ dist_pos_control <- function(physeq, samples_names, method = "bray") {
 #' @export
 #'
 #' @examples
-#' # data(data_fungi)
+#' 
 #'
 #' subset_taxa_tax_control(data_fungi,
 #'   as.numeric(data_fungi@otu_table[, 300]),