clean up help files following R CMD check

mainly cleaning wrong `param` tags, links etc

.Rbuildignore

@@ -6,3 +6,5 @@
 ^pkgdown$
 ^data-raw$
 ^.github$
+^doc$
+^Meta$

.gitignore

@@ -55,3 +55,5 @@ rsconnect/
 tests/my_tests.R
 docs
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -22,7 +22,6 @@ Imports:
   cli,
   dplyr,
   glue,
-  here,
   hms,
   lubridate,
   purrr,
@@ -31,19 +30,21 @@ Imports:
   stringr,
   tibble,
   tidyr,
-  nanoparquet,
   uuid
 Suggests:
   gt,
+  here,
   knitr,
+  nanoparquet,
+  ozmaps,
   readr,
   rmarkdown,
   testthat (>= 3.0.0)
 License: GPL-3 + file LICENSE
 URL: https://corella.ala.org.au
 Encoding: UTF-8
+VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Config/testthat/edition: 3
-VignetteBuilder: knitr
 LazyData: true

NAMESPACE

@@ -82,6 +82,7 @@ importFrom(lubridate,ymd_hms)
 importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,pluck)
+importFrom(rlang,.data)
 importFrom(rlang,abort)
 importFrom(rlang,as_label)
 importFrom(rlang,caller_env)
@@ -109,5 +110,6 @@ importFrom(sf,st_geometry_type)
 importFrom(sf,st_is)
 importFrom(stringr,str_remove_all)
 importFrom(tibble,lst)
+importFrom(tibble,tibble)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,unnest)

NEWS.md

@@ -0,0 +1,3 @@
+# corella 0.1.0
+
+Welcome to {corella}!

R/check_occurrences.R

@@ -32,7 +32,7 @@ check_dataset <- function(.df){
   fields <- colnames(.df)
   available_checks <- fn_to_term_table() |>
     bind_rows() |>
-    select(dwc_term) |>
+    select("dwc_term") |>
     pull()
   checkable_fields <- fields[fields %in% available_checks]
 
@@ -63,12 +63,10 @@ check_dataset <- function(.df){
   summary_message(check_results, checkable_fields)
   cat_line()
 
-
   ## Darwin Core compliance
   # dwc_spinny_message(c("Meets minimum requirements for Darwin Core terms"))
   check_min_req_dwc(checkable_fields)
 
-
   ## Error Messages
 
   # truncate
@@ -81,11 +79,11 @@ check_dataset <- function(.df){
 
   # split messages by function for message formatting
     results_split <- check_results |>
-      unnest(messages) |>
+      unnest(.data$messages) |>
       mutate(
         term = factor(term, levels = unique(term)) # maintain original term order
         ) |>
-      group_split(term)
+      group_split(.data$term)
 
   # print preserved errors in a nice format
     results_split |>
@@ -114,9 +112,10 @@ check_dataset <- function(.df){
 #' @importFrom cli cli_progress_update
 #' @importFrom cli ansi_align
 #' @importFrom cli ansi_nchar
-#' @importFrom stringr str_remove_all
 #' @importFrom rlang cnd_muffle
 #' @importFrom rlang exec
+#' @importFrom stringr str_remove_all
+#' @importFrom tibble tibble
 #' @noRd
 #' @keywords Internal
 check_all <- function(fn, .df, checkable_fields) {

R/corella-package.R

@@ -29,7 +29,7 @@
 #'
 #'   * [use_events()] basic information on observation events (`eventID`, `parentEventID`, `eventType`)
 #'   * [use_occurrences()] basic information on observations (`occurrenceID`, `basisOfRecord`)
-#'   * [use_scientificName()] record the highest level of taxonomic specificity in the dataset (`scientificName`, `scientificNameAuthorship`, `taxonRank`)
+#'   * [use_scientific_name()] record the highest level of taxonomic specificity in the dataset (`scientificName`, `scientificNameAuthorship`, `taxonRank`)
 #'   * [use_taxonomy()] to specify higher taxonomic columns (`kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, `specificEpithet`, `vernacularName`)
 #'   * [use_coordinates()] for spatial data (`decimalLatitude`, `decimalLongitude`, `geodeticDatum`, `coordinateUncertaintyInMeters`, `coordinatePrecision`)
 #'   * [use_sf()] for spatial data in `sf` format

R/darwin_core_terms.R

@@ -15,8 +15,8 @@
 #'   \item{comments}{Further information from TDWG.}
 #'   \item{examples}{Examples of how the field should be populated.}
 #' }
-#' @seealso [occurrence_fields()] and [event_fields()] to get terms for use in
-#' `[dplyr::select()]`
+#' @seealso [occurrence_terms()] and [event_terms()] to get terms for use in
+#' [dplyr::select()]
 #' @source Slightly modified version of a table supplied by TDWG at
 #' [this link](https://github.com/tdwg/dwc/blob/master/vocabulary/term_versions.csv).
 "darwin_core_terms"

