Fixed species_family to return latest db version

DESCRIPTION

@@ -1,35 +1,49 @@
-Package: rFishTaxa
 Type: Package
+Package: rFishTaxa
 Title: R Interface to 'Eschmeyer's Catalog of Fishes'
 Version: 0.1.0
 Date: 2022-09-08
-Authors@R: c(person(given = "Liuyong",     family = "Ding",   email = "[email protected]",              role = c("aut", "cre"), comment = c(ORCID="0000-0002-5490-182X")),
-             person(given = "Zhixin",      family = "Zhang",  email = "[email protected]", role = "ctb")
-             )
+Authors@R: 
+    c(person(given = "Liuyong",
+             family = "Ding",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-5490-182X")),
+      person(given = "Zhixin",
+             family = "Zhang",
+             role = "ctb",
+             email = "[email protected]"))
 Maintainer: Liuyong Ding <[email protected]>
-Description: `Eschmeyer's Catalog of Fishes` <https://www.calacademy.org/scientists/projects/catalog-of-fishes> is the authoritative reference for taxonomic fish names, featuring a searchable online database. This package helps users to query valid taxonomic fish information for biodiversity estimates, conservation issues, etc.
-Depends: R (>= 4.0.0)
+Description: `Eschmeyer's Catalog of Fishes`
+    <https://www.calacademy.org/scientists/projects/catalog-of-fishes> is
+    the authoritative reference for taxonomic fish names, featuring a
+    searchable online database. This package helps users to query valid
+    taxonomic fish information for biodiversity estimates, conservation
+    issues, etc.
+License: Artistic-2.0
+URL: https://otoliths.github.io/rFishTaxa/
+BugReports: https://github.com/Otoliths/rFishTaxa/issues
+Depends: 
+    R (>= 4.0.0)
 Imports: 
-  httr,
-  tibble,
-  magrittr,
-  xml2,
-  dplyr,
-  stringr,
-  rvest,
-  janitor
+    dplyr,
+    httr,
+    janitor,
+    magrittr,
+    rvest,
+    stringr,
+    tibble,
+    tidyr,
+    xml2
 Suggests:
-    utils,
-    testthat,
-    rmarkdown,
+    devtools,
     knitr,
     prettydoc,
-    devtools
+    rmarkdown,
+    testthat,
+    utils
 VignetteBuilder:
-    knitr, 
+    knitr,
     rmarkdown
-License: Artistic-2.0
-URL: https://otoliths.github.io/rFishTaxa/
-BugReports: https://github.com/Otoliths/rFishTaxa/issues
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -18,6 +18,7 @@ importFrom(stringr,str_sub)
 importFrom(stringr,str_trim)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
+importFrom(tidyr,fill)
 importFrom(utils,browseURL)
 importFrom(xml2,read_html)
 importFrom(xml2,xml_find_all)

R/species_family.R

@@ -26,6 +26,8 @@
 #' @importFrom utils browseURL
 #' @importFrom janitor clean_names
 #' @importFrom dplyr filter
+#' @importFrom dplyr mutate
+#' @importFrom tidyr fill
 #' @details See for website \url{https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp} details.
 #' @references \url{https://github.com/curso-r/lives/blob/6e042cf5f0bae0d957ff487a39b6601ac6f514ea/drafts/20210915_webscraping_ichthyology.R}
 #' @examples
@@ -61,8 +63,28 @@ species_family <- function(){
       rvest::html_table() %>%
       janitor::clean_names() %>%
       dplyr::filter(class != "Totals")
-    r <- readRDS(paste0(system.file("extdata",package = "rFishTaxa"),"/","db_2022_09.rds"))
-    return(tibble::as_tibble(r))
+    result %>%
+      dplyr::mutate(order = ifelse(endsWith(order, "formes") | endsWith(order, "*"),
+                                   order,
+                                   NA),
+                    class = ifelse(is.na(available_genera) & is.na(order),
+                                   class,
+                                   NA),
+                    # "Percalates-clade" among families as of 6 February 2024
+                    family = ifelse(endsWith(family, "idae") | endsWith(family, '-clade"'),
+                                    family,
+                                    NA),
+                    subfamily = ifelse(!is.na(available_genera) & is.na(family),
+                                       subfamily,
+                                       NA)
+                    # subfamily = ifelse(endsWith(subfamily, "inae") | endsWith(subfamily, " sedis"),
+                    #                    subfamily,
+                    #                    NA)
+                    ) %>%
+      tidyr::fill("class", "order", "family") %>%
+      dplyr::filter(!is.na(available_genera))
+    # r <- readRDS(paste0(system.file("extdata",package = "rFishTaxa"),"/","db_2022_09.rds"))
+    # return(tibble::as_tibble(r))
   }else{
     cat("Error request - the parameter query is not valid")
     browseURL(url)