herbParse_v2<-
## DPUT output, 14sept08 11:48pm
function (oracleIn, dbaseIn, edIn = NULL, usdaIn = NULL, file.names = F) 
{
    require(cba)
    if (file.names) {
        oracle <- read.csv(oracleIn, header = T)
        dbase = vector("list", length(dbaseIn))
        for (i in seq(length(dbaseIn))) dbase[[i]] <- read.csv(dbaseIn, 
            header = T)
        names(dbase) <- names(dbaseIn)
        ed <- read.csv(edIn, header = T)
        if (!identical(usdaIn, NULL)) 
            usda <- read.csv(usdaIn, header = T)
    }
    else {
        if (class(dbaseIn) != "list") 
            stop("dbaseIn must be a list of dbase tables, preferably named")
        oracle <- oracleIn
        dbase <- dbaseIn
        ed <- edIn
        usda <- usdaIn
    }
    for (i in seq(length(dbaseIn))) dbase[[i]]$SN_CONCAT_FULL <- paste(toupper(dbase[[i]]$GENUS), 
        toupper(dbase[[i]]$HYBRID), toupper(dbase[[i]]$SPECIES), 
        toupper(dbase[[i]]$AUTHOR1), toupper(dbase[[i]]$IFS), 
        toupper(dbase[[i]]$TRINOM), toupper(dbase[[i]]$AUTHOR2), 
        sep = " ")
    dbaseWorking <- dbase[[1]][, c("DIVISION", "CLASS", "FAMILY", 
        "GENUS", "HYBRID", "SPECIES", "AUTHOR1", "IFS", "TRINOM", 
        "AUTHOR2", "SN_CONCAT_FULL")]
    if (length(dbase) > 1) {
        for (i in 2:length(dbase)) dbaseWorking <- rbind(dbaseWorking, 
            dbase[[i]][, c("DIVISION", "CLASS", "FAMILY", "GENUS", 
                "HYBRID", "SPECIES", "AUTHOR1", "IFS", "TRINOM", 
                "AUTHOR2", "SN_CONCAT_FULL")])
    }
    oracle <- as.data.frame(apply(oracle, c(1, 2), function(x) gsub("(null)", 
        "", x, fixed = T)), stringsAsFactors = F)
    names(usda) <- toupper(names(usda))
    names(ed) <- toupper(names(ed))
    G <- length(dbaseWorking$GENUS)
    dbaseWorking$SN_CONCAT <- paste(toupper(dbaseWorking$GENUS), 
        toupper(dbaseWorking$HYBRID), toupper(dbaseWorking$SPECIES), 
        toupper(dbaseWorking$TRINOM), sep = " ")
    dbaseWorking$SN_CONCAT_NOWHITE <- gsub(" ", "", dbaseWorking$SN_CONCAT)
    dbaseWorking$SN_CONCAT_FULL_NOWHITE <- gsub(" ", "", dbaseWorking$SN_CONCAT_FULL)
    dbaseWorking$SN_CONCAT_FULL_NOWHITE <- gsub("'", "", dbaseWorking$SN_CONCAT_FULL)
    oracleHybGENUS <- unlist(lapply(oracle$GEN_HYB_CD, function(x) {
        if (as.character(x) == "HY") 
            "x"
        else ""
    }))
    oracleHybSPECIES <- unlist(lapply(oracle$SPEC_HYB_CD, function(x) {
        if (as.character(x) == "HY") 
            "x"
        else ""
    }))
    oracleSSP <- unlist(lapply(oracle$SSP, function(x) {
        if (nchar(as.character(x)) > 0) 
            "ssp."
        else ""
    }))
    oracleVAR <- unlist(lapply(oracle$VAR, function(x) {
        if (nchar(as.character(x)) > 0) 
            "var."
        else ""
    }))
    oracleCULTIVAR <- unlist(lapply(oracle$CULTIVAR, function(x) {
        if (nchar(as.character(x)) > 0) 
            "cv."
        else ""
    }))
    oracleFMA <- unlist(lapply(oracle$FMA, function(x) {
        if (nchar(as.character(x)) > 0) 
            "f."