R/suggest_workflow.R

@@ -69,15 +69,15 @@ check_dataframe <- function(.df,
 #'
 #' @param .df vector of values
 #' @param dwc_terms vector of valid Darwin Core terms against which .df should be compared
-#' @importFrom dplyr pull
-#' @importFrom dplyr filter
-#' @importFrom dplyr distinct
-#' @importFrom rlang is_empty
 #' @importFrom cli cli_div
 #' @importFrom cli cli_h1
 #' @importFrom cli cli_h2
 #' @importFrom cli cli_h3
 #' @importFrom cli cli_end
+#' @importFrom dplyr pull
+#' @importFrom dplyr filter
+#' @importFrom dplyr distinct
+#' @importFrom rlang is_empty
 #' @noRd
 #' @keywords Internal
 check_contains_terms <- function(.df,
@@ -106,23 +106,21 @@ check_contains_terms <- function(.df,
   # retrieve required term match results
   req_terms_results <- check_required_terms(user_column_names)
 
-
   ## Suggested workflow & Additional functions
 
   # Function matching for suggested workflow
   main_functions <- fn_to_term_table()$main
   other_functions <- fn_to_term_table()$optional
 
   suggested_functions <- main_functions |>
-    filter(!dwc_term %in% matched_values) |>
-    distinct(use_function) |>
-    pull(use_function)
+    filter(!.data$dwc_term %in% matched_values) |>
+    distinct(.data$use_function) |>
+    pull("use_function")
 
   optional_functions <- other_functions |>
-    filter(dwc_term %in% matched_values) |>
-    distinct(use_function) |>
-    pull(use_function)
-
+    filter(.data$dwc_term %in% matched_values) |>
+    distinct(.data$use_function) |>
+    pull("use_function")
 
   # this wraps text (which might not be optimal for this table)
   # withr::with_options(
@@ -385,43 +383,41 @@ fn_to_term_table <- function() {
 }
 
 
-
-
 #' Build table for messaging about minimum required terms
 #'
-#' @importFrom tidyr unnest
-#' @importFrom dplyr case_when
-#' @importFrom dplyr group_by
-#' @importFrom dplyr select
-#' @importFrom dplyr full_join
-#' @importFrom dplyr join_by
-#' @importFrom tidyr replace_na
-#' @importFrom tidyr unnest
 #' @importFrom cli ansi_align
 #' @importFrom cli ansi_collapse
 #' @importFrom cli ansi_nchar
 #' @importFrom cli col_blue
 #' @importFrom cli col_green
 #' @importFrom cli col_red
 #' @importFrom cli symbol
+#' @importFrom dplyr case_when
+#' @importFrom dplyr group_by
+#' @importFrom dplyr select
+#' @importFrom dplyr full_join
+#' @importFrom dplyr join_by
+#' @importFrom rlang .data
+#' @importFrom tidyr replace_na
+#' @importFrom tidyr unnest
 #' @noRd
 #' @keywords Internal
 build_req_terms_table <- function(req_terms) {
 
   # Unnest & concatenate terms by group
   missing_results <- req_terms |>
-    select(-matched) |>
+    select(-"matched") |>
     unnest(cols = c(missing)) |>
-    group_by(term_group) |>
+    group_by(.data$term_group) |>
     mutate( # glue names
       missing = ansi_collapse(missing, sep = ", ", last = ", ")
     ) |>
     unique()
 
   matched_results <- req_terms |>
-    select(-missing) |>
+    select(-"missing") |>
     unnest(cols = c(matched)) |>
-    group_by(term_group) |>
+    group_by(.data$term_group) |>
     mutate( # glue names
       matched = ansi_collapse(matched, sep = ", ", last = ", ")
     ) |>

R/use_abundance.R

@@ -9,7 +9,12 @@
 #' @param individualCount The number of individuals present
 #' @param organismQuantity A number or enumeration value for the quantity of
 #' organisms. Used together with `organismQuantityType` to provide context.
-#' @param organismQuantityType The type of quantification system used for `organismQuantity`
+#' @param organismQuantityType The type of quantification system used for
+#' `organismQuantity`.
+#' @param .keep Control which columns from .data are retained in the output.
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
+#' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
+#' generate them.
 #' @returns A tibble with the requested fields (see details).
 #'
 #' @details

R/use_collection.R

@@ -8,15 +8,15 @@
 #' informative errors, and serves as a useful lookup for fields in
 #' the Darwin Core Standard.
 #'
-#' @param df a `data.frame` or `tibble` that the column should be appended to.
+#' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param datasetID An identifier for the set of data. May be a global unique
 #' identifier or an identifier specific to a collection or institution.
 #' @param datasetName The name identifying the data set from which the record
 #' was derived.
 #' @param catalogNumber A unique identifier for the record within the data set
 #' or collection.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields added.

