rename non-internal functions

previously named with a preceding <dot> these helper functions were renamed to prevent giving the impression that they are internal functions

Author: grlloyd

NAMESPACE

@@ -1,23 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(.cache_as_is)
-export(.collapse)
-export(.count)
-export(.greek_dictionary)
-export(.mean)
-export(.median)
-export(.mode)
-export(.nothing)
-export(.prioritise)
-export(.racemic_dictionary)
-export(.select_exact)
-export(.select_grade)
-export(.select_match)
-export(.select_max)
-export(.select_min)
-export(.tripeptide_dictionary)
-export(.unique)
-export(.unzip)
 export(AnnotationDb_database)
 export(AnnotationDb_select)
 export(BiocFileCache_database)
@@ -36,6 +18,7 @@ export(annotation_source)
 export(annotation_table)
 export(annotation_upset_chart)
 export(annotation_venn_chart)
+export(cache_as_is)
 export(calc_ppm_diff)
 export(calc_rt_diff)
 export(cd_source)
@@ -44,7 +27,11 @@ export(combine_columns)
 export(combine_records)
 export(combine_sources)
 export(compute_column)
+export(compute_mean)
+export(compute_median)
+export(compute_mode)
 export(compute_record)
+export(count_records)
 export(database_lookup)
 export(eutils_lookup)
 export(excel_database)
@@ -53,7 +40,10 @@ export(filter_na)
 export(filter_range)
 export(filter_records)
 export(filter_venn)
+export(fuse)
+export(fuse_unique)
 export(github_file)
+export(greek_dictionary)
 export(hmdb_lookup)
 export(id_counts)
 export(import_source)
@@ -69,14 +59,17 @@ export(mz_match)
 export(mzrt_match)
 export(normalise_lipids)
 export(normalise_strings)
+export(nothing)
 export(openbabel_structure)
 export(opsin_lookup)
 export(pivot_columns)
+export(prioritise)
 export(prioritise_columns)
 export(pubchem_compound_lookup)
 export(pubchem_property_lookup)
 export(pubchem_structure)
 export(pubchem_widget)
+export(racemic_dictionary)
 export(rdata_database)
 export(rds_cache)
 export(rds_database)
@@ -85,11 +78,18 @@ export(rename_columns)
 export(rest_api)
 export(rt_match)
 export(select_columns)
+export(select_exact)
+export(select_grade)
+export(select_match)
+export(select_max)
+export(select_min)
 export(split_column)
 export(split_records)
 export(sqlite_database)
 export(trim_whitespace)
+export(tripeptide_dictionary)
 export(unique_records)
+export(unzip_before_cache)
 export(wherever)
 exportMethods(chart_plot)
 exportMethods(check_for_columns)

R/BiocFileCache_database_class.R

@@ -5,7 +5,7 @@
 BiocFileCache_database <- function(source,
     bfc_path = NULL,
     resource_name,
-    bfc_fun = .cache_as_is,
+    bfc_fun = cache_as_is,
     import_fun = read.csv,
     offline = FALSE,
     ...) {
@@ -78,7 +78,7 @@ BiocFileCache_database <- function(source,
                 "See [BiocFileCache::bfcdownload()] for details."
             ),
             type = c("function"),
-            value = .cache_as_is,
+            value = cache_as_is,
             max_length = 1
         ),
         import_fun = entity(

R/BiocFileCache_database_helpers.R

@@ -25,11 +25,11 @@
 #' M <- BiocFileCache_database(
 #'     source = tempfile(),
 #'     resource_name = "example",
-#'     bfc_fun = .unzip
+#'     bfc_fun = unzip_before_cache
 #' )
 #'
 #' @export
-.unzip <- function(from, to) {
+unzip_before_cache <- function(from, to) {
     # temp folder
     fldr <- tempdir()
     # unzip
@@ -51,11 +51,11 @@
 #' M <- BiocFileCache_database(
 #'     source = tempfile(),
 #'     resource_name = "example",
-#'     bfc_fun = .cache_as_is
+#'     bfc_fun = cache_as_is
 #' )
 #'
 #' @export
-.cache_as_is <- function(from, to) {
+cache_as_is <- function(from, to) {
     file.copy(from = from, to = to, overwrite = TRUE)
     return(TRUE)
 }

R/MTox700plus_database_class.R

@@ -75,7 +75,7 @@ MTox700plus_database <- function(version = "latest",
         bfc_fun = .set_entity_value(
             obj = "BiocFileCache_database",
             param_id = "bfc_fun",
-            value = .cache_as_is
+            value = cache_as_is
         )
     )
 )

