R/TPLck2.R

In frmunoz/TreeGhats: Taxonomic name resolution and phylogeny generator for Western Ghats trees

TPLck2<-function (sp, corr = TRUE, diffchar = 2, max.distance = 1, infra = TRUE, 
            abbrev = TRUE, version = "1.1", encoding = "UTF-8") 
  {
    sp <- as.character(sp)
    abbr <- NA
    Homonym<- NA
    if (abbrev == TRUE) {
      vec0 <- c("nothossp. ", "nothossp.", " nothossp ", "nothosubsp. ", 
                "nothosubsp.", " nothosubsp ", "cultivar. ", "cultivar.", 
                " cultivar ", "subfo. ", " subfo ", "subf. ", "subf.", 
                " subf ", " subproles ", "cf. ", "cf.", " cf ", "aff. ", 
                "aff.", " aff ", "s.l. ", "s.l.", "s.l ", "s.str. ", 
                "s.str.", "s.str ", "?", "x. ", "x.", " x ", "X. ", 
                "X.", " X ", "f. ", "f.", " f ", "fo. ", "fo.", " fo ", 
                " forma ", "subvar.", " subvar ", "var. ", "var.", 
                " var ", "subsp. ", "subsp.", " subsp ", "ssp. ", 
                "ssp.", " ssp ", " gama ", " grex ", "lus. ", "lus.", 
                " lus ", " lusus ", "monstr. ", " monstr ", "nm. ", 
                "nm.", " nm ", "prol. ", "prol.", " prol ", " proles ", 
                " race ", "subvar. ", "cv. ", "cv.", " cv ")
      for (j in 1:length(vec0)) {
        abbr <- ifelse(length(grep(vec0[j], sp, fixed = TRUE)) > 
                         0, vec0[j], abbr)
        sp <- sub(vec0[j], " ", sp, fixed = TRUE)
      }
      abbr <- gsub(" ", "", abbr, fixed = TRUE)
      sp <- gsub("      ", " ", sp, fixed = TRUE)
      sp <- gsub("     ", " ", sp, fixed = TRUE)
      sp <- gsub("    ", " ", sp, fixed = TRUE)
      sp <- gsub("   ", " ", sp, fixed = TRUE)
      sp <- gsub("  ", " ", sp, fixed = TRUE)
      sp <- gsub("_", "", sp, fixed = TRUE)
      sp <- ifelse(substr(sp, 1, 1) == " ", substr(sp, 2, nchar(sp)), 
                   sp)
    }
    Abbrev <- abbr
    genus <- unlist(strsplit(sp, " "))[1]
    species <- unlist(strsplit(sp, " "))[2]
    if (corr == TRUE) {
      species <- tolower(species)
    }
    infrasp <- ifelse(length(unlist(strsplit(sp, " "))) > 2, 
                      unlist(strsplit(sp, " "))[3], "")
    if (corr == TRUE) {
      infrasp <- tolower(infrasp)
    }
    vv <- ifelse(version == "1.0", "", version)
    searchstring <- paste("http://www.theplantlist.org/tpl", 
                          vv, "/search?q=", genus, "+", species, "&csv=true", sep = "")
    table.sp <- NULL
    try(table.sp <- read.csv(searchstring, header = TRUE, sep = ",", 
                             fill = TRUE, colClasses = "character", as.is = TRUE, 
                             encoding = encoding), silent = TRUE)
    Genus <- genus
    Species <- species
    Infraspecific <- infrasp
    New.Hybrid.marker <- ""
    marker <- FALSE
    marker.infra <- FALSE
    if (is.null(table.sp)) {
      Family <- ""
      Taxonomic.status <- ""
      Plant.Name.Index <- FALSE
      New.Genus <- Genus
      New.Species <- Species
      New.Infraspecific <- Infraspecific
      Authority <- ""
      Typo <- FALSE
      WFormat <- TRUE
      ID <- ""
      New.ID <- ""
    }
    else if (!is.null(table.sp)) {
      k <- dim(table.sp)[2]
      z <- dim(table.sp)[1]
      if (k == 1) {
        Family <- ""
        Plant.Name.Index <- FALSE
        Taxonomic.status <- ""
        New.Genus <- Genus
        New.Species <- Species
        New.Infraspecific <- Infraspecific
        Authority <- ""
        Typo <- FALSE
        WFormat <- FALSE
        ID <- ""
        New.ID <- ""
      }
      else if (k > 1) {
        if (z == 0) {
          Family <- ""
          Plant.Name.Index <- FALSE
          Taxonomic.status <- ""
          New.Genus <- Genus
          New.Species <- Species
          New.Infraspecific <- Infraspecific
          Authority <- ""
          Typo <- FALSE
          WFormat <- FALSE
          ID <- ""
          New.ID <- ""
        }
        else if (z > 1) {
          if (length(unique(paste(table.sp$Genus, table.sp$Species))) > 
              1 && corr == TRUE) {
            spx <- length(agrep(species, "sp", max.distance = 0)) + 
              length(agrep(species, "sp.", max.distance = 0))
            mf <- c(as.character(1:1000))
            is.mf <- agrep(species, mf, max.distance = list(deletions = 1), 
                           value = TRUE)
            cck <- agrep(species, table.sp$Species, value = TRUE, 
                         max.distance = max.distance)
            ddf <- abs(nchar(cck) - nchar(species))
            if (length(cck) > 0) {
              cck <- cck[ddf == min(ddf)]
