From 70adfbac9cf2c2cd55b9c9030d2f7578b182e37a Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 13:59:47 +1100
Subject: [PATCH 01/10] Changed class name and generic name

---
 NAMESPACE                                         | 2 +-
 R/extract_data.R                                  | 2 +-
 R/load_austraits.R                                | 2 +-
 R/print.austraits.R                               | 7 ++++---
 man/{print.austraits.Rd => print.traits.build.Rd} | 6 +++---
 5 files changed, 10 insertions(+), 9 deletions(-)
 rename man/{print.austraits.Rd => print.traits.build.Rd} (79%)

diff --git a/NAMESPACE b/NAMESPACE
index cf686d9..8653e64 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/extract_data.R b/R/extract_data.R
index e202310..f276932 100644
--- a/R/extract_data.R
+++ b/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"
 
   }
   
diff --git a/R/load_austraits.R b/R/load_austraits.R
index 020fd06..2f332a3 100644
--- a/R/load_austraits.R
+++ b/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
 }
diff --git a/R/print.austraits.R b/R/print.austraits.R
index 58f14a2..eb15730 100644
--- a/R/print.austraits.R
+++ b/R/print.austraits.R
@@ -1,13 +1,14 @@
 #' @title Generic for outputting a nice summary for austraits objects
 #'
-#' @name print.austraits
+#' @name print.traits.build
 #' @param database traits.build database
 #' @param \dots passed to print
 #'
 #' @return nicely printed table
 #' @export
 
-print.austraits <- function(database, ...){
+print.traits.build <- function(database, ...){
+  browser()
   
   # Setting up
   version <- database$build_info$version %>% as.character()
@@ -18,7 +19,7 @@ print.austraits <- function(database, ...){
   cat("This is version",
          version, 
          "of austraits!\n", 
-         "\nThis object contains a total of",
+         "\nThis database contains a total of",
          nrecords, "records",
          "for", nspecies, "taxa and",
          ntraits, "traits.\n")
diff --git a/man/print.austraits.Rd b/man/print.traits.build.Rd
similarity index 79%
rename from man/print.austraits.Rd
rename to man/print.traits.build.Rd
index 37d4cf4..01904d4 100644
--- a/man/print.austraits.Rd
+++ b/man/print.traits.build.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/print.austraits.R
-\name{print.austraits}
-\alias{print.austraits}
+\name{print.traits.build}
+\alias{print.traits.build}
 \title{Generic for outputting a nice summary for austraits objects}
 \usage{
-\method{print}{austraits}(database, ...)
+\method{print}{traits.build}(database, ...)
 }
 \arguments{
 \item{database}{traits.build database}

From 8ce6ca98dd88a5783a039e2e859ae9444ee659b0 Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 14:27:30 +1100
Subject: [PATCH 02/10] Replacing cat with cli

---
 R/print.austraits.R | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/R/print.austraits.R b/R/print.austraits.R
index eb15730..58fef9f 100644
--- a/R/print.austraits.R
+++ b/R/print.austraits.R
@@ -8,7 +8,7 @@
 #' @export
 
 print.traits.build <- function(database, ...){
-  browser()
+  # browser()
   
   # Setting up
   version <- database$build_info$version %>% as.character()
@@ -16,13 +16,21 @@ print.traits.build <- function(database, ...){
   nspecies <- unique(database$traits$taxon_name) %>% length()
   ntraits <- unique(database$traits$trait_name) %>% length()
   
-  cat("This is version",
-         version, 
-         "of austraits!\n", 
-         "\nThis database contains a total of",
-         nrecords, "records",
-         "for", nspecies, "taxa and",
-         ntraits, "traits.\n")
+  database_name <- database$metadata$title
+  
+  traits.build_version <- at_six$metadata$related_identifiers |> 
+    convert_list_to_df2() |> 
+    dplyr::filter(resource_type == "software") |> 
+    dplyr::pull(version)
+  
+  # Formulate message
+  cli::cli_h1("This is {database_name}!")
+  
+  cli::cli_bullets(c(
+    "i" = "A database built using traits.build version {traits.build_version}",
+    "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits."
+  )
+  )
   
   if(package_version(version) <= '3.0.2'){
   
@@ -43,7 +51,6 @@ print.traits.build <- function(database, ...){
     )
   }
 
-  
   cat("\n\nTo access a component, try using the $ e.g. austraits$traits")  
 }
 

From 047dbb14ddd89c2b592b3dd306194dfb1b21a3a2 Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 14:54:07 +1100
Subject: [PATCH 03/10] Using cli altogether

