Major upgrades to {austraits} (#131)

As discussed in issue #92, the goal of this upgrade was to:

  1. Discontinue support for AusTraits version < 4.2.0
    - Mass removal of switch functions that controlled function behaviour depending on AusTraits version (Issue #102, issue #91)
    - Creation of check_compatibility() (Issue #100)
    - Console messaging alerting user which version of AusTraits is supported by which functions (Issue #100)
    - Updated documentation guiding user on how to install an older version of the R package for backwards compatibility (Issue #93)

  2. Introduce new traits.build 'wrangling output' functions into austraits
    -  flatten_database added to austraits (Issue #105)
    -  bind_databases added to austraits (Issue #106)

  3. Reduce redundancy across traits.build and austraits to streamline codebase maintenance
    -  plot_trait_beeswarm moved back to austraits
    -  trait_pivot_ moved back to austraits

  4. Refactor {austraits} functions to support other traits.build databases and allow functionality across more tables and columns.
    -  join_ functions (Issue #91)
    -  extract_ functions (Issue #107)
    -  Rename argument names (Issue #115)

  5. Update documentation accordingly    -  Pointing to APD and traits.build-book directly in README and vignette 

Update documentation in {austraits} for changes in version 3.0.0 #96
Update documentation with reference to manual #74
Added cheatsheet
________________________
co-authored by @ehwenk and @dfalster

.Rbuildignore

@@ -11,3 +11,4 @@
 ^ignore$
 ^austraits$
 ^codecov\.yml$
+

.github/workflows/test-coverage.yml

@@ -3,7 +3,6 @@ on:
     branches:
       - master
       - develop
-      - upgrade
   pull_request:
     branches:
       - master

.gitignore

@@ -53,3 +53,5 @@ data/austraits/
 #
 *.pdf
 *.svg
+inst/cheatsheet/austraits-cheatsheet.pptx
+inst/cheatsheet/austraits-cheatsheet.pptx

DESCRIPTION

@@ -1,12 +1,17 @@
 Package: austraits
-Title: Helpful functions to access, summarise and wrangle austraits data
-Version: 2.2.3
+Title: Helpful functions to access the AusTraits database and wrangle data from other traits.build databases
+Version: 3.0.0
 Authors@R:
     c(person(given = "Daniel",
              family = "Falster",
              role = "aut",
              email = "[email protected]",
              comment = c(ORCID = "0000-0002-9814-092X")),
+      person(given = "Elizabeth", 
+            family = "Wenk", 
+            role = "ctb",
+            email = "[email protected]", 
+            comment = c(ORCID = "0000-0001-5640-5910")),
       person(given = "Fonti",
              family = "Kar",
              role = c("aut", "cre"),
@@ -16,13 +21,13 @@ Authors@R:
              family = "Indiarto",
              role = c("aut"),
              comment = c(ORCID = "0000-0001-9546-8201")))
-Description: austraits is a package for accessing, summarising and wrangling austraits data. The package allows users to explore the scope and type of data available, as well as subset and wrangle relevant specific data for furture research. This package is still under development. See README and vignette('austraits') for further information.
+Description: `austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.0.0),
     RefManageR
@@ -32,19 +37,21 @@ Imports:
     rlang,
     purrr,
     tidyselect,
-    assertthat,
     stringr,
     stats,
     jsonlite,
     utils,
     magrittr,
     janitor,
-    lifecycle
+    lifecycle,
+    tibble,
+    cli
 Suggests: 
     ggplot2,
     ggpointdensity,
     ggbeeswarm (>= 0.7.1),
     gridExtra,
+    readr,
     scales,
     forcats,
     viridis,

NAMESPACE

@@ -1,41 +1,42 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,austraits)
+S3method(print,traits.build)
 export("%>%")
 export(as_wide_table)
+export(bind_databases)
 export(bind_trait_values)
+export(convert_df_to_list)
+export(convert_list_to_df1)
+export(convert_list_to_df2)
+export(extract_data)
 export(extract_dataset)
 export(extract_taxa)
 export(extract_trait)
+export(flatten_database)
 export(get_version_latest)
 export(get_versions)
-export(join_all)
-export(join_contexts)
-export(join_locations)
+export(join_context_properties)
+export(join_contributors)
+export(join_location_coordinates)
+export(join_location_properties)
 export(join_methods)
-export(join_sites)
-export(join_taxonomy)
+export(join_taxa)
+export(join_taxonomic_updates)
 export(load_austraits)
+export(lookup_context_property)
+export(lookup_location_property)
 export(lookup_trait)
 export(plot_locations)
 export(plot_site_locations)
 export(plot_trait_distribution_beeswarm)
 export(separate_trait_values)
-export(summarise_austraits)
-export(summarise_trait_means)
+export(summarise_database)
 export(trait_pivot_longer)
 export(trait_pivot_wider)
 import(RefManageR)
-importFrom(dplyr,arrange)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,select)
-importFrom(dplyr,summarise)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)
 importFrom(stats,family)
-importFrom(stringr,str_detect)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
-importFrom(tidyselect,all_of)
 importFrom(utils,methods)

NEWS.md

@@ -1,2 +1,17 @@
-# austraits 2.2.1
+# austraits 3.0.0
 - Updated dependencies, placing graphics related packages in Suggests
+- Added internal function to check the compatibility of databases
+- Added internal function notify users that some database versions will not be supported
+- The following functions will no longer support AusTraits version < 5.0.0:
+    - `extract_*` 
+    - `trait_pivot_wider`
+    - `join_*`
+    - `plot_site/locations`
+    - `plot_trait_beeswarm`
+    - `as_wide_table`
+- `trait_pivot_longer` is deprecated
+- `summarise_trait_means` will trigger warning due to uninformed calculations
+- Added new function `extract_data`
+- Added new function `bind_databases`
+- Added new function `flatten_databases`
+- Updated print function `print.traits.build`