              ddf <- abs(nchar(cck) - nchar(species))
            }
            levs <- length(unique(cck))
            if (length(is.mf) == 0 && length(cck) > 0 && 
                ddf <= diffchar && levs == 1 && spx == 0) {
              searchstring <- paste("http://www.theplantlist.org/tpl", 
                                    vv, "/search?q=", genus, "+", cck[1], "&csv=true", 
                                    sep = "")
              try(table.sp <- read.table(searchstring, 
                                         header = TRUE, sep = ",", fill = TRUE, 
                                         colClasses = "character", as.is = TRUE, 
                                         encoding = encoding), silent = T)
              k <- dim(table.sp)[2]
              z <- dim(table.sp)[1]
              marker <- TRUE
            }
          }
          if (length(unique(paste(table.sp$Genus, table.sp$Species))) > 
              1) {
            Family <- ""
            Plant.Name.Index <- FALSE
            Taxonomic.status <- ""
            New.Genus <- Genus
            New.Species <- Species
            New.Infraspecific <- Infraspecific
            Authority <- ""
            Typo <- FALSE
            WFormat <- FALSE
            ID <- ""
            New.ID <- ""
          }
          if (length(unique(paste(table.sp$Genus, table.sp$Species))) == 
              1) {
            grep1 <- grep(infrasp, table.sp$Infraspecific.epithet, 
                          value = TRUE)
            ngrep <- nchar(grep1)
            if ((length(ngrep) == 0 || abs(ngrep - nchar(infrasp)) > 
                 0) && corr == TRUE && !is.na(infrasp) && 
                nchar(infrasp) > 0) {
              cck.infra <- agrep(infrasp, table.sp$Infraspecific.epithet, 
                                 value = TRUE, max.distance = max.distance)
              ddf.infra <- abs(nchar(cck.infra) - nchar(infrasp))
              if (length(cck.infra) > 0) {
                cck.infra <- cck.infra[ddf.infra == min(ddf.infra)]
                ddf.infra <- abs(nchar(cck.infra) - nchar(infrasp))
              }
              levs <- length(unique(cck.infra))
              if (length(cck.infra) > 0 && levs == 1) {
                infrasp <- unique(cck.infra)
                grep1 <- grep(infrasp, table.sp$Infraspecific.epithet, 
                              value = TRUE)
                ngrep <- nchar(grep1)
                marker.infra <- TRUE
              }
            }
            if (infra == TRUE && length(grep(infrasp, table.sp$Infraspecific.epithet)) > 
                0 && abs(ngrep - (nchar(infrasp))) == 0) {
              table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                     infrasp, ]
              if (dim(table.sp)[1] > 1 && sum(!is.na(grep(Abbrev, 
                                                          table.sp$Infraspecific.rank, ignore.case = TRUE))) > 
                  0) {
                table.sp <- table.sp[table.sp$Infraspecific.rank == 
                                       Abbrev, ]
              }
            }
            else if (infra == FALSE || length(grep(infrasp, 
                                                   table.sp$Infraspecific.epithet)) == 0 || 
                     abs(ngrep - (nchar(infrasp))) > 0) {
              if ((table.sp$Infraspecific.epithet == "" || 
                   is.na(table.sp$Infraspecific.epithet)) == 
                  FALSE && length(grep(Species, table.sp$Infraspecific.epithet)) == 
                  0) {
                table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                       "" || is.na(table.sp$Infraspecific.epithet), 
                                     ]
                table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
              }
              else if ((table.sp$Infraspecific.epithet == 
                        "" || is.na(table.sp$Infraspecific.epithet)) == 
                       FALSE && length(grep(Species, table.sp$Infraspecific.epithet)) > 
                       0) {
                table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                       Species, ]
                table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
              }
            }
            k <- dim(table.sp)[2]
            z <- dim(table.sp)[1]
            if (z == 0) {
              Family <- ""
              Plant.Name.Index <- FALSE
              Taxonomic.status <- ""
              New.Genus <- Genus
              New.Species <- Species
              New.Infraspecific <- Infraspecific
              Authority <- ""