R/PathBank_metabolite_database_class.R

@@ -82,7 +82,7 @@ PathBank_metabolite_database <- function(version = "primary",
         bfc_fun = .set_entity_value(
             "BiocFileCache_database",
             "bfc_fun",
-            value = .unzip
+            value = unzip_before_cache
         )
     )
 )

R/combine_records_class.R

@@ -2,7 +2,7 @@
 #' @export
 #' @include annotation_source_class.R
 combine_records <- function(group_by,
-    default_fcn = .collapse(separator = " || "),
+    default_fcn = fuse(separator = " || "),
     fcns = list(),
     ...) {
     # check fcns are all functions
@@ -206,7 +206,7 @@ NULL
 #' and placed last if `ties = FALSE` (values are returned preferentially over
 #' NA).
 #'
-.mode <- function(ties = FALSE, na.rm = TRUE) {
+compute_mode <- function(ties = FALSE, na.rm = TRUE) {
     fcn <- expr(function(x) {
         if (length(x) <= 2) {
             return(x[1])
@@ -232,9 +232,9 @@ NULL
 #' @export
 #' @describeIn combine_records_helper_functions calculates the mean value,
 #' excluding NA if `na.rm = TRUE`
-.mean <- function() {
+compute_mean <- function(na.rm = TRUE) {
     fcn <- expr(function(x) {
-        mean(x, na.rm = TRUE)
+        mean(x, na.rm = !!na.rm)
     })
     return(eval(fcn))
 }
@@ -243,9 +243,9 @@ NULL
 #' @describeIn combine_records_helper_functions calculates the median value,
 #' excluding NA if `na.rm = TRUE`
 #' @export
-.median <- function() {
+compute_median <- function(na.rm = TRUE) {
     fcn <- expr(function(x) {
-        stats::median(x, na.rm = TRUE)
+        stats::median(x, na.rm = !!na.rm)
     })
     return(eval(fcn))
 }
@@ -256,7 +256,7 @@ NULL
 #' @param separator (character) a string used to separate multiple matches.
 #' @param na_string (character) a string used to represent NA values.
 #' @export
-.collapse <- function(separator, na_string = "NA") {
+fuse <- function(separator, na_string = "NA") {
     fcn <- expr(function(x) {
         x[is.na(x)] <- !!na_string
         paste0(x, collapse = !!separator)
@@ -272,7 +272,7 @@ NULL
 #' @param keep_NA (logical) If TRUE then records with NA are returned as well as
 #' the record with the maximum value.
 #' @export
-.select_max <- function(max_col, use_abs = FALSE, keep_NA = FALSE) {
+select_max <- function(max_col, use_abs = FALSE, keep_NA = FALSE) {
     fcn <- expr(function(x) {
         # get values
         vals <- as.numeric(pick(!!max_col)[[1]])
@@ -311,7 +311,7 @@ NULL
 #' @param keep_NA (logical) If TRUE then records with NA are returned as well as
 #' the record with the minimum value.
 #' @export
-.select_min <- function(min_col, use_abs = FALSE, keep_NA = FALSE) {
+select_min <- function(min_col, use_abs = FALSE, keep_NA = FALSE) {
     fcn <- expr(function(x) {
         # get values
         vals <- as.numeric(pick(!!min_col)[[1]])
@@ -342,13 +342,13 @@ NULL
 #' Select matching annotations
 #' @describeIn combine_records_helper_functions returns all records based on
 #' the indices of identical matches in a second column and collapses them
-#' useing the provided separator.
+#' using the provided separator.
 #' @param match_col (character) the name of a column to search for matches to
 #' the search column.
 #' @param search_col (character) the name of a column to use as a reference for
 #' locating values in the matching column.
 #' @export
-.select_match <- function(match_col, search_col, separator, na_string = "NA") {
+select_match <- function(match_col, search_col, separator, na_string = "NA") {
     fcn <- expr(function(x) {
         x <- x[which(pick(!!search_col)[[1]] == pick(!!match_col)[[1]])]
         if (!is.null(!!separator)) {
@@ -374,15 +374,15 @@ NULL
 #' # Select matching records
 #' M <- combine_records(
 #'     group_by = "example",
-#'     default_fcn = .select_exact(
+#'     default_fcn = select_exact(
 #'         match_col = "match_column",
 #'         match = "find_me",
 #'         separator = ", ",
 #'         na_string = "NA"
 #'     )
 #' )
 #' @export
-.select_exact <- function(match_col, match, separator, na_string = "NA") {
+select_exact <- function(match_col, match, separator, na_string = "NA") {
     fcn <- expr(function(x) {
         x <- x[which(pick(!!match_col) == !!match)]
 
