Updates for austraits 3.0 (#21)

Update austraits package vignette & AusTraits tutorial vignette to match austraits version 3.0 release.

data/extra_functions.R

@@ -4,7 +4,7 @@ austraits_weighted_means <- function(austraits, traits) {
 
   # any data that is a mean, median or raw, create a site mean
   data_means <- 
-    (austraits %>% austraits::join_locations())$traits %>% 
+    (austraits %>% austraits::join_location_coordinates())$traits %>% 
     dplyr::filter(trait_name %in% traits) %>%
     dplyr::filter(value_type %in% c("mean", "raw", "median")) %>%
     dplyr::mutate(

database_structure.qmd

@@ -79,7 +79,7 @@ print_schema_element <- function(elements) {
       writeLines()
 
     elements$elements %>%
-      util_list_to_df1() %>%
+      austraits::convert_list_to_df1() %>%
       my_kable_styling() %>%
       writeLines()
   }
@@ -112,7 +112,7 @@ In detail:
 
 ```{r entity_type}
 schema$entity_type$values %>%
-  util_list_to_df1() %>%
+  austraits::convert_list_to_df1() %>%
   my_kable_styling() %>%
   writeLines()
 ```
@@ -158,7 +158,7 @@ Possible values are:
 
 ```{r basis_of_record}
 schema$basis_of_record$values %>%
-  util_list_to_df1() %>%
+  austraits::convert_list_to_df1() %>%
   my_kable_styling() %>%
   writeLines()
 ```
@@ -177,7 +177,7 @@ Possible value types are:
 
 ```{r value_type}
 schema$value_type$values %>%
-  util_list_to_df1() %>%
+  austraits::convert_list_to_df1() %>%
   my_kable_styling() %>%
   writeLines()
 ```
@@ -188,7 +188,7 @@ Possible values are:
 
 ```{r basis_of_value}
 schema$basis_of_value$values %>%
-  util_list_to_df1() %>%
+  austraits::convert_list_to_df1() %>%
   my_kable_styling() %>%
   writeLines()
 ```

dictionary.qmd

@@ -2,6 +2,9 @@
 
 A core component of the traits.build database structure is a trait dictionary that clearly defines and describes each trait concept included within the trait database.
 
+A description of the trait dictionary is available at: Wenk, E.H., Sauquet, H., Gallagher, R.V., Brownlee, R., Boettiger, C., Coleman, D., Yang, S., Auld, T., Barrett, R., Brodribb, T., Choat, B., Dun, L., Ellsworth, D., Gosper, C., Guja, L., Jordan, G.J., Le Breton, T., Leigh, A., Lu-Irving, P., Medlyn, B., Nolan, R., Ooi, M., Sommerville, K.D., Vesk, P., White, M., Wright, I.J., Falster, D.S., 2024. The AusTraits plant dictionary. Sci Data 11, 537. [DOI: 10.1038/s41597-024-03368-z](https://doi.org/10.1038/s41597-024-03368-z).
+
+
 Building upon the standard outlined by the ETS [Ecological Trait-data Standard](https://doi.org/10.1111/2041-210X.13288), all numeric traits must have standard units and an allowable range. Categorical traits must have a list of allowable trait values.
 
 Each trait concept must have a complete, explicit definition to eliminate confusion between trait concepts.

file_structure_data_metadata.qmd

@@ -96,7 +96,7 @@ This section provides `r tolower(schema$metadata$elements$contributors$descripti
 
 ```{r, echo=FALSE, results="show"}
 schema$metadata$elements$contributors$elements$data_collectors$elements %>%
-  util_list_to_df1() %>%
+  austraits::convert_list_to_df1() %>%
   my_kable_styling()
 ```
 

index.qmd

@@ -6,6 +6,9 @@ Imagine you wanted to build a database of traits. You might start by compiling d
 
 `traits.build` is a data standard, R package, and workflow that is desgined to help you build a harmonised, relational database from disparate datasets. The package was first developed to create  [`austraits.build`](https://github.com/traitecoevo/austraits.build/) an, open-source database of Australian plant traits. The code has been transformed into a standalone package allowing anyone to build a relational, tabular database for any taxonomic group and any collection of traits.
 
+A description of this package is available at: Wenk, E., Bal, P., Coleman, D., Gallagher, R., Yang, S., Falster, D., 2024. Traits.build: A data model, workflow and R package for building harmonised ecological trait databases. Ecological Informatics 83, 102773. [DOI: j.ecoinf.2024.102773](https://doi.org/10.1016/j.ecoinf.2024.102773)
+
+
 ## About this manual
 
 This manual is a step-by-step user guide to the `traits.build` standard, R package and workflow manual. Alongside this manual, you may find the following resources useful: