doc

DESCRIPTION

@@ -74,6 +74,7 @@ X-schema.org-keywords: metabolite annotation, chemotaxonomy, scoring
  distance, specialized metabolome
 Collate:
  'round_reals.R'
+ 'log_pipe.R'
  'harmonize_adducts.R'
  'parse_yaml_params.R'
  'parse_cli_params.R'
@@ -126,7 +127,6 @@ Collate:
  'install.R'
  'load_yaml_files.R'
  'log_debug.R'
- 'log_pipe.R'
  'pre_harmonize_names_sirius.R'
  'select_annotations_columns.R'
  'prepare_annotations_gnps.R'

NAMESPACE

@@ -2,57 +2,23 @@
 
 export(annotate_masses)
 export(annotate_spectra)
-export(benchmark_taxize_spectra)
-export(calculate_entropy)
 export(calculate_mass_of_m)
-export(clean_bio)
-export(clean_chemo)
-export(clean_collapse)
-export(columns_model)
-export(complement_metadata_structures)
-export(copy_backbone)
 export(create_components)
 export(create_dir)
-export(create_edges)
 export(create_edges_spectra)
-export(decorate_bio)
-export(decorate_chemo)
-export(decorate_masses)
-export(dist_get)
-export(dist_groups)
 export(export_output)
-export(export_params)
-export(export_spectra_rds)
-export(extract_spectra)
-export(fake_annotations_columns)
-export(fake_ecmdb)
-export(fake_hmdb)
-export(fake_lotus)
-export(fake_sop_columns)
 export(filter_annotations)
-export(filter_high_confidence_only)
 export(get_default_paths)
 export(get_example_files)
-export(get_example_sirius)
 export(get_file)
-export(get_gnps_tables)
 export(get_last_version_from_zenodo)
-export(get_massbank_spectra)
 export(get_organism_taxonomy_ott)
 export(get_params)
 export(go_to_cache)
-export(harmonize_adducts)
-export(harmonize_names_sirius)
-export(harmonize_spectra)
 export(import_spectra)
 export(install)
-export(load_yaml_files)
 export(log_debug)
-export(log_pipe)
 export(parse_adduct)
-export(parse_cli_params)
-export(parse_yaml_params)
-export(pre_harmonize_names_sirius)
 export(prepare_annotations_gnps)
 export(prepare_annotations_sirius)
 export(prepare_annotations_spectra)
@@ -66,24 +32,11 @@ export(prepare_libraries_sop_hmdb)
 export(prepare_libraries_sop_lotus)
 export(prepare_libraries_sop_merged)
 export(prepare_libraries_spectra)
-export(prepare_params)
 export(prepare_taxa)
-export(read_from_sirius_zip)
-export(replace_id)
-export(round_reals)
 export(run_app)
 export(sanitize_spectra)
-export(select_annotations_columns)
-export(select_sirius_columns_canopus)
-export(select_sirius_columns_formulas)
-export(select_sirius_columns_structures)
-export(select_sop_columns)
-export(split_tables_sop)
 export(tima_full)
-export(transform_score_sirius_csi)
 export(weight_annotations)
-export(weight_bio)
-export(weight_chemo)
 import(rlang)
 importFrom(MetaboCoreUtils,calculateMass)
 importFrom(MsBackendMgf,readMgf)

NEWS.md

@@ -4,6 +4,7 @@
 
 * Improved documentation
 * Reduced dependencies
+* Reduced exports
 * Removed `CompoundDb` dependency as it was causing too many issues
 * Removed `pak` install and switched to `r-universe`
 * Replaced internal functions by `Spectra` equivalents (#166)

R/annotate_masses.R

@@ -55,6 +55,7 @@ import::from(tidytable, where, .into = environment())
 #' @include dist_groups.R
 #' @include get_params.R
 #' @include harmonize_adducts.R
+#' @include log_pipe.R
 #' @include round_reals.R
 #'
 #' @param features Table containing your previous annotation to complement

R/benchmark_taxize_spectra.R

@@ -14,8 +14,6 @@ import::from(tidytable, slice_sample, .into = environment())
 #'
 #' @details Because they are still quite dirty
 #'
-#' @export
-#'
 #' @importFrom stringi stri_sub
 #' @importFrom tidytable bind_rows
 #' @importFrom tidytable distinct
@@ -26,8 +24,6 @@ import::from(tidytable, slice_sample, .into = environment())
 #' @importFrom tidytable select
 #' @importFrom tidytable slice_sample
 #'
-#' @noRd
-#'
 #' @param input Initial features
 #' @param keys SOP keys
 #' @param org_tax_ott Taxonomy

