Merge pull request #103 from adrientaudiere/dev

refactor: Better lint

.lintr

@@ -0,0 +1,18 @@
+linters: linters_with_tags(
+      tags = c("default", "common_mistakes", "package_development", "consistency", "correctness", "robustness"),
+      undesirable_operator_linter = NULL,
+      line_length_linter(120),
+      keyword_quote_linter = NULL,
+      condition_message_linter = NULL,
+      paste_linter = NULL,
+      implicit_integer_linter = NULL,
+      packages = "lintr",
+      exclude_tags = "deprecated"
+    )
+encoding: "UTF-8"
+
+exclusions: list(
+    # excluded from all lints:
+    "tests/testthat.R"
+    )
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.10.1
+Version: 0.10.2
 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>.

NEWS.md

@@ -1,5 +1,10 @@
 
-# MiscMetabar 0.10.1 (in development)
+# MiscMetabar 0.10.2 (in development)
+
+- Improve code thanks to {lintr} package
+# MiscMetabar 0.10.1
+
+> CRAN 2024-09-10
 
 - Delete function `heat_tree_pq()` because {metacoder} package is archived from CRAN.
 

R/alpha_div_test.R

@@ -302,7 +302,9 @@ hill_test_rarperm_pq <- function(physeq,
 #'   Package leaps must then be loaded, and this can only be applied to linear models
 #'   with covariates and no interactions. If "d", a simple summary of the candidate set
 #'   is printed, including the number of candidate models.
-#' @param crit The Information Criterion to be used. Default is the small-sample corrected AIC (aicc). This should be a function that accepts a fitted model as first argument. Other provided functions are the classic AIC, the Bayes IC (bic), and QAIC/QAICc (qaic and qaicc).
+#' @param crit The Information Criterion to be used. Default is the small-sample corrected AIC (aicc).
+#'   This should be a function that accepts a fitted model as first argument.
+#'   Other provided functions are the classic AIC, the Bayes IC (bic), and QAIC/QAICc (qaic and qaicc).
 #' @param ... Other arguments passed on to [glmulti::glmulti()] function
 #'
 #' @return A data.frame summarizing the glmulti results with columns
@@ -380,7 +382,7 @@ glmutli_pq <-
     if (fitfunction == "lm") {
       test <- vector("list", nrow(top_glmulti))
       R2__h0 <- NULL
-      for (i in 1:nrow(top_glmulti)) {
+      for (i in seq_along(nrow(top_glmulti))) {
         test[[i]] <- summary(res_glmulti@objects[[i]])
         R2__h0[i] <- test[[i]]$adj.r.squared
       }

R/beta_div_test.R

@@ -75,9 +75,7 @@ graph_test_pq <- function(physeq,
     nperm = nperm,
     ...
   )
-  if (!return_plot) {
-    return(res_graph_test)
-  } else {
+  if (return_plot) {
     p <- phyloseqGraphTest::plot_test_network(res_graph_test) +
       labs(
         title = title,
@@ -90,6 +88,8 @@ graph_test_pq <- function(physeq,
         )
       )
     return(p)
+  } else {
+    return(res_graph_test)
   }
 }
 ################################################################################
@@ -831,11 +831,8 @@ signif_ancombc <- function(ancombc_res,
   clnames <- colnames(signif_ancombc_res)
 
   name_modality <-
-    gsub(
-      "passed_ss", "",
-      clnames[grepl("passed_ss", clnames) &
-        !grepl("Intercept", clnames)]
-    )
+    gsub("passed_ss", "", clnames[grepl("passed_ss", clnames) &
+      !grepl("Intercept", clnames)])
 
   if (filter_passed) {
     signif_ancombc_res <- signif_ancombc_res %>%
@@ -1356,13 +1353,6 @@ var_par_rarperm_pq <-
       )
     }
 
-    if (dist_method %in% c("robust.aitchison", "aitchison")) {
-      dist_physeq <-
-        vegdist(as(otu_table(physeq, taxa_are_rows = FALSE), "matrix"), method = dist_method)
-    } else {
-      dist_physeq <- phyloseq::distance(physeq, method = dist_method)
-    }
-
     res_perm <- vector("list", nperm)
     for (i in 1:nperm) {
       res_perm[[i]] <-

R/blast.R

@@ -115,12 +115,12 @@ blast_to_phyloseq <- function(physeq,
     blast_tab_OK <- FALSE
   }
 
-  if (!keep_temporary_files) {
+  if (keep_temporary_files) {
+    message(paste0("Temporary files are located at ", tempdir()))
+  } else {
     unlink(paste0(tempdir(), "/", "blast_result.txt"))
     unlink(list.files(tempdir(), pattern = "dbase"))
     unlink(paste0(tempdir(), "/", "db.fasta"))
-  } else {
-    message(paste0("Temporary files are located at ", tempdir()))
   }
 
   if (!blast_tab_OK) {
@@ -292,12 +292,12 @@ blast_pq <- function(physeq,
     blast_tab_OK <- FALSE
   }
 
-  if (!keep_temporary_files) {
+  if (keep_temporary_files) {
+    message(paste0("Temporary files are located at ", tempdir()))
+  } else {
     unlink(paste0(tempdir(), "/", "blast_result.txt"))
     unlink(list.files(tempdir(), pattern = "dbase"))
     unlink(paste0(tempdir(), "/", "db.fasta"))
-  } else {
-    message(paste0("Temporary files are located at ", tempdir()))
   }
 
   if (!blast_tab_OK) {
@@ -542,12 +542,12 @@ blast_to_derep <- function(derep,
     blast_tab_OK <- FALSE
   }
 
-  if (!keep_temporary_files) {
+  if (keep_temporary_files) {
+    message(paste0("Temporary files are located at ", tempdir()))
+  } else {
     unlink(paste0(tempdir(), "/", "blast_result.txt"))
     unlink(list.files(tempdir(), pattern = "dbase"))
     unlink(paste0(tempdir(), "/", "db.fasta"))
-  } else {
-    message(paste0("Temporary files are located at ", tempdir()))
   }
 
   if (!blast_tab_OK) {