              Typo <- ifelse(marker == TRUE || marker.infra == 
                               TRUE, TRUE, FALSE)
              WFormat <- FALSE
              ID <- ""
              New.ID <- ""
            }
            else if (any(table.sp$Taxonomic.status.in.TPL == 
                         "Accepted")) {
              table.sp <- table.sp[table.sp$Taxonomic.status.in.TPL == 
                                     "Accepted", ]
              Plant.Name.Index <- TRUE
              Taxonomic.status <- table.sp$Taxonomic.status.in.TPL[1]
              Family <- table.sp$Family[1]
              New.Genus <- table.sp$Genus[1]
              New.Hybrid.marker <- table.sp$Species.hybrid.marker[1]
              New.Species <- table.sp$Species[1]
              if (infra == T && length(grep(infrasp, table.sp$Infraspecific.epithet)) > 
                  0) {
                New.Infraspecific <- table.sp$Infraspecific.epithet[1]
              }
              else if (infra == F || length(grep(infrasp, 
                                                 table.sp$Infraspecific.epithet)) == 0) {
                New.Infraspecific <- ""
              }
              Authority <- table.sp$Authorship[1]
              Typo <- ifelse(marker == TRUE || marker.infra == 
                               TRUE, TRUE, FALSE)
              WFormat <- FALSE
              ID <- table.sp[1, 1]
              New.ID <- ID
            }
            else if (sum(table.sp$Taxonomic.status.in.TPL == 
                         "Accepted") == 0 && (sum(table.sp$Taxonomic.status.in.TPL == 
                                                  "Synonym") > 0 || sum(table.sp$Taxonomic.status.in.TPL == 
                                                                        "Misapplied") > 0)) {
              if (sum(table.sp$Taxonomic.status.in.TPL == 
                      "Synonym") > 0) {
                table.sp <- table.sp[table.sp$Taxonomic.status.in.TPL == 
                                       "Synonym", ]
              }
              else if (sum(table.sp$Taxonomic.status.in.TPL == 
                           "Misapplied") > 0) {
                table.sp <- table.sp[table.sp$Taxonomic.status.in.TPL == 
                                       "Misapplied", ]
              }
              if (sum(table.sp$Confidence.level == "H") > 
                  0) {
                table.sp <- table.sp[table.sp$Confidence.level == 
                                       "H", ]
              }
              else if (sum(table.sp$Confidence.level == 
                           "M") > 0) {
                table.sp <- table.sp[table.sp$Confidence.level == 
                                       "M", ]
              }
              if (nrow(table.sp) > 1) {
                Homonym=nrow(table.sp)
                warning(paste(sp, "has more than one valid synonym"))
              }
              table.sp.id <- table.sp[1, 1]
              ID <- table.sp.id
              at <- readLines(paste("http://www.theplantlist.org/tpl", 
                                    vv, "/record/", table.sp.id, sep = ""), 
                              encoding = encoding)
              if (sum(table.sp$Taxonomic.status.in.TPL == 
                      "Synonym") > 0) {
                if (version == "1.1") {
                  az <- "<p>This name is a <a href=\"/1.1/about/#synonym\">synonym</a> of"
                }
                else if (version == "1.0") {
                  az <- "<p>This name is a <a href=\"/about/#synonym\">synonym</a> of"
                }
              }
              else if (sum(table.sp$Taxonomic.status.in.TPL == 
                           "Misapplied") > 0) {
                if (version == "1.1") {
                  az <- "<p>In the past this name has been <a href=\"/1.1/about/#misapplied\">erroneously used</a> to refer to"
                }
                else if (version == "1.0") {
                  az <- "<p>In the past this name has been <a href=\"/about/#misapplied\">erroneously used</a> to refer to"
                }
              }
              n <- pmatch(az, at)
              nsen <- at[n]
              nsen <- unlist(strsplit(unlist(strsplit(nsen, 
                                                      split = ">")), "<"))
              if (version == "1.1") {
                searchstring <- paste("http://www.theplantlist.org/tpl", 
                                      vv, "/search?q=", nsen[13], "+", ifelse(nsen[17] == 
                                                                                "?", nsen[21], nsen[17]), "&csv=true", 
                                      sep = "")