R/calculate_entropy.R

@@ -5,13 +5,9 @@ import::from(tidytable, tidytable, .into = environment())
 #'
 #' @description This function calculates entropy similarity between two spectra
 #'
-#' @export
-#'
 #' @importFrom msentropy calculate_entropy_similarity
 #' @importFrom tidytable tidytable
 #'
-#' @noRd
-#'
 #' @param index Index of the first spectrum
 #' @param target Index of the second spectrum
 #' @param frags List of fragments

R/clean_bio.R

@@ -23,8 +23,6 @@ import::from(tidytable, where, .into = environment())
 #' @description This function cleans the results
 #' obtained after biological weighting
 #'
-#' @export
-#'
 #' @importFrom stats setNames
 #' @importFrom tidytable across
 #' @importFrom tidytable add_count
@@ -45,7 +43,7 @@ import::from(tidytable, where, .into = environment())
 #' @importFrom tidytable ungroup
 #' @importFrom tidytable where
 #'
-#' @noRd
+#' @include log_pipe.R
 #'
 #' @param annot_table_wei_bio Table containing your
 #' biologically weighted annotation

R/clean_chemo.R

@@ -23,8 +23,6 @@ import::from(tidytable, where, .into = environment())
 #' @description This function cleans the results
 #' obtained after chemical weighting
 #'
-#' @export
-#'
 #' @importFrom tidytable across
 #' @importFrom tidytable any_of
 #' @importFrom tidytable arrange
@@ -48,8 +46,7 @@ import::from(tidytable, where, .into = environment())
 #' @include clean_collapse.R
 #' @include columns_model.R
 #' @include filter_high_confidence_only.R
-#'
-#' @noRd
+#' @include log_pipe.R
 #'
 #' @param annot_table_wei_chemo Table containing your
 #' chemically weighted annotation

R/clean_collapse.R

@@ -10,8 +10,6 @@ import::from(tidytable, where, .into = environment())
 #'
 #' @description This function collapses a grouped dataframe and trims it
 #'
-#' @export
-#'
 #' @importFrom tidytable across
 #' @importFrom tidytable everything
 #' @importFrom tidytable mutate
@@ -20,8 +18,6 @@ import::from(tidytable, where, .into = environment())
 #' @importFrom tidytable ungroup
 #' @importFrom tidytable where
 #'
-#' @noRd
-#'
 #' @param grouped_df Grouped dataframe
 #' @param cols Column(s) to apply collapse to
 #'

R/columns_model.R

@@ -2,10 +2,6 @@
 #'
 #' @description This function models columns
 #'
-#' @export
-#'
-#' @noRd
-#'
 #' @return The columns model
 #'
 #' @examples NULL

R/complement_metadata_structures.R

@@ -26,8 +26,6 @@ import::from(tidytable, where, .into = environment())
 #'
 #' @include clean_collapse.R
 #'
-#' @noRd
-#'
 #' @param df Data frame with structural metadata to be complemented
 #' @param str_stereo File containing structures stereo
 #' @param str_met File containing structures metadata
@@ -37,8 +35,6 @@ import::from(tidytable, where, .into = environment())
 #'
 #' @return Data frame with complemented structural metadata
 #'
-#' @export
-#'
 #' @examples NULL
 complement_metadata_structures <- function(df,
  str_stereo = get("str_stereo", envir = parent.frame()),

R/copy_backbone.R

@@ -6,14 +6,10 @@ import::from(fs, path_home, .into = environment())
 #'
 #' @description This function copies backbone
 #'
-#' @export
-#'
 #' @importFrom fs dir_copy
 #' @importFrom fs dir_create
 #' @importFrom fs path_home
 #'
-#' @noRd
-#'
 #' @param cache_dir Cache directory
 #' @param package Package
 #' @param copy_dir Copy directory

R/create_edges.R

@@ -5,14 +5,10 @@ import::from(tidytable, bind_rows, .into = environment())
 #' @description This function applies similarity calculation to a list of
 #' spectra to create edges
 #'
-#' @export
-#'
 #' @importFrom tidytable bind_rows
 #'
 #' @include calculate_entropy.R
 #'
-#' @noRd
-#'
 #' @param index Indices
 #' @param frags Fragments
 #' @param precs Precursors

