Merge pull request #97 from stitam/dev

Update documentation

Author: stitam

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: taxizedb
 Type: Package
 Title: Offline Access to Taxonomic Databases
-Description: Download taxonomic databases such as CoL, GBIF, ITIS, NCBI, WFO, or 
-    Wikidata, convert them into SQLite format, and query them locally for fast, 
-    reliable, and reproducible access to taxonomic data.
+Description: Download taxonomic databases, convert them into 'SQLite' format, 
+    and query them locally for fast, reliable, and reproducible access to 
+    taxonomic data.
 Version: 0.3.2
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut"),

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(children)
 export(classification)
 export(db_download_col)

R/ap_children.R

@@ -89,6 +89,7 @@ gbif_children <- function(src, x, ...){
   stats::setNames(lapply(x, FUN, src = src), x)
 }
 
+#' @importFrom magrittr %>%
 ncbi_children <- function(src, x, ...){
 
   FUN <- function(src, x, ambiguous=FALSE, ...){

R/ap_classification.R

@@ -162,6 +162,7 @@ gbif_classification <- function(src, x, ...) {
   stats::setNames(lapply(x, FUN, src = src), x)
 }
 
+#' @importFrom magrittr %>%
 ncbi_classification <- function(src, x, ...){
 
   FUN <- function(src, x, ...){

R/ap_core.R

@@ -4,6 +4,7 @@
 # c("Arabidopsis", "Peridermium sp. 'Ysgr-4'") -> "'Arabidopsis',
 # 'Peridermium sp. ''Ysgr-4'''"
 # Note that double quoting is the SQL convention for escaping quotes in strings
+#' @importFrom magrittr %>%
 sql_character_list <- function(x){
   if(any(is.na(x))){
     stop("Cannot pass NA into SQL query")
@@ -73,6 +74,7 @@ run_with_db <- function(FUN, db, ...) {
   FUN(src, ...)
 }
 
+#' @importFrom magrittr %>%
 ncbi_apply <- function(src, x, FUN, missing=NA, die_if_ambiguous=TRUE, ...){
   # preserve original names (this is important when x is a name vector)
   namemap <- x

R/ap_downstream.R

@@ -255,6 +255,7 @@ gbif_downstream <- function(src, x, ...){
   stats::setNames(lapply(x, FUN, src = src, ...), x)
 }
 
+#' @importFrom magrittr %>%
 ncbi_downstream <- function(src, x, ...){
 
   FUN <- function(

R/caching.R

@@ -4,6 +4,8 @@
 #'
 #' @export
 #' @name tdb_cache
+#' 
+#' @return An object of classes `HoardClient` and `R6`.
 #'
 #' @details `cache_delete` only accepts 1 file name, while
 #' `cache_delete_all` doesn't accept any names, but deletes all files.

R/db_download.R

@@ -12,35 +12,36 @@
 #' sqlite database you can still use the rest of the TPL functions with it. We 
 #' suggest using the World Flora Online (WFO) database as a replacement.
 #' @seealso [tdb_cache]
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # ITIS
-#' # db_download_itis()
-#' # src_itis()
+#' db_download_itis()
+#' src_itis()
 #'
 #' # Plantlist
-#' # db_download_tpl()
-#' # src_tpl()
+#' db_download_tpl()
+#' src_tpl()
 #'
 #' # COL
-#' # db_download_col()
-#' # src_col()
+#' db_download_col()
+#' src_col()
 #'
 #' # GBIF
-#' # db_download_gbif()
-#' # src_gbif()
+#' db_download_gbif()
+#' src_gbif()
 #'
 #' # NCBI
-#' # db_download_ncbi()
-#' # src_ncbi()
+#' db_download_ncbi()
+#' src_ncbi()
 #'
 #' # Wikidata
-#' # db_download_wikidata()
-#' # db_download_wikidata(overwrite=TRUE) # overwrite - download again
-#' # src_wikidata()
+#' db_download_wikidata()
+#' db_download_wikidata(overwrite=TRUE) # overwrite - download again
+#' src_wikidata()
 #' 
 #' # World Flora Online
-#' # db_download_wfo()
-#' # src_wfo()
+#' db_download_wfo()
+#' src_wfo()
 #' }
 
 #' @export
@@ -127,7 +128,7 @@ db_download_ncbi <- function(verbose = TRUE, overwrite = FALSE) {
   hierarchs <- list()
   # set up the base table with columns 'tax_id', 'ancestor', and 'level', where
   # level is 1 for immediate parent
-  hierarchs[[1]] <- ncbi_nodes[, c('tax_id', 'parent_tax_id')] %>%
+  hierarchs[[1]] <- ncbi_nodes[, c('tax_id', 'parent_tax_id')] |>
     magrittr::set_names(c('tax_id', 'ancestor'))
   hierarchs[[1]]$level <- 1
   # make a child to parent map

R/db_load.R

@@ -5,6 +5,7 @@
 #'
 #' @export
 #' @param ... ignored
+#' @return An error message.
 #' @name db_load-defunct
 
 #' @export