Extract from single table only (#121)

*    extract_ functions can now work with a single table or an entire traits.build database; the single table can have any columns, any number of columns
*    required a tweak to check_compatibility to allow single tables to be declared compatible. A extra parameter was added that indicates if the incoming data is allowed to be a single table
*   lots of documentation that was supposed to be on the previous commit

Closes issue #120

R/bind_databases.R

@@ -4,7 +4,7 @@
 #' database object as a large list.
 #'
 #' @param ... Arguments passed to other functions
-#' @param databases List of traits.build databases to bind together
+#' @param database_1 List of traits.build databases to bind together
 #'
 #' @return Compiled database as a single large list
 #' @importFrom rlang .data

R/check_compatibility.R

@@ -2,6 +2,7 @@
 #' @description Function to check whether the data object has been compiled by the traits.build workflow and 
 #' therefore has a data structure that is appropriate for use with austraits functions.
 #' @param database traits.build database (list object)
+#' @param single_table_allowed logical for when the input might be a single table instead of a complete database; defaults to FALSE
 #'
 #' @return logical (T/F) output and messaging for uncompatible versions
 #'
@@ -11,28 +12,36 @@
 #' }
 #' @author Elizabeth Wenk - [email protected]
 
-check_compatibility <- function(database) {
+check_compatibility <- function(database, single_table_allowed = FALSE) {
 
-  if (is.null(database$metadata)) {
+  if (!is.null(dim(database)) & single_table_allowed == TRUE) {
 
-    compatible <- FALSE
-
-    # message("You are working with AusTraits version 3.0 or earlier. \nThis database structure is unsupported by the current version of this package. \nPlease see https://github.com/traitecoevo/austraits for details on installing old versions of the package.")
+    compatible <- TRUE
 
   } else {
 
-    compiled_by_traits.build <-
-      database$metadata$related_identifiers %>% 
-      convert_list_to_df2() %>%
-      dplyr::filter(relation_type == "isCompiledBy") %>% 
-      dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
-
-    if(is.null(compiled_by_traits.build) | nrow(compiled_by_traits.build) > 0) {
-      compatible <- TRUE
-    } else{
+    if (is.null(database$metadata)) {
+
       compatible <- FALSE
 
-      # message("You are working with AusTraits version 4, which is unsupported by the current version of this package. \nPlease see https://github.com/traitecoevo/austraits for details on installing old versions of the package.")
+      # message("You are working with AusTraits version 3.0 or earlier. \nThis database structure is unsupported by the current version of this package. \nPlease see https://github.com/traitecoevo/austraits for details on installing old versions of the package.")
+
+    } else {
+
+      compiled_by_traits.build <-
+        database$metadata$related_identifiers %>% 
+        convert_list_to_df2() %>%
+        dplyr::filter(relation_type == "isCompiledBy") %>% 
+        dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
+
+      if(is.null(compiled_by_traits.build) | nrow(compiled_by_traits.build) > 0) {
+        compatible <- TRUE
+      } else{
+        compatible <- FALSE
+
+        # message("You are working with AusTraits version 4, which is unsupported by the current version of this package. \nPlease see https://github.com/traitecoevo/austraits for details on installing old versions of the package.")
+      }
+
     }
 
   }