Add BibType as a column in methods table (#193)

As described [here](#192), the `BibType ` associated with a dataset is used by the R package `RefManageR` to process the references, but is not displayed anywhere within the traits.build database. A column recording the BibType of the
primary citation is now included within the reference table. 
This change has not effected any dataset metadata.yml files, but is
simply capturing and outputting data that was already documented in
them.

Note that `austraits` functions still work and the function
`extract_data` lets you filter data based on `BibType`.

R/process.R

@@ -1633,6 +1633,7 @@ process_format_methods <- function(metadata, dataset_id, sources, contributors)
     )
 
   source_primary_key <- metadata$source$primary$key
+  source_primary_type <- metadata$source$primary$bibtype
   source_secondary_keys <- citation_types %>%
     dplyr::filter(.data$type == "secondary") %>%
     purrr::pluck("source_id")
@@ -1676,6 +1677,7 @@ process_format_methods <- function(metadata, dataset_id, sources, contributors)
         tibble::tibble(
           dataset_id = dataset_id,
           source_primary_key = source_primary_key,
+          source_primary_type = source_primary_type,
           source_primary_citation = bib_print(sources[[source_primary_key]]),
           source_secondary_key = ifelse(
             length(source_secondary_keys) > 0,

inst/support/traits.build_schema.yml

@@ -115,6 +115,7 @@ austraits:
         description: &description A 1-2 sentence description of the purpose of the study.
         sampling_strategy: &sampling_strategy A written description of how study locations were selected and how study individuals were selected. When available, this information is lifted verbatim from a published manuscript. For preserved specimens, this field ideally indicates which records were 'sampled' to measure a specific trait.
         source_primary_key: Citation key for the primary source in `sources`. The key is typically formatted as `Surname_year`.
+        source_primary_type: Citation type for the primary source in `sources`, using standard BibTex citation types (Article, Book, Misc, Online, Report, Techreport, Thesis, Unpublished).
         source_primary_citation: Citation for the primary source. This detail is generated from the primary source in the metadata.
         source_secondary_key: Citation key for the secondary source in `sources`.  The key is typically formatted as `Surname_year`.
         source_secondary_citation: Citations for the secondary source. This detail is generated from the secondary source in the metadata.

tests/testthat/examples/Test_2023_5/output/methods.csv

@@ -1,3 +1,3 @@
-dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators
-Test_2023_5,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
-Test_2023_5,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
+dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators
+Test_2023_5,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,Unpublished,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
+Test_2023_5,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,Unpublished,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright

tests/testthat/examples/Test_2023_6/output/methods.csv

@@ -1,3 +1,3 @@
-dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators
-Test_2023_6,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
-Test_2023_6,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
+dataset_id,trait_name,methods,method_id,description,sampling_strategy,source_primary_key,source_primary_type,source_primary_citation,source_secondary_key,source_secondary_citation,source_original_dataset_key,source_original_dataset_citation,data_collectors,assistants,dataset_curators
+Test_2023_6,leaf_mass_per_area,unknown,01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,Unpublished,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright
+Test_2023_6,leaf_lifespan,"From Richards_2008_2 (unpublished); See original references, listed alphabetically under 'additional references'",01,Collection of trait data on Australian plants compiled by Anna Richards and Ian Wright from papers,See the individual 'additional references' for the individual study motivations.,Richards_2008,Unpublished,"A. Richards and I. J. Wright. ""Unpublished data: Transcription of Australian plant functional trait data from Ian Wright's collection of papers, Macquarie University"". 2009.",Leuning_1991; Meakins_0000,"R. Leuning, R. N. Cromer, and S. Rance. ""Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis"".   _Oecologia_ 88.4 (1991), pp. 504-510.  doi:  [10.1007/bf00317712](https://doi.org/10.1007%2Fbf00317712); Meakins. ""Unpublished data: Study of Brindabella species"".",Bell_1985; Bevege_1978; Lambert_1979,"Bell. ""Nutrient requirements for the establishment of native flora at Weipa"". In: _Conference proceedings of N Australian mine rehab workshop 9_. 1985; D. I. Bevege. _Biomass and nutrient distribution in indigenous forest ecosystems_. Tech. rep. Queensland Department of Forestry, 1978, p. 20; M. J. Lambert. ""Sulphur relationships of native and exotic tree species"". Masters. Macquarie University, Sydney, 1979.",Anna Richards (contact),,Ian Wright