        else ""
    }))
    oracle$SN_CONCAT <- paste(toupper(oracleHybGENUS), toupper(oracle$GENUS), 
        toupper(oracleHybSPECIES), toupper(oracle$SPECIES), toupper(oracle$SSP), 
        toupper(oracle$VAR), toupper(oracle$FMA), toupper(oracleCULTIVAR), 
        toupper(oracle$CULTIVAR), sep = " ")
    oracle$SN_CONCAT_NOWHITE <- gsub(" ", "", oracle$SN_CONCAT)
    oracle$SN_CONCAT_FULL <- paste(toupper(oracleHybGENUS), toupper(oracle$GENUS), 
        toupper(oracleHybSPECIES), toupper(oracle$SPECIES), toupper(oracle$AUTHOR), 
        toupper(oracleSSP), toupper(oracle$SSP), toupper(oracle$SSP_AUTHOR), 
        toupper(oracleVAR), toupper(oracle$VAR), toupper(oracle$VAR_AUTHOR), 
        toupper(oracleFMA), toupper(oracle$FMA), toupper(oracle$FMA_AUTHOR), 
        toupper(oracleCULTIVAR), toupper(oracle$CULTIVAR), sep = " ")
    oracle$SN_CONCAT_FULL_NOWHITE <- gsub(" ", "", oracle$SN_CONCAT_FULL)
    usdaHybGENUS <- unlist(lapply(usda$XGENUS, function(x) {
        if (nchar(as.character(x)) > 0) 
            "x"
        else ""
    }))
    usdaHybSPECIES <- unlist(lapply(usda$XSPECIES, function(x) {
        if (nchar(as.character(x)) > 0) 
            "x"
        else ""
    }))
    usdaFORMA <- unlist(lapply(usda$FORMA, function(x) {
        if (nchar(as.character(x)) > 0) 
            "f."
        else ""
    }))
    usdaVarAUTH <- as.character(usda$QUADRANOMIAL.AUTHOR)
    usdaSspAUTH <- character(length(usda$GENUS))
    usdaFormaAUTH <- character(length(usda$GENUS))
    for (i in 1:length(usda$GENUS)) {
        if (usdaVarAUTH[i] != "") 
            usdaSspAUTH[i] <- as.character(usda$TRINOMIAL.AUTHOR[i])
        else {
            if (as.character(usda$SUBSPECIES[i]) != "") 
                usdaSspAUTH[i] <- as.character(usda$TRINOMIAL.AUTHOR[i])
            if (as.character(usda$VARIETY[i]) != "") 
                usdaVarAUTH[i] <- as.character(usda$TRINOMIAL.AUTHOR[i])
            if (as.character(usda$FORMA[i]) != "") 
                usdaFormaAUTH[i] <- as.character(usda$TRINOMIAL.AUTHOR[i])
        }
    }
    usda$SN_CONCAT <- paste(toupper(usda$GENUS), toupper(usdaHybSPECIES), 
        toupper(usda$SPECIES), toupper(usda$SUBSPECIES), toupper(usda$VARIETY), 
        toupper(usda$FORMA), sep = " ")
    usda$SN_CONCAT_NOWHITE <- gsub(" ", "", usda$SN_CONCAT)
    usda$SN_CONCAT_FULL <- paste(toupper(usdaHybGENUS), toupper(usda$GENUS), 
        toupper(usdaHybSPECIES), toupper(usda$SPECIES), toupper(usda$BINOMIAL.AUTHOR), 
        toupper(usda$SSP), toupper(usda$SUBSPECIES), toupper(usdaSspAUTH), 
        toupper(usda$VAR), toupper(usda$VARIETY), toupper(usdaVarAUTH), 
        toupper(usdaFORMA), toupper(usda$FORMA), toupper(usdaFormaAUTH), 
        sep = " ")
    edHybGENUS <- unlist(lapply(ed$GEN_DSG, function(x) {
        if (nchar(as.character(x)) > 0) 
            "x"
        else ""
    }))
    edHybSPECIES <- unlist(lapply(ed$SP_DSG, function(x) {
        if (nchar(as.character(x)) > 0) 
            "x"
        else ""
    }))
    edAUTHOR <- as.character(ed$AUTHOR)
    for (i in 1:length(edAUTHOR)) {
        if (nchar(as.character(ed$BASONYM[i])) > 0) 
            edAUTHOR[i] <- paste("(", ed$BASONYM[i], ") ", edAUTHOR[i], 
                sep = "")
    }
    ed$SN_CONCAT <- paste(toupper(ed$GENUS_NAME), toupper(edHybSPECIES), 
        toupper(ed$SP_NAME), toupper(ed$SSP_NAME), toupper(ed$CV_NAME), 
        sep = " ")
    ed$SN_CONCAT_NOWHITE <- gsub(" ", "", ed$SN_CONCAT)
    ed$SN_CONCAT_FULL <- paste(toupper(edHybGENUS), toupper(ed$GENUS_NAME), 
        toupper(edHybSPECIES), toupper(ed$SP_NAME), toupper(ed$SSP_DSG), 
        toupper(ed$SSP_NAME), toupper(ed$CV_NAME), toupper(edAUTHOR), 
        sep = " ")
    ed$SN_CONCAT_FULL_NOWHITE <- gsub(" ", "", ed$SN_CONCAT_FULL)
    concatSort <- sort(unique(dbaseWorking$SN_CONCAT_FULL))
    N = length(concatSort)
    message("Making matchlist")
    matchList <- match(concatSort, dbaseWorking$SN_CONCAT_FULL)
    message("Matchlist made")
    # save(matchList, file='matchList.Rdata')
    dbaseTaxa <- data.frame(CONCAT_FULL = concatSort, CONCAT_FULL_NOWHITE = dbaseWorking$SN_CONCAT_FULL_NOWHITE[matchList], 
