fungi taxonomy working - tested on vida LCs

R/get_name_keys.R

@@ -20,7 +20,7 @@
 #' to get native ranges. To see a wider range of plausible matches adjust 'tax_status' and 'match' to 'any'.
 
 # add option to determine which sources you want to search e.g. WCVP for plants, or IF for fungi
-get_name_keys <- function(df, name_column, tax_status = "accepted", match = "single", kingdom = "plantae") {
+get_name_keys <- function(df, name_column, tax_status = "any", match = "single", kingdom = "plantae") {
   # search terms
   search_names <- as.vector(unlist(df[, name_column]))
 

R/make_sis_csvs.R

@@ -15,7 +15,9 @@
 
 make_sis_csvs <-
   function(unique_id, wcvp_ipni_id, first_name, second_name, email,
-           institution, gbif_ref, native_ranges, kingdom = "plantae", powo_ref = FALSE) {
+           institution, gbif_ref = NULL, native_ranges,
+           family, genus, species, taxonomicAuthority,
+           kingdom = "plantae", powo_ref = FALSE) {
 
     if (kingdom == "plantae") {
 
@@ -26,9 +28,9 @@ make_sis_csvs <-
       plantspecific <- sis_plantspecific(unique_id, kingdom)
       habitats <- sis_habitats(unique_id)
       credits <- sis_credits(unique_id, first_name, second_name, email, affiliation = institution)
+      taxonomy <- sis_taxonomy(unique_id, family, genus, species, taxonomicAuthority)
 
       # need to embed map into the function, but these are a bit awkward - try again later
-      taxonomy <- purrr::map2(unique_id, wcvp_ipni_id, sis_taxonomy) %>%  dplyr::bind_rows()
       references <- purrr::map_dfr(unique_id, sis_references, powo_ref = powo_ref, gbif_ref)
 
       return(
@@ -48,14 +50,14 @@ make_sis_csvs <-
       plantspecific <- sis_plantspecific(unique_id, kingdom)
       habitats <- sis_habitats(unique_id)
       credits <- sis_credits(unique_id, first_name, second_name, email, affiliation = institution)
+      taxonomy <- sis_taxonomy(unique_id, family,genus, species, taxonomicAuthority)
 
       # need to embed map into the function, but these are a bit awkward - try again later
-      #taxonomy <- purrr::map2(unique_id, wcvp_ipni_id, sis_taxonomy) %>%  dplyr::bind_rows()
       references <- purrr::map_dfr(unique_id, sis_references, gbif_ref, powo_ref)
 
       return(
         list(allfields = allfields, assessments = assessments, plantspecific = plantspecific,
-             habitats = habitats, credits = credits, references = references
+             habitats = habitats, credits = credits, taxonomy = taxonomy, references = references
         )
       )
   }

R/name_search_gbif.R

@@ -25,8 +25,7 @@ name_search_gbif = function(name, species_rank = TRUE, match = "single", gbif_ta
   default_tbl = gbif_name_tbl_(name)
 
   # search using verbose to get fuzzy alternatives
-  matches = rgbif::name_backbone_verbose(name = name,
-                                         strict = FALSE)
+  matches = rgbif::name_backbone_verbose(name = name, strict = FALSE, rank = 'species')
 
   # bind together in case there are missing data
   matches = dplyr::bind_rows(matches$alternatives, matches$data)
@@ -47,26 +46,50 @@ name_search_gbif = function(name, species_rank = TRUE, match = "single", gbif_ta
 
     results$searchName = name # adding the search name back in to results table
 
-    results = dplyr::select(results, colnames(default_tbl))
-    results = dplyr::arrange(results, dplyr::desc(confidence))
-  }
+    # check if family column exists (not for some fungi)
+    if ("family" %in% colnames(results)) {
+      # family column exists
+      results = dplyr::select(results, colnames(default_tbl))
+      results = dplyr::arrange(results, dplyr::desc(confidence))
+    }
+       else
+      # family column does not exist (for some fungi)
+    {
+      default_tbl = default_tbl %>% dplyr::select(-family)
+      results = dplyr::select(results, colnames(default_tbl))
+      results$family <- "incertae sedis"
+      results = dplyr::arrange(results, dplyr::desc(confidence))
+      }
 
   # option to filter on GBIF accepted species only
   if (gbif_tax_stat == "any"){
     results = results
   } else {
     if (gbif_tax_stat == "accepted") {
-      results = dplyr::filter(results, status == "ACCEPTED")}
+      results = dplyr::filter(results, status == "ACCEPTED")
+      }
   }
 
   # option to filter on maximum confidence from GBIF search - one option only "single"
   # or allow list of options "any"
   if (match == "single") {
     results = dplyr::slice_max(results, confidence, n = 1, with_ties = FALSE)
   } else {
-    if (match == "any")
+    if (match == "any") {
       results = results
   }
+}
+
+    #Check if the 'scientificName' column contains NA values
+     if (!is.na(results$scientificName)) {
+      gen_sp_auth <- rgbif::name_parse(results$scientificName) %>%
+        dplyr::select(genusorabove, specificepithet, authorship) %>%
+        dplyr::rename(genus = genusorabove,
+                      species = specificepithet,
+                      taxonomicAuthority = authorship)
+      #results <- results %>% dplyr::select(-genus, -species, -taxonomicAuthority)
+      results <- dplyr::bind_cols(results, gen_sp_auth)
+      }
 
   return(results)
 