              }
              else if (version == "1.0") {
                searchstring <- paste("http://www.theplantlist.org/tpl", 
                                      vv, "/search?q=", nsen[11], "+", ifelse(nsen[15] == 
                                                                                "?", nsen[19], nsen[15]), "&csv=true", 
                                      sep = "")
              }
              kup <- length(grep("var.", nsen)) + length(grep("subsp.", 
                                                              nsen))
              if (infra == T && kup > 0) {
                if (version == "1.1") {
                  infrasp <- ifelse(nsen[17] == "?", nsen[29], 
                                    nsen[25])
                }
                else if (version == "1.0") {
                  infrasp <- ifelse(nsen[15] == "?", nsen[27], 
                                    nsen[23])
                }
              }
              else if (kup == 0) {
                infrasp <- ""
              }
              if (sum(table.sp$Taxonomic.status.in.TPL == 
                      "Synonym") > 0) {
                Taxonomic.status <- "Synonym"
              }
              else if (sum(table.sp$Taxonomic.status.in.TPL == 
                           "Misapplied") > 0) {
                Taxonomic.status <- "Misapplied"
              }
              try(table.sp <- read.table(searchstring, 
                                         header = TRUE, sep = ",", fill = TRUE, 
                                         colClasses = "character", as.is = TRUE, 
                                         encoding = encoding), silent = TRUE)
              if(min(dim(table.sp))>0) {
                if (version == "1.1" && nsen[17] == "?") {
                  table.sp <- table.sp[table.sp$Species.hybrid.marker == 
                                       "?", ]
                }
               else if (version == "1.0" && nsen[15] == 
                        "?") {
                 table.sp <- table.sp[table.sp$Species.hybrid.marker == 
                                       "?", ]
                }
                grep1 <- grep(infrasp, table.sp$Infraspecific.epithet, 
                            value = TRUE)
                ngrep <- nchar(grep1)
                if (infra == TRUE && length(grep(infrasp, 
                                                 table.sp$Infraspecific.epithet)) > 0 && 
                    abs(ngrep - (nchar(infrasp))) == 0) {
                  table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                         infrasp, ]
                  table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
                }
                else if (infra == FALSE || length(grep(infrasp, 
                                                       table.sp$Infraspecific.epithet)) == 0 || 
                         abs(ngrep - (nchar(infrasp))) > 0) {
                  table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                         "" || is.na(table.sp$Infraspecific.epithet), 
                                       ]
                  table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
                }
                Plant.Name.Index <- TRUE
                Family <- table.sp$Family[1]
                New.Genus <- table.sp$Genus[1]
                New.Hybrid.marker <- table.sp$Species.hybrid.marker[1]
                New.Species <- table.sp$Species[1]
                New.Infraspecific <- table.sp$Infraspecific.epithet[1]
                Authority <- table.sp$Authorship[1]
                Typo <- ifelse(marker == TRUE || marker.infra == 
                                 TRUE, TRUE, FALSE)
                WFormat <- FALSE
                New.ID <- table.sp[1, 1]
              } else {
                Plant.Name.Index <- F
                Family <- NA
                New.Genus <- NA
                New.Hybrid.marker <- NA
                New.Species <- NA
                New.Infraspecific <- NA
                Authority <- NA
                Typo <- NA
                WFormat <- NA
                New.ID <- NA
              }
            }
            else if (sum(table.sp$Taxonomic.status.in.TPL == 
                         "Accepted") == 0 && sum(table.sp$Taxonomic.status.in.TPL == 
                                                 "Synonym") == 0 && sum(table.sp$Taxonomic.status.in.TPL == 
                                                                        "Unresolved") > 0) {
              Plant.Name.Index <- TRUE
              Taxonomic.status <- "Unresolved"
