Updating print function and messaging style

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,austraits)
+S3method(print,traits.build)
 export("%>%")
 export(as_wide_table)
 export(bind_databases)
@@ -30,7 +30,7 @@ export(plot_locations)
 export(plot_site_locations)
 export(plot_trait_distribution_beeswarm)
 export(separate_trait_values)
-export(summarise_austraits)
+export(summarise_database)
 export(summarise_trait_means)
 export(trait_pivot_longer)
 export(trait_pivot_wider)

R/austraits-package.R

@@ -6,7 +6,7 @@
 if(getRversion() >= "2.15.1")  utils::globalVariables(c(".", "dplyr::n()"))
 
 .onAttach <- function(libname, pkgname) {
-  packageStartupMessage("Thanks for showing interest in `austraits`! Please consider citing this package - citation('austraits')")
+    cli::cli_inform("Thanks for showing interest in `austraits`! Please consider citing this package - citation('austraits')", class = "packageStartupMessage")
 }
 
 #' @keywords internal

R/extract_data.R

@@ -232,7 +232,7 @@ extract_data <- function(database, table = NA, col, col_value) {
                  "taxa","contributors","sources","definitions","schema", "metadata","build_info")]
 
     # Assign class
-    attr(ret, "class") <- "austraits"
+    attr(data, "class") <- "traits.build"
 
   }
 

R/load_austraits.R

@@ -82,7 +82,7 @@ load_austraits <- function(doi = NULL, version = NULL, path = "data/austraits",
   data <- readRDS(file_nm) 
 
   # Assign class
-  attr(data, "class") <- "austraits"
+  attr(data, "class") <- "traits.build"
 
   data
 }

R/print.austraits.R

@@ -1,49 +1,89 @@
 #' @title Generic for outputting a nice summary for austraits objects
 #'
-#' @name print.austraits
-#' @param database traits.build database
+#' @name print.traits.build
+#' @param x traits.build database
 #' @param \dots passed to print
 #'
 #' @return nicely printed table
 #' @export
 
-print.austraits <- function(database, ...){
-
+print.traits.build <- function(x, ...){
+  # browser()
   # Setting up
-  version <- database$build_info$version %>% as.character()
-  nrecords <- nrow(database$traits)
-  nspecies <- unique(database$traits$taxon_name) %>% length()
-  ntraits <- unique(database$traits$trait_name) %>% length()
-
-  cat("This is version",
-         version, 
-         "of austraits!\n", 
-         "\nThis object contains a total of",
-         nrecords, "records",
-         "for", nspecies, "taxa and",
-         ntraits, "traits.\n")
+  version <- x$build_info$version %>% as.character()
+  nrecords <- nrow(x$traits)
+  nspecies <- unique(x$traits$taxon_name) %>% length()
+  ntraits <- unique(x$traits$trait_name) %>% length()
+
 
-  if(package_version(version) <= '3.0.2'){
+  if(package_version(version) < '5.0.0'){
+
+    # Setting up
+    database_name <- x$definitions$austraits$description
 
-  cat("\nThis object is a 'list' with the following components:\n\n",
-  database$definitions$austraits$elements %>%
-  purrr::map(~.x[["description"]]) %>% 
-  as.vector() %>% 
-  sprintf("- `%s`: %s", names(.), .) %>%
-  paste(collapse="\n")
-  )
+    fun <- function() {
+      cli::cli_h1("This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits.")
+
+      cli::cli_h2("This object is a 'list' with the following components:")
+      cli::cli_div(theme = list(span.emph = list(color = "forestgreen")))
+      cli::cli_ul()
+      cli::cli_li("{.emph traits}: A table containing measurements of traits.")
+      cli::cli_li("{.emph locations}: A table containing observations of location/site characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `location_name`.")
+      cli::cli_li("{.emph contexts}: A table containing observations of contextual characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `link_id`, and `link_vals`.")
+      cli::cli_li("{.emph methods}: A table containing details on methods with which data were collected, including time frame and source. Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id`, `trait_name`.")
+      cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.")
+      cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).")
+      cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.")
+      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
+      cli::cli_li("{.emph contributors}: A table of people contributing to each study.")
+      cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.")
+      cli::cli_li("{.emph build_info}:  A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
+      cli::cli_end()
+
+      cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits")
+    }
+
+    fun()
   } else{
-    cat("\nThis object is a 'list' with the following components:\n\n",
-        database$schema$austraits$elements %>%
-          purrr::map(~.x[["description"]]) %>% 
-          as.vector() %>% 
-          sprintf("- `%s`: %s", names(.), .) %>%
-          paste(collapse="\n")
-    )
+    database_name <- x$metadata$title
+
+    traits.build_version <- x$metadata$related_identifiers |> 
+      convert_list_to_df2() |> 
+      dplyr::filter(resource_type == "software") |> 
+      dplyr::pull(version)
+
+    fun <- function() {
+            cli::cli_h1("This is {version} of {database_name}!")
+
+      cli::cli_bullets(c(
+        "i" = "This database is built using traits.build version {traits.build_version}",
+        "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits."
+      )
+      )
+
+      cli::cli_h2("This object is a 'list' with the following components:")
+      cli::cli_div(theme = list(span.emph = list(color = "forestgreen")))
+      cli::cli_ul()
+      cli::cli_li("{.emph traits}: A table containing measurements of traits.")
+      cli::cli_li("{.emph locations}: A table containing observations of location/site characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `location_name`.")
+      cli::cli_li("{.emph contexts}: A table containing observations of contextual characteristics associated with information in `traits`. Cross referencing between the two dataframes is possible using combinations of the variables `dataset_id`, `link_id`, and `link_vals`.")
+      cli::cli_li("{.emph methods}: A table containing details on methods with which data were collected, including time frame and source. Cross referencing with the `traits` table is possible using combinations of the variables `dataset_id`, `trait_name`.")
+      cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.")
+      cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).")
+      cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.")
+      cli::cli_li("{.emph contributors}: A table of people contributing to each study.")
+      cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.")
+      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
+      cli::cli_li("{.emph schema}: A copy of the schema for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
+      cli::cli_li("{.emph metadata}: Metadata associated with the dataset, including title, creators, license, subject, funding sources.")
+      cli::cli_li("{.emph build_info}: A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
+      cli::cli_end()
+
+      cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits")
+    }
+
+    fun()
   }
-
-
-  cat("\n\nTo access a component, try using the $ e.g. austraits$traits")  
 }
 
