Reduce warnings

R/prepare_taxa.R

@@ -37,12 +37,10 @@
 #' github <- "https://raw.githubusercontent.com/"
 #' repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
 #' dir <- paste0(github, repo)
-#' org_tax_ott <- get_params(step = "prepare_taxa")$files$libraries$sop$merged$organisms$taxonomies$ott |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
+#' org_tax_ott <- paste0(
+#'   "data/interim/libraries/",
+#'   "sop/merged/organisms/taxonomies/ott.tsv"
+#' )
 #' get_file(url = paste0(dir, org_tax_ott), export = org_tax_ott)
 #' get_file(
 #'   url = get_default_paths()$urls$examples$features,

R/weight_annotations.R

@@ -102,54 +102,38 @@
 #'     replacement = "",
 #'     fixed = TRUE
 #'   )
-#' org_tax_ott <- get_params(step = "weight_annotations")$files$libraries$sop$merged$organisms$taxonomies$ott |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' str_stereo <- get_params(step = "weight_annotations")$files$libraries$sop$merged$structures$stereo |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' annotations <- get_params(step = "weight_annotations")$files$annotations$filtered |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' canopus <- get_params(step = "weight_annotations")$files$annotations$prepared$canopus |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' formula <- get_params(step = "weight_annotations")$files$annotations$prepared$formula |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' components <- get_params(step = "weight_annotations")$files$networks$spectral$components$prepared |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' edges <- get_params(step = "weight_annotations")$files$networks$spectral$edges$prepared |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
-#' taxa <- get_params(step = "weight_annotations")$files$metadata$prepared |>
-#'   gsub(
-#'     pattern = ".gz",
-#'     replacement = "",
-#'     fixed = TRUE
-#'   )
+#' org_tax_ott <- paste0(
+#'   "data/interim/libraries/",
+#'   "sop/merged/organisms/taxonomies/ott.tsv"
+#' )
+#' str_stereo <- paste0(
+#'   "data/interim/libraries/",
+#'   "sop/merged/structures/stereo.tsv"
+#' )
+#' annotations <- paste0(
+#'   "data/interim/annotations/",
+#'   "example_annotationsFiltered.tsv"
+#' )
+#' canopus <- paste0(
+#'   "data/interim/annotations/",
+#'   "example_canopusPrepared.tsv"
+#' )
+#' formula <- paste0(
+#'   "data/interim/annotations/",
+#'   "example_formulaPrepared.tsv"
+#' )
+#' components <- paste0(
+#'   "data/interim/features/",
+#'   "example_componentsPrepared.tsv"
+#' )
+#' edges <- paste0(
+#'   "data/interim/features/",
+#'   "example_edges.tsv"
+#' )
+#' taxa <- paste0(
+#'   "data/interim/taxa/",
+#'   "example_taxed.tsv"
+#' )
 #' get_file(url = paste0(dir, library), export = library)
 #' get_file(url = paste0(dir, org_tax_ott), export = org_tax_ott)
 #' get_file(url = paste0(dir, str_stereo), export = str_stereo)