              Family <- table.sp$Family[1]
              New.Genus <- table.sp$Genus[1]
              New.Hybrid.marker <- table.sp$Species.hybrid.marker[1]
              New.Species <- table.sp$Species[1]
              New.Infraspecific <- table.sp$Infraspecific.epithet[1]
              Authority <- table.sp$Authorship[1]
              Typo <- ifelse(marker == TRUE || marker.infra == 
                               TRUE, TRUE, FALSE)
              WFormat <- FALSE
              ID <- table.sp[1, 1]
              New.ID <- ID
            }
          }
        }
        else if (z == 1) {
          if (is.na(table.sp$Taxonomic.status.in.TPL)) {
            Taxonomic.status <- ""
            Plant.Name.Index <- FALSE
            Family <- ""
            New.Genus <- Genus
            New.Species <- Species
            New.Infraspecific <- Infraspecific
            Authority <- ""
            Typo <- ifelse(marker == TRUE || marker.infra == 
                             TRUE, TRUE, FALSE)
            WFormat <- FALSE
            ID <- ""
            New.ID <- ""
          }
          else if (table.sp$Taxonomic.status.in.TPL == 
                   "Synonym" || table.sp$Taxonomic.status.in.TPL == 
                   "Misapplied") {
            ID <- table.sp[1, 1]
            at <- readLines(paste("http://www.theplantlist.org/tpl", 
                                  vv, "/search?q=", genus, "+", species, sep = ""), 
                            encoding = encoding)
            if (table.sp$Taxonomic.status.in.TPL == "Synonym") {
              if (version == "1.1") {
                az <- "<p>This name is a <a href=\"/1.1/about/#synonym\">synonym</a> of"
              }
              else if (version == "1.0") {
                az <- "<p>This name is a <a href=\"/about/#synonym\">synonym</a> of"
              }
            }
            else if (table.sp$Taxonomic.status.in.TPL == 
                     "Misapplied") {
              if (version == "1.1") {
                az <- "<p>In the past this name has been <a href=\"/1.1/about/#misapplied\">erroneously used</a> to refer to"
              }
              else if (version == "1.0") {
                az <- "<p>In the past this name has been <a href=\"/about/#misapplied\">erroneously used</a> to refer to"
              }
            }
            n <- pmatch(az, at)
            nsen <- at[n]
            nsen <- unlist(strsplit(unlist(strsplit(nsen, 
                                                    split = ">")), "<"))
            if (version == "1.1") {
              searchstring <- paste("http://www.theplantlist.org/tpl", 
                                    vv, "/search?q=", nsen[13], "+", ifelse(nsen[17] == 
                                                                              "?", nsen[21], nsen[17]), "&csv=true", 
                                    sep = "")
            }
            else if (version == "1.0") {
              searchstring <- paste("http://www.theplantlist.org/tpl", 
                                    vv, "/search?q=", nsen[11], "+", ifelse(nsen[15] == 
                                                                              "?", nsen[19], nsen[15]), "&csv=true", 
                                    sep = "")
            }
            kup <- length(grep("var.", nsen)) + length(grep("subsp.", 
                                                            nsen))
            if (infra == T && kup > 0) {
              if (version == "1.1") {
                infrasp <- ifelse(nsen[17] == "?", nsen[29], 
                                  nsen[25])
              }
              else if (version == "1.0") {
                infrasp <- ifelse(nsen[15] == "?", nsen[27], 
                                  nsen[23])
              }
            }
            else if (kup == 0) {
              infrasp <- ""
            }
            if (table.sp$Taxonomic.status.in.TPL == "Synonym") {
              Taxonomic.status <- "Synonym"
            }
            else if (table.sp$Taxonomic.status.in.TPL == 
                     "Misapplied") {
              Taxonomic.status <- "Misapplied"
            }
            try(table.sp <- read.table(searchstring, header = TRUE, 
                                       sep = ",", fill = TRUE, colClasses = "character", 
                                       encoding = encoding), silent = TRUE)
            if(is.na(nsen))
              return(NA)
            if (version == "1.1" && nsen[17] == "?") {
              table.sp <- table.sp[table.sp$Species.hybrid.marker == 
                                     "?", ]
              New.Hybrid.marker <- "?"