 

R/summarise_austraits.R

@@ -1,35 +1,35 @@
 #' @title Summarise counts for a particular variable of interest
 #'
-#' @name summarise_austraits
+#' @name summarise_database
 #' @param database traits.build database (list object)
 #' @param var variable you use wish to see summary of (trait_name, genus, family)
 #'
 #' @return dataframe of unique levels of variable with counts and percentage
 #' @export
 #' @examples
 #' \dontrun{
-#' summarise_austraits(database = austraits, "trait_name")
-#' summarise_austraits(database = austraits, "family")
+#' summarise_database(database = austraits, "trait_name")
+#' summarise_database(database = austraits, "family")
 #' }
 
 
-summarise_austraits <- function(database, var){
+summarise_database <- function(database, var){
 
   if(!var %in% c("trait_name", "family", "genus")){
     stop(paste0("Print summary for ", var, " has not been implemented! see examples)"))
   }
 
   switch(var,
-         trait_name = summarise_austraits_traits(database, var),
-         genus =  summarise_austraits_taxa(database, var),
-         family = summarise_austraits_taxa(database, var)
+         trait_name = summarise_database_traits(database, var),
+         genus =  summarise_database_taxa(database, var),
+         family = summarise_database_taxa(database, var)
   )
 }
 
 #' @noRd
 #' @keywords internal
 
-summarise_austraits_traits <-function(database, var) {
+summarise_database_traits <-function(database, var) {
 
   ret <- 
     database[["traits"]] %>% 
@@ -60,7 +60,7 @@ summarise_austraits_traits <-function(database, var) {
 #' @noRd
 #' @keywords internal
 
-summarise_austraits_taxa <-function(database, var) {
+summarise_database_taxa <-function(database, var) {
 
   #Join taxonomic info
   database <- database %>% join_taxa()

tests/testthat/test-summarise_austraits.R

@@ -4,24 +4,24 @@ not_supported_austraits <- list(austraits_3.0.2_lite, austraits_4.2.0_lite)
 
 
 test_that("Function works", {
-    expect_visible(austraits_5.0.0_lite %>% summarise_austraits("family"))
-    expect_visible(austraits_5.0.0_lite %>% summarise_austraits("genus"))
-    expect_visible(austraits_5.0.0_lite %>% summarise_austraits("trait_name"))
+    expect_visible(austraits_5.0.0_lite %>% summarise_database("family"))
+    expect_visible(austraits_5.0.0_lite %>% summarise_database("genus"))
+    expect_visible(austraits_5.0.0_lite %>% summarise_database("trait_name"))
   })
 
 
 test_that("Throws errors", {
-    expect_error(austraits_5.0.0_lite %>% summarise_austraits("observation_id"))
-    expect_error(austraits_5.0.0_lite %>% summarise_austraits("trait"))
-    expect_error(austraits_5.0.0_lite %>% summarise_austraits("unit"))
-    expect_error(austraits_5.0.0_lite %>% summarise_austraits("source"))
+    expect_error(austraits_5.0.0_lite %>% summarise_database("observation_id"))
+    expect_error(austraits_5.0.0_lite %>% summarise_database("trait"))
+    expect_error(austraits_5.0.0_lite %>% summarise_database("unit"))
+    expect_error(austraits_5.0.0_lite %>% summarise_database("source"))
 
   })
 
 test_that("Output correct", {
-    family <- austraits_5.0.0_lite %>% summarise_austraits("family")
-    genus <- austraits_5.0.0_lite %>% summarise_austraits("genus")
-    trait_nm <- austraits_5.0.0_lite %>% summarise_austraits("trait_name")
+    family <- austraits_5.0.0_lite %>% summarise_database("family")
+    genus <- austraits_5.0.0_lite %>% summarise_database("genus")
+    trait_nm <- austraits_5.0.0_lite %>% summarise_database("trait_name")
 
     expect_length(family, 5)
     expect_length(genus, 5)