        CONCAT = dbaseWorking$SN_CONCAT[matchList], CONCAT_NOWHITE = dbaseWorking$SN_CONCAT_NOWHITE[matchList], 
        summaryVerdict = character(N), GENUS = dbaseWorking$GENUS[matchList], 
        SPECIES = dbaseWorking$SPECIES[matchList], AUTHOR1 = dbaseWorking$AUTHOR1[matchList], 
        TRINOM = dbaseWorking$TRINOM[matchList], AUTHOR2 = dbaseWorking$AUTHOR2[matchList], 
        generationDate = rep(date(), N))
    dbaseTaxa$SN_CHECKED_DATE <- character(N)
    dbaseTaxa$SN_CHECKED_USER <- character(N)
    dbaseTaxa$WORK_NEEDED <- character(N)
    dbaseTaxa$BEST_ORACLE_MATCH <- character(N)
    dbaseTaxa$BEST_ED_MATCH <- character(N)
    dbaseTaxa$BEST_USDA_MATCH <- character(N)
    dbaseTaxa <- dbaseTaxa[-(nchar(gsub(" ","",(as.character(dbaseTaxa$CONCAT_FULL)))) == 0), ] # gets rid of blank rows
    N <- length(dbaseTaxa$CONCAT_FULL) # needed so that loops run the right length of time
    # save(dbaseTaxa,file='dbaseTaxaMidstream.Rdata')
    
    oracleGenera <- sort(toupper(unique(gsub(" ", "", oracle$GENUS))))
    oracleEpithets <- sort(toupper(unique(c(gsub(" ", "", oracle$SPECIES), 
        gsub(" ", "", oracle$SSP), gsub(" ", "", oracle$VAR), 
        gsub(" ", "", oracle$FMA), gsub(" ", "", oracle$CULTIVAR)))))
    oracleAuthors <- sort(toupper(unique(c(gsub(" ", "", oracle$AUTHOR), 
        gsub(" ", "", oracle$SSP_AUTHOR), gsub(" ", "", oracle$VAR_AUTHOR), 
        gsub(" ", "", oracle$FMA_AUTHOR)))))
    
    for (i in seq(N)) {
        oracleMatch = match(dbaseTaxa$CONCAT_FULL_NOWHITE[i], 
            oracle$SN_CONCAT_FULL_NOWHITE)
        if (!is.na(oracleMatch)) {
            dbaseTaxa$BEST_ORACLE_MATCH[i] <- oracle$SN_CONCAT_FULL[oracleMatch[1]]
            dbaseTaxa$WORK_NEEDED[i] <- "Oracle match"
        }
        else {
            oracleClose <- agrep(dbaseTaxa$CONCAT_NOWHITE[i], 
                oracle$SN_CONCAT_NOWHITE, value = F, max.distance = 0.05)
            if (length(oracleClose) == 0) {
                dbaseTaxa$BEST_ORACLE_MATCH[i] <- "0"
            }
            else {
                oracleClosest <- oracleClose[sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                  oracle$SN_CONCAT_FULL[oracleClose], weight = c(1, 
                    1, 1)) == min(sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                  oracle$SN_CONCAT_FULL[oracleClose], weight = c(1, 
                    1, 1)))][1]
                dbaseTaxa$BEST_ORACLE_MATCH[i] <- oracle$SN_CONCAT_FULL[oracleClosest]
                dbaseTaxa$WORK_NEEDED[i] <- "Oracle close"
            }
            if (!identical(usda, NULL)) {
                usdaClose <- agrep(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                  usda$SN_CONCAT_NOWHITE, value = F, max.distance = 0.05)
                if (length(usdaClose) == 0) {
                  dbaseTaxa$BEST_USDA_MATCH[i] <- "0"
                }
                else {
                  usdaClosest <- usdaClose[sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                    usda$SN_CONCAT_FULL[usdaClose], weight = c(1, 
                      1, 1)) == min(sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                    usda$SN_CONCAT_FULL[usdaClose], weight = c(1, 
                      1, 1)))][1]
                  dbaseTaxa$BEST_USDA_MATCH[i] <- usda$SN_CONCAT_FULL[usdaClosest]
                }
            }
            if (!identical(ed, NULL)) {
                edClose <- agrep(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                  ed$SN_CONCAT_NOWHITE, value = F, max.distance = 0.05)
                if (length(edClose) == 0) {
                  dbaseTaxa$BEST_ED_MATCH[i] <- "0"
                }
                else {
                  edClosest <- edClose[sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                    ed$SN_CONCAT_FULL[edClose], weight = c(1, 
                      1, 1)) == min(sdists(as.character(dbaseTaxa$CONCAT_NOWHITE[i]), 
                    ed$SN_CONCAT_FULL[edClose], weight = c(1, 
                      1, 1)))][1]
                  dbaseTaxa$BEST_ED_MATCH[i] <- ed$SN_CONCAT_FULL[edClosest]
                }
            }
        }
        message(paste("Matched name", i, "of