---
 R/print.austraits.R | 97 +++++++++++++++++++++++++++++++--------------
 1 file changed, 67 insertions(+), 30 deletions(-)

diff --git a/R/print.austraits.R b/R/print.austraits.R
index 58fef9f..62de1c0 100644
--- a/R/print.austraits.R
+++ b/R/print.austraits.R
@@ -8,14 +8,8 @@
 #' @export
 
 print.traits.build <- function(database, ...){
-  # 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$trait_name) %>% length()
-  
   database_name <- database$metadata$title
   
   traits.build_version <- at_six$metadata$related_identifiers |> 
@@ -23,35 +17,78 @@ print.traits.build <- function(database, ...){
     dplyr::filter(resource_type == "software") |> 
     dplyr::pull(version)
   
-  # Formulate message
-  cli::cli_h1("This is {database_name}!")
-  
-  cli::cli_bullets(c(
-    "i" = "A database built using traits.build version {traits.build_version}",
-    "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits."
-  )
-  )
+  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()
+
   
   if(package_version(version) <= '3.0.2'){
+    
+    # Setting up
+    database_name <- database$definitions$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 is {version} of {database_name}!")
+      
+      cli::cli_bullets(c(
+        "i" = "A database 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 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")
-    )
+    fun <- function() {
+            cli::cli_h1("This is {version} of {database_name}!")
+      
+      cli::cli_bullets(c(
+        "i" = "A database 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 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 sources}:  Bibtex entries for all primary and secondary sources in the compilation.")
+      cli::cli_li("{.emph contributors}:  A table of people contributing to each study.")
+      cli::cli_li("{.emph taxonomic_updates}:   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 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")  
 }
 
 

From 8da52aae799f6592f5b2dacfb152079002e425eb Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:00:00 +1100
Subject: [PATCH 04/10] Updated formating in cli

---
 R/print.austraits.R | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/print.austraits.R b/R/print.austraits.R
index 62de1c0..3becb4b 100644
--- a/R/print.austraits.R
+++ b/R/print.austraits.R
@@ -47,9 +47,9 @@ print.traits.build <- function(database, ...){
       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 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 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()
       
@@ -74,14 +74,15 @@ print.traits.build <- function(database, ...){
       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 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 sources}:  Bibtex entries for all primary and secondary sources in the compilation.")
-      cli::cli_li("{.emph contributors}:  A table of people contributing to each study.")
-      cli::cli_li("{.emph taxonomic_updates}:   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 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_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")

From 6e19f28c4af0b6a5ccd147a77a64b86da15c58a9 Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:15:09 +1100
Subject: [PATCH 05/10] Rename summarise_austraits to summarise_database

---
 NAMESPACE                                     |  2 +-
 R/summarise_austraits.R                       | 18 ++++++++---------
 ...ise_austraits.Rd => summarise_database.Rd} | 10 +++++-----
 tests/testthat/test-summarise_austraits.R     | 20 +++++++++----------
 4 files changed, 25 insertions(+), 25 deletions(-)
 rename man/{summarise_austraits.Rd => summarise_database.Rd} (71%)

diff --git a/NAMESPACE b/NAMESPACE
index 8653e64..998dc4a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -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)
diff --git a/R/summarise_austraits.R b/R/summarise_austraits.R
index 519b50d..85b6da8 100644
--- a/R/summarise_austraits.R
+++ b/R/summarise_austraits.R
@@ -1,6 +1,6 @@
 #' @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)
 #'
@@ -8,28 +8,28 @@
 #' @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()
diff --git a/man/summarise_austraits.Rd b/man/summarise_database.Rd
similarity index 71%
rename from man/summarise_austraits.Rd
rename to man/summarise_database.Rd
index 43f1b65..af70696 100644
--- a/man/summarise_austraits.Rd
+++ b/man/summarise_database.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/summarise_austraits.R
-\name{summarise_austraits}
-\alias{summarise_austraits}
+\name{summarise_database}
+\alias{summarise_database}
 \title{Summarise counts for a particular variable of interest}
 \usage{
-summarise_austraits(database, var)
+summarise_database(database, var)
 }
 \arguments{
 \item{database}{traits.build database (list object)}
@@ -19,7 +19,7 @@ Summarise counts for a particular variable of interest
 }
 \examples{
 \dontrun{
-summarise_austraits(database = austraits, "trait_name")
-summarise_austraits(database = austraits, "family")
+summarise_database(database = austraits, "trait_name")
+summarise_database(database = austraits, "family")
 }
 }
diff --git a/tests/testthat/test-summarise_austraits.R b/tests/testthat/test-summarise_austraits.R
index f6e182e..7690604 100644
--- a/tests/testthat/test-summarise_austraits.R
+++ b/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)