@@ -411,15 +411,15 @@ NULL
 #' # Collapse unique values
 #' M <- combine_records(
 #'     group_by = "example",
-#'     default_fcn = .unique(
+#'     default_fcn = fuse_unique(
 #'         digits = 6,
 #'         separator = ", ",
 #'         na_string = "NA",
 #'         sort = FALSE
 #'     )
 #' )
 #' @export
-.unique <- function(separator,
+fuse_unique <- function(separator,
     na_string = "NA",
     digits = 6,
     drop_na = FALSE,
@@ -463,14 +463,14 @@ NULL
 #' # Prioritise by source
 #' M <- combine_records(
 #'     group_by = "InChiKey",
-#'     default_fcn = .prioritise(
+#'     default_fcn = prioritise(
 #'         match_col = "source",
 #'         priority = c("CD", "LS"),
 #'         separator = "  || "
 #'     )
 #' )
 #' @export
-.prioritise <- function(match_col,
+prioritise <- function(match_col,
     priority,
     separator,
     no_match = NA,
@@ -522,10 +522,10 @@ NULL
 #' # Do nothing to all columns
 #' M <- combine_records(
 #'     group_by = "InChiKey",
-#'     default_fcn = .nothing()
+#'     default_fcn = nothing()
 #' )
 #' @export
-.nothing <- function() {
+nothing <- function() {
     fcn <- expr(function(x) {
         return(x)
     })
@@ -542,11 +542,11 @@ NULL
 #' M <- combine_records(
 #'     group_by = "InChiKey",
 #'     fcns = list(
-#'         count = .count()
+#'         count = count_records()
 #'     )
 #' )
 #' @export
-.count <- function() {
+count_records <- function() {
     fcn <- expr(function(x) {
         y <- pick(everything())
         return(nrow(y))
@@ -569,14 +569,14 @@ NULL
 #' # Select annotation with highest (best) grade
 #' M <- combine_records(
 #'     group_by = "InChiKey",
-#'     default_fcn = .select_grade(
+#'     default_fcn = select_grade(
 #'         grade_col = "grade",
 #'         keep_NA = FALSE,
 #'         upper_case = TRUE
 #'     )
 #' )
 #' @export
-.select_grade <- function(grade_col, keep_NA = FALSE, upper_case = TRUE) {
+select_grade <- function(grade_col, keep_NA = FALSE, upper_case = TRUE) {
     fcn <- expr(function(x) {
         # get values
         vals <- pick(!!grade_col)

R/dictionaries.R

@@ -8,12 +8,12 @@
 #' M <- normalise_strings(
 #'     search_column = "example",
 #'     output_column = "result",
-#'     dictionary = .tripeptide_dictionary
+#'     dictionary = tripeptide_dictionary
 #' )
 #'
 #' @return A dictionary for use with [`normalise_strings()`]
 #' @export
-.tripeptide_dictionary <- list(
+tripeptide_dictionary <- list(
     list(
         pattern = "^[ABCDEFGHIJKLMNOPQRSTVWXYZ]{3}$",
         replace = function(x) {
@@ -71,12 +71,12 @@
 #' M <- normalise_strings(
 #'     search_column = "example",
 #'     output_column = "result",
-#'     dictionary = .racemic_dictionary
+#'     dictionary = racemic_dictionary
 #' )
 #'
 #' @return A dictionary for use with [`normalise_strings()`]
 #' @export
-.racemic_dictionary <- list(
+racemic_dictionary <- list(
     list(pattern = "-(-)-", replace = "-", fixed = TRUE),
     list(pattern = "-(+)-", replace = "-", fixed = TRUE),
     list(pattern = "^L(+)-", replace = "L-", fixed = TRUE),
@@ -94,12 +94,12 @@
 #' M <- normalise_strings(
 #'     search_column = "example",
 #'     output_column = "result",
-#'     dictionary = .greek_dictionary
+#'     dictionary = greek_dictionary
 #' )
 #'
 #' @return A dictionary for use with [`normalise_strings()`]
 #' @export
-.greek_dictionary <- list(
+greek_dictionary <- list(
     list(pattern = "\\x{03b1}", replace = "alpha"),
     list(pattern = "\\x{03b2}", replace = "beta"),
     list(pattern = "\\x{03b3}", replace = "gamma"),

R/excel_database_class.R

@@ -88,7 +88,7 @@ setMethod(
             colNames = obj$colNames,
             startRow = obj$startRow
         )
-        colnames(IN) <- make.unique(colnames(IN))
+        colnames(IN) <- makefuse_unique(colnames(IN))
         IN$.row_id <- seq_len(nrow(IN))
 
         # return