🦀

Author: cboettig

R/common_names.R

@@ -15,7 +15,7 @@
 #' common_to_sci(c("Bicolor cleaner wrasse", "humphead parrotfish"), Language="English")
 #' common_to_sci(c("Coho Salmon", "trout"))
 #' }
-#' @seealso \code{\link{species_list}}, \code{\link{synonyms}}
+#' @seealso \code{\link{synonyms}}
 #' @export
 #' @importFrom dplyr filter select distinct collect
 #' @importFrom stringr str_to_lower

R/distribution.R

@@ -20,8 +20,6 @@ Ecosystemname <- NA
 #' \dontrun{
 #' country("Bolbometopon muricatum")
 #' }
-#' @details 
-#' e.g. http://www.fishbase.us/Country
 country <- endpoint("country", join = country_names())
 
 #' countrysub
@@ -61,11 +59,7 @@ countrysubref <- function(server = getOption("FISHBASE_API", "fishbase"),
 #' @param c_code a C_Code or list of C_Codes (FishBase country code)
 #' @export
 #' @examplesIf interactive() 
-#' \dontrun{
 #' c_code(440)
-#' }
-#' @details 
-#' e.g. http://www.fishbase.us/Country
 c_code <- function(c_code = NULL, 
                    server = getOption("FISHBASE_API", "fishbase"), 
                    version = get_latest_release(),
@@ -101,10 +95,7 @@ country_names <- function(server = getOption("FISHBASE_API", "fishbase"),
 #' @export
 #' @return a tibble, empty tibble if no results found
 #' @examplesIf interactive() 
-#' \dontrun{
 #'   faoareas()
-#' }
-#' e.g. http://www.fishbase.us/Country/FaoAreaList.php?ID=5537
 faoareas <- function(species_list = NULL, fields = NULL, 
                      server = getOption("FISHBASE_API", "fishbase"), 
                      version = "latest",

R/fb_tbl.R

@@ -1,5 +1,17 @@
 #' Access a fishbase or sealifebase table
 #' 
+#' 
+#' Please note that rfishbase accesses static snapshots of the raw database
+#' tables used by FishBase and Sealifebase websites. Because these are static
+#' snapshots, they may lag behind the latest available information on the web
+#' interface, but should provide stable results.  
+#' 
+#' Please also note that the website pages are not organized precisely along
+#' the lines of these tables.  A given page for a species may draw on data from
+#' multiple tables, and sometimes presents the data in a processed or summarized
+#' form.  Following RDB design, it is often
+#' necessary to join multiple tables.  Other data cleaning steps are sometimes
+#' necessary as well.  
 #' @param tbl table name, as it appears in the database. See [fb_tables()]
 #' for a list.
 #' @param server Access data from fishbase or sealifebase?
@@ -25,6 +37,13 @@ fb_tbl <- function(tbl,
   out  
 }
 
+#' List the tables available on fishbase/sealifebase
+#' 
+#' These table names can be used to access each of the corresponding tables
+#' using `[fb_tbl()]`.  Please note that following RDB design, it is often
+#' necessary to join multiple tables.  Other data cleaning steps are sometimes
+#' necessary as well.  
+#' @inheritParams fb_tbl
 #' @export
 #' @examplesIf interactive()
 #' fb_tables()

R/load_taxa.R

@@ -26,7 +26,11 @@ load_taxa <- memoise::memoise(load_taxa_)
 
 
 
-
+dummy_fn <- function(f) {
+  # CRAN check doesn't recognize memoise use in the above and throws note:
+  # Namespace in Imports field not imported from: ‘memoise’
+  memoise::memoise(f)
+}
 
 
 

R/species.R

@@ -6,6 +6,7 @@
 #' @param version a version string for the database. See [available_releases()] for details.
 #' @param fields subset to these columns.  (recommend to omit this and handle manually)
 #' @param db database connection, now deprecated.
+#' @param ... additional arguments, currently ignored
 #' @return a data.frame with rows for species and columns for the fields returned by the query (FishBase 'species' table)
 #' @details 
 #' The Species table is the heart of FishBase. This function provides a convenient way to 

R/synonyms.R

@@ -50,8 +50,10 @@ synonyms <- function(species_list = NULL,
 
   df <- data.frame(synonym = species_list, stringsAsFactors = FALSE)
   codes <- fb_species(server, version)
-  left_join(df, syn, by="synonym") %>%
-    left_join(codes, by = "SpecCode")
+  dplyr::left_join(df, syn, by="synonym", 
+            relationship = "many-to-many" 
+            ) %>%
+    dplyr::left_join(codes, by = "SpecCode")
 }