From c1b4b7e6aac4d335653a608ca79a2ed8cd6085ec Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:31:27 +1100
Subject: [PATCH 06/10] Updated format for print message for v<5

---
 R/print.austraits.R | 42 ++++++++++++++++++------------------------
 1 file changed, 18 insertions(+), 24 deletions(-)

diff --git a/R/print.austraits.R b/R/print.austraits.R
index 3becb4b..11030e6 100644
--- a/R/print.austraits.R
+++ b/R/print.austraits.R
@@ -1,41 +1,28 @@
 #' @title Generic for outputting a nice summary for austraits objects
 #'
 #' @name print.traits.build
-#' @param database traits.build database
+#' @param x traits.build database
 #' @param \dots passed to print
 #'
 #' @return nicely printed table
 #' @export
 
-print.traits.build <- function(database, ...){
-  
+print.traits.build <- function(x, ...){
+  # browser()
   # Setting up
-  database_name <- database$metadata$title
-  
-  traits.build_version <- at_six$metadata$related_identifiers |> 
-    convert_list_to_df2() |> 
-    dplyr::filter(resource_type == "software") |> 
-    dplyr::pull(version)
-  
-  version <- database$build_info$version %>% as.character()
-  nrecords <- nrow(database$traits)
-  nspecies <- unique(database$traits$taxon_name) %>% length()
-  ntraits <- unique(database$traits$trait_name) %>% length()
+  version <- x$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 <- database$definitions$austraits$description
+    database_name <- x$definitions$austraits$description
   
     fun <- function() {
-      cli::cli_h1("This is {version} of {database_name}!")
-      
-      cli::cli_bullets(c(
-        "i" = "A database 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_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")))
@@ -58,11 +45,18 @@ print.traits.build <- function(database, ...){
     
     fun()
   } else{
+    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" = "A database built using traits.build version {traits.build_version}",
+        "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."
       )
       )

From cbc3094fa6e6fba440a6248e0b95bd45909a8b3e Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:32:19 +1100
Subject: [PATCH 07/10] Updated start up message

---
 R/austraits-package.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/austraits-package.R b/R/austraits-package.R
index cfd5fc7..f61fe31 100644
--- a/R/austraits-package.R
+++ b/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_alert_success("Thanks for showing interest in `austraits`! Please consider citing this package - citation('austraits')")
 }
 
 #' @keywords internal

From 46e638c4bc14740651c1403824cd16c2e0331a30 Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:34:22 +1100
Subject: [PATCH 08/10] Updated documentation

---
 man/print.traits.build.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/print.traits.build.Rd b/man/print.traits.build.Rd
index 01904d4..bf16dc7 100644
--- a/man/print.traits.build.Rd
+++ b/man/print.traits.build.Rd
@@ -4,10 +4,10 @@
 \alias{print.traits.build}
 \title{Generic for outputting a nice summary for austraits objects}
 \usage{
-\method{print}{traits.build}(database, ...)
+\method{print}{traits.build}(x, ...)
 }
 \arguments{
-\item{database}{traits.build database}
+\item{x}{traits.build database}
 
 \item{\dots}{passed to print}
 }

From ccaefe326749b995b7964b5f9ca1ea042f2175e0 Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:38:02 +1100
Subject: [PATCH 09/10] Revered start up message

---
 R/austraits-package.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/austraits-package.R b/R/austraits-package.R
index f61fe31..cfd5fc7 100644
--- a/R/austraits-package.R
+++ b/R/austraits-package.R
@@ -6,7 +6,7 @@
 if(getRversion() >= "2.15.1")  utils::globalVariables(c(".", "dplyr::n()"))
 
 .onAttach <- function(libname, pkgname) {
-  cli::cli_alert_success("Thanks for showing interest in `austraits`! Please consider citing this package - citation('austraits')")
+  packageStartupMessage("Thanks for showing interest in `austraits`! Please consider citing this package - citation('austraits')")
 }
 
 #' @keywords internal

From 0089f60be07a55af87b3071c0efd8ab6ae16e8ec Mon Sep 17 00:00:00 2001
From: Fonti Kar <f.kar@unsw.edu.au>
Date: Thu, 14 Nov 2024 15:47:22 +1100
Subject: [PATCH 10/10] Updated start up message

---
 R/austraits-package.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/austraits-package.R b/R/austraits-package.R
index cfd5fc7..f81f19e 100644
--- a/R/austraits-package.R
+++ b/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