V 0.0.148 Cran recomentations #147, #148 and #149

Author: vijaybarve

DESCRIPTION

@@ -1,16 +1,17 @@
 Package: taxotools
 Type: Package
 Title: Taxonomic List Processing
-Version: 0.0.147
-Date: 2025-05-19
+Version: 0.0.148
+Date: 2025-05-23
 Authors@R: c(
     person("Vijay", "Barve", ,"vijay.barve@gmail.com", role = c("aut", "cre"), 
       comment = c(ORCID = "0000-0002-4852-2567")))
 Maintainer: Vijay Barve <vijay.barve@gmail.com>
 Description: Taxonomic lists matching and merging, casting and melting 
   scientific names, managing taxonomic lists from  Global Biodiversity 
-  Information Facility 'GBIF' or Integrated Taxonomic Information System 'ITIS',
-  harvesting names from Wikipedia and fuzzy matching.
+  Information Facility 'GBIF' <https://www.gbif.org/> or Integrated Taxonomic 
+  Information System 'ITIS', <https://itis.gov/> harvesting names from 
+  Wikipedia and fuzzy matching.
 License: CC0
 Imports: taxize, wikitaxa, plyr, sqldf, stringr, stringdist, rmarkdown, stringi
 Encoding: UTF-8

NEWS

@@ -1,4 +1,4 @@
-taxotools 0.0.147
+taxotools 0.0.148
 =================
 * Bug fixes in melt_canonical, melt_scientificname, syn2taxo, get_synonym, resolve_names
 * Function syn2taxo now carries order and family if present in original data

R/get_accepted_names.R

@@ -168,11 +168,11 @@ get_accepted_names <- function(namelist, master, gen_syn=NA, namelookup=NA,
     if("source" %in% names(master) ){
       master <- master[which(master$source %in% mastersource),]
       if(nrow(master)==0){
-        cat("\nProblem matching mastersource")
+        warning("\nProblem matching mastersource")
         return(NULL)
       }
     } else {
-      cat("\nmaster data frame needs to have source column to use mastersource option")
+      warning("\nmaster data frame needs to have source column to use mastersource option")
       return(NULL)
     }
   }

R/list_wiki_syn.R

@@ -14,10 +14,10 @@
 #' @importFrom wikitaxa wt_wikipedia
 #' @importFrom taxize gbif_parse
 #' @examples
-#' \dontrun{
-#'  #list_wiki_syn("Abrothrix illutea")
-#'  #list_wiki_syn(c("Abditomys latidens", "Abeomelomys sevia",
-#'  #                "Abrocoma schistacea"))
+#' \donttest{
+#'  list_wiki_syn("Abrothrix illutea")
+#'  list_wiki_syn(c("Abditomys latidens", "Abeomelomys sevia",
+#'                  "Abrocoma schistacea"))
 #' }
 #'
 #' @export

R/melt_scientificname.R

@@ -89,7 +89,7 @@ melt_scientificname <- function(dat,sciname="",genus="genus",
             words <- words[-1]
             next
           } else {
-            cat(paste("\n Name: ",newdat$sciname[i]," is not well formated"))
+            if(verbose){cat(paste("\n Name: ",newdat$sciname[i]," is not well formated"))}
             words <- words[-1]
             next
           }
@@ -151,7 +151,7 @@ melt_scientificname <- function(dat,sciname="",genus="genus",
     }
     setTxtProgressBar(pb,i)
   }
-  cat("\n")
+  if(verbose){cat("\n")}
   newdat <- rename_column(newdat,"genus_",genus)
   newdat <- rename_column(newdat,"species_",species)
   if(subspecies!=""){

R/syn2taxo.R

@@ -4,6 +4,7 @@
 #' @param synlist Synonym list with Accepted name (canonical) and Synonym columns
 #' @param canonical Accepted names column name, Default: 'canonical'
 #' @param synonym Synonym column name , Default: 'synonym'
+#' @param verbose verbose output on the console
 #' @return returns a data frame in taxolist format with all the names in 
 #'  canonical column and accepted names linked to synonyms using id and accid
 #'  fields. Order, family and (guessed) taxonlevel are added if missing. Genus,
@@ -33,7 +34,8 @@
 #' @export
 syn2taxo <- function(synlist,
                      canonical="canonical",
-                     synonym="synonym"){
+                     synonym="synonym",
+                     verbose=FALSE){
   synlist <- rename_column(synlist,canonical,"Name_")
   synlist <- rename_column(synlist,synonym,"Syn_")
   # Accepeted Names
@@ -83,7 +85,7 @@ syn2taxo <- function(synlist,
     }
     setTxtProgressBar(pb,i)
   }
-  cat("\n")
+  if(verbose){cat("\n")}
   taxo <- melt_canonical(taxo,"canonical","genus","species","subspecies")
   taxo$Id <- as.numeric(taxo$Id)
   taxo$AccId <- as.numeric(taxo$AccId)

R/synonymize_subspecies.R

@@ -78,10 +78,10 @@ synonymize_subspecies <- function(master,
   master <- master[which(master$id %!in% remrec$id),]
   if(return_unmatched){
     if(nrow(remrec)==0){
-      cat("\nNO Orphan subspecies\n")
+      if(verbose){cat("\nNO Orphan subspecies\n")}
       return(NULL)
     } else {
-      cat("\nReturning",nrow(remrec),"Orphan subspecies\n")
+      if(verbose){cat("\nReturning",nrow(remrec),"Orphan subspecies\n")}
       return(remrec)
     }
   } else {