            }
            else if (version == "1.0" && nsen[15] == "?") {
              table.sp <- table.sp[table.sp$Species.hybrid.marker == 
                                     "?", ]
              New.Hybrid.marker <- "?"
            }
            Plant.Name.Index <- TRUE
            Family <- table.sp$Family[1]
            if (version == "1.1") {
              New.Genus <- nsen[13]
              New.Species <- ifelse(nsen[17] == "?", nsen[21], 
                                    nsen[17])
              Authority <- ifelse(nsen[17] == "?", nsen[25], 
                                  nsen[21])
            }
            else if (version == "1.0") {
              New.Genus <- nsen[11]
              New.Species <- ifelse(nsen[15] == "?", nsen[19], 
                                    nsen[15])
              Authority <- ifelse(nsen[15] == "?", nsen[23], 
                                  nsen[19])
            }
            grep1 <- grep(infrasp, table.sp$Infraspecific.epithet, 
                          value = TRUE)
            ngrep <- nchar(grep1)
            if (length(ngrep) == 0 && corr == TRUE && !is.na(infrasp) && 
                nchar(infrasp) > 0) {
              cck.infra <- agrep(infrasp, table.sp$Infraspecific.epithet, 
                                 value = TRUE, max.distance = max.distance)
              ddf.infra <- abs(nchar(cck.infra) - nchar(infrasp))
              if (length(cck.infra) > 0) {
                cck.infra <- cck.infra[ddf.infra == min(ddf.infra)]
                ddf.infra <- abs(nchar(cck.infra) - nchar(infrasp))
              }
              levs <- length(unique(cck.infra))
              if (length(cck.infra) > 0 && ddf.infra <= 
                  diffchar && levs == 1) {
                infrasp <- cck.infra
                grep1 <- grep(infrasp, table.sp$Infraspecific.epithet, 
                              value = TRUE)
                ngrep <- nchar(grep1)
                marker.infra <- TRUE
              }
            }
            if (infra == TRUE && length(grep(infrasp, table.sp$Infraspecific.epithet)) > 
                0 && abs(ngrep - (nchar(infrasp))) == 0) {
              table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                     infrasp, ]
              table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
              if (dim(table.sp)[1] > 1 && sum(!is.na(grep(Abbrev, 
                                                          table.sp$Infraspecific.rank, ignore.case = TRUE))) > 
                  0) {
                table.sp <- table.sp[table.sp$Infraspecific.rank == 
                                       Abbrev, ]
              }
            }
            else if (infra == FALSE || length(grep(infrasp, 
                                                   table.sp$Infraspecific.epithet)) == 0 || 
                     abs(ngrep - (nchar(infrasp))) > 0) {
              table.sp <- table.sp[table.sp$Infraspecific.epithet == 
                                     "" || is.na(table.sp$Infraspecific.epithet), 
                                   ]
              table.sp$Taxonomic.status.in.TPL <- table.sp$Taxonomic.status.in.TPL
            }
            New.Infraspecific <- table.sp$Infraspecific.epithet[1]
            Typo <- ifelse(marker == TRUE || marker.infra == 
                             TRUE, TRUE, FALSE)
            WFormat <- FALSE
            New.ID <- table.sp[1, 1]
          }
          else if (table.sp$Taxonomic.status.in.TPL == 
                   "Accepted" || table.sp$Taxonomic.status.in.TPL == 
                   "Unresolved") {
            Plant.Name.Index <- TRUE
            Taxonomic.status <- table.sp$Taxonomic.status.in.TPL[1]
            Family <- table.sp$Family
            New.Genus <- table.sp$Genus
            New.Hybrid.marker <- table.sp$Species.hybrid.marker[1]
            New.Species <- table.sp$Species
            New.Infraspecific <- table.sp$Infraspecific.epithet
            Authority <- table.sp$Authorship
            Typo <- ifelse(marker == TRUE || marker.infra == 
                             TRUE, TRUE, FALSE)
            WFormat <- FALSE
            ID <- table.sp[1, 1]
            New.ID <- ID
          }
        }
      }
    }
    results <- data.frame(Genus, Species, Abbrev, Infraspecific, 
                          ID, Plant.Name.Index, TPL_version = version, Taxonomic.status, 
                          Family, New.Genus, New.Hybrid.marker, New.Species, New.Infraspecific, 
                          Authority, New.ID, Typo, WFormat, stringsAsFactors = FALSE,Homonym)
  }