@@ -85,6 +108,10 @@ gbif_name_tbl_ = function(query) {
     status =  NA_character_,
     rank = NA_character_,
     confidence = NA_integer_,
-    #family = NA_character_
+    family = NA_character_
+    #genus = NA_character_,
+    #species = NA_character_,
+    #taxonomicAuthority = NA_character_
   )
 }
+}

R/sis_references.R

@@ -9,7 +9,7 @@
 #' @export
 #'
 
-sis_references = function(unique_id, gbif_ref, powo_ref) {
+sis_references = function(unique_id, gbif_ref = NULL, powo_ref = NULL) {
 
   LCr_ref <-
   tibble::tibble(

R/sis_taxonomy.R

@@ -6,27 +6,21 @@
 #' @return Returns an SIS compliant csv file
 #' @export
 
-sis_taxonomy = function(unique_id, wcvp_ipni_id){
-
-  name_info <- powo_lookup(wcvp_ipni_id)
+sis_taxonomy = function(unique_id, family, genus, species, taxonomicAuthority){
 
   tax = tibble::tibble(
     internal_taxon_id = unique_id,
-    family = name_info$family,
-    genus = name_info$genus,
-    species = name_info$species,
-    taxonomicAuthority = name_info$authors)
+    family = family,
+    genus = genus,
+    species = species,
+    taxonomicAuthority = taxonomicAuthority
+    )
 
   tax = dplyr::inner_join(tax, iucn_taxonomy, by="family")
-  tax = tax[c(1, 7:10, 2:5)]
 
   tax$infratype = ""
   tax$infra_name = ""
   tax$infra_authority = ""
 
-  tax <- tax %>%
-    dplyr::rename("kingdom" = "kingdomName") %>%
-    dplyr::rename("phylum" = "phylumName")
-
   return(tax)
 }

data-raw/fungi_workflow.R

@@ -13,22 +13,51 @@ institution = "Royal Botanic Gardens, Kew"
 # species list
 lc_species <-
   data.frame(sp = c(
-    "Russula amethystina",
-    "Lactarius decipiens",
-    "Poa annua"
+    "Asplenium longissimum  Blume",
+    "Asplenium macrophyllum  Sw.",
+    "Asplenium nidus  L.",
+    "Boerhavia repens L. ",
+    "Canavalia cathartica  Thouars",
+    "Cassytha filiformis L.",
+    "Dactyloctenium ctenoides  (Steud.) Bosser",
+    "Euphorbia stoddartii  Fosberg",
+    "Ipomoea violacea L.",
+    "test test",
+    "Lagrezia micrantha (Bak.)Schinz."
+    #"lntsia bijuga  Colebr.) Kuntze",
+#     "Lepturus repens G.Forst.) R.Br.",
+#     "Triumfetta procumbens Forst.",
+# #"lpomoea pes-caprae  (L.) R.Br.",
+# #"Pisonia grandis R.Br.",
+# "Pteris tripartita  Sw.",
+# "Scaevola taccada  (Gaertn.) Roxb.",
+# "Sida pusilla Cav.",
+# "Stenotaphrum micranthum (Desv.) C.E. Hubb.",
+# #"Thelypteris opulentum  (Kaulf.) J.P.Roux",
+# "Triumfetta procumbens Forst."
   ))
 print(lc_species)
 
+# gbif_names_out <- purrr::map_dfr(chagos_names$name_in,
+#                                  name_search_gbif,
+#                                  match = match,
+#                                  gbif_tax_stat = "any")
+
 # get the keys
 lc_keys <-
   get_name_keys(
-    lc_species,
-    name_column = "sp",
-    tax_status = "accepted",
+    #lc_species,
+    Confident.LC.fungi.1.3.24_VS,
+    #name_column = "sp",
+    name_column = "acceptedNameAuthor",
+    tax_status = "any",
     match = "single",
-    kingdom = "fungi" # note this needs to change to remove the WCVP name check
+    kingdom = "fungi" # setting to fungi removes the WCVP check
   )
 
+# filter out the not accepted if you like
+lc_keys <- lc_keys %>% dplyr::filter(GBIF_status == "ACCEPTED")
+
 # make the LC points csv file
 lc_points <- make_LC_points(lc_keys, range_check = FALSE)
 
@@ -42,7 +71,11 @@ sis_occs <- make_sis_csvs(unique_id = lc_keys$GBIF_usageKey,
                               second_name = "Bachman",
                               email = "[email protected]",
                               institution = "Royal Botanic Gardens, Kew",
-                              gbif_ref = lc_points$citation,
+                              family = lc_keys$GBIF_family,
+                              genus = lc_keys$GBIF_genus,
+                              species = lc_keys$GBIF_species,
+                              taxonomicAuthority = lc_keys$GBIF_taxonomicAuthority,
+                              #gbif_ref = lc_points$citation,
                               #native_ranges = lc_points$native_ranges, # remove this for fungi
                               kingdom = "fungi" # set to fungi
 )