R/use_coordinates.R

@@ -2,11 +2,10 @@
 #'
 #' This function helps format standard location fields to a `tibble`.
 #'
-#' In
-#' practice this is no different from using `mutate()`, but gives some
+#' In practice this is no different from using `mutate()`, but gives some
 #' informative errors, and serves as a useful lookup for how spatial fields are
 #' represented in the Darwin Core Standard.
-#' @param df a `data.frame` or `tibble` that the column should be appended to.
+#' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param decimalLatitude The latitude in decimal degrees
 #' @param decimalLongitude The longitude in decimal degrees
 #' @param geodeticDatum The datum or spatial reference system that coordinates
@@ -21,7 +20,7 @@
 #' `decimalLongitude` are supplied to. `coordinatePrecision` should be no less
 #' than 0.00001 if data were collected using GPS.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields added.

R/use_datetime.R

@@ -2,18 +2,17 @@
 #'
 #' This function helps format standard date/time fields to a `tibble`.
 #'
-#' In
-#' practice this is no different from using `mutate()`, but gives some
+#' In practice this is no different from using `mutate()`, but gives some
 #' informative errors, and serves as a useful lookup for how spatial fields are
 #' represented in the Darwin Core Standard.
 #' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param eventDate The date or date + time that the observation/event occurred.
 #' @param year The year of the observation/event.
 #' @param month The month of the observation/event.
 #' @param day The day of the observation/event.
-#' @param time The time of the observation/event.
+#' @param eventTime The time of the observation/event.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @param .messages (logical) Should informative messages be shown? Defaults to

R/use_individual_traits.R

@@ -10,7 +10,7 @@
 #' informative errors, and serves as a useful lookup for fields in
 #' the Darwin Core Standard.
 #'
-#' @param df a `data.frame` or `tibble` that the column should be appended to.
+#' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param individualID An identifier for an individual or named group of
 #' individual organisms represented in the Occurrence. Meant to accommodate
 #' resampling of the same individual or group for monitoring purposes. May
@@ -23,7 +23,7 @@
 #' @param reproductiveCondition The reproductive condition of the biological
 #' individual.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields added.

R/use_locality.R

@@ -2,14 +2,14 @@
 #'
 #' Locality information refers to a description of a place, rather than a
 #' spatial coordinate.
-#' @param df a `data.frame` or `tibble` that the column should be appended to.
+#' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param continent (string) Valid continent. See details.
 #' @param country Valid country name. See `country_codes`.
 #' @param countryCode Valid country code. See `country_codes`.
 #' @param stateProvince A sub-national region.
 #' @param locality A specific location, such as a property or address.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields.

R/use_measurements.R

@@ -4,8 +4,11 @@
 #' This function is a work in progress, and should be used with caution.
 #'
 #' @param .df a `data.frame` or `tibble` that the column should be appended to.
+#' @param cols vector of column names to be included as 'measurements'. Unquoted.
+#' @param unit vector of strings giving units for each variable
+#' @param type vector of strings giving a description for each variable
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields added.
@@ -19,8 +22,8 @@
 use_measurements <- function(
     .df,
     cols = NULL,
-    type = NULL,
     unit = NULL,
+    type = NULL,
     .keep = "unused"
 ){
   if(missing(.df)){

R/use_observer.R

@@ -6,14 +6,14 @@
 #' In practice this is no different from using `mutate()`, but gives some
 #' informative errors, and serves as a useful lookup for fields in
 #' the Darwin Core Standard.
-#' @param df a `data.frame` or `tibble` that the column should be appended to.
+#' @param .df a `data.frame` or `tibble` that the column should be appended to.
 #' @param recordedBy Names of people, groups, or organizations responsible for
 #' recording the original occurrence. The primary collector or observer should
 #' be listed first.
 #' @param recordedByID The globally unique identifier for the person, people,
 #' groups, or organizations responsible for recording the original occurrence.
 #' @param .keep Control which columns from .data are retained in the output.
-#' Note that unlike `dplyr::mutate`, which defaults to `"all"` this defaults to
+#' Note that unlike [dplyr::mutate()], which defaults to `"all"` this defaults to
 #' `"unused"`; i.e. only keeps Darwin Core fields, and not those fields used to
 #' generate them.
 #' @returns A tibble with the requested fields added.