R/create_edges_spectra.R

@@ -48,7 +48,12 @@ import::from(tidytable, tidytable, .into = environment())
 #'
 #' @export
 #'
-#' @examples NULL
+#' @examples
+#' get_file(
+#' url = get_default_paths()$urls$examples$spectra_mini,
+#' export = get_params(step = "create_edges_spectra")$files$spectral$raw
+#' )
+#' create_edges_spectra()
 create_edges_spectra <- function(input = get_params(step = "create_edges_spectra")$files$spectral$raw,
  output = get_params(step = "create_edges_spectra")$files$networks$spectral$edges$raw,
  name_source = get_params(step = "create_edges_spectra")$names$source,

R/decorate_bio.R

@@ -13,8 +13,6 @@ import::from(tidytable, filter, .into = environment())
 #'
 #' @description This function outputs information about biological weighting
 #'
-#' @export
-#'
 #' @importFrom crayon blue
 #' @importFrom crayon cyan
 #' @importFrom crayon green
@@ -26,8 +24,6 @@ import::from(tidytable, filter, .into = environment())
 #' @importFrom tidytable distinct
 #' @importFrom tidytable filter
 #'
-#' @noRd
-#'
 #' @param annot_table_wei_bio Table to decorate
 #' @param score_biological_kingdom Kingdom score
 #' @param score_biological_phylum Phylum score

R/decorate_chemo.R

@@ -12,8 +12,6 @@ import::from(tidytable, filter, .into = environment())
 #'
 #' @description This function outputs information about chemical weighting
 #'
-#' @export
-#'
 #' @importFrom crayon blue
 #' @importFrom crayon cyan
 #' @importFrom crayon green
@@ -24,8 +22,6 @@ import::from(tidytable, filter, .into = environment())
 #' @importFrom tidytable distinct
 #' @importFrom tidytable filter
 #'
-#' @noRd
-#'
 #' @param annot_table_wei_chemo Table to decorate
 #' @param score_chemical_cla_kingdom Classyfire kingdom score
 #' @param score_chemical_cla_superclass Classyfire superclass score

R/decorate_masses.R

@@ -7,15 +7,11 @@ import::from(tidytable, filter, .into = environment())
 #'
 #' @description This function outputs information about MS1 annotation
 #'
-#' @export
-#'
 #' @importFrom crayon blue
 #' @importFrom crayon green
 #' @importFrom tidytable distinct
 #' @importFrom tidytable filter
 #'
-#' @noRd
-#'
 #' @param annotation_table_ms1 Table to decorate
 #'
 #' @return Message indicating the number of annotations obtained by MS1

R/dist_groups.R

@@ -7,12 +7,8 @@ import::from(stats, as.dist, .into = environment())
 #'
 #' @details Credit goes to usedist package
 #'
-#' @export
-#'
 #' @importFrom stats as.dist
 #'
-#' @noRd
-#'
 #' @param d Distance matrix
 #' @param idx1 Index of the first element
 #' @param idx2 Index of the second element
@@ -43,13 +39,9 @@ import::from(utils, combn, .into = environment())
 #'
 #' @description This function gets distances per group
 #'
-#' @export
-#'
 #' @importFrom stats as.dist
 #' @importFrom utils combn
 #'
-#' @noRd
-#'
 #' @param d A distance object
 #' @param g A grouping vector for the distance object
 #'

R/export_params.R

@@ -6,15 +6,11 @@ import::from(yaml, write_yaml, .into = environment())
 #' @description This function writes the parameters
 #' to a YAML file in the specified directory.
 #'
-#' @export
-#'
 #' @importFrom crayon green
 #' @importFrom yaml write_yaml
 #'
 #' @include get_default_paths.R
 #'
-#' @noRd
-#'
 #' @param parameters list of parameters to be exported
 #' @param directory directory where the YAML file will be saved
 #' @param step step identifier to be included in the YAML file name

R/export_spectra_rds.R

@@ -13,8 +13,6 @@ import::from(tidytable, filter, .into = environment())
 #'
 #' @return NULL
 #'
-#' @export
-#'
 #' @examples NULL
 export_spectra_rds <- function(file, spectra) {
  if (nrow(spectra |>

R/extract_spectra.R

@@ -24,8 +24,6 @@ import::from(tidytable, select, .into = environment())
 #'
 #' @return Data frame containing spectra data
 #'
-#' @export
-#'
 #' @examples NULL
 extract_spectra <- function(object) {
  ## issues

R/fake_annotations_columns.R

@@ -2,10 +2,6 @@
 #'
 #' @description This function fakes annotations columns
 #'
-#' @export
-#'
-#' @noRd
-#'
 #' @return NULL
 #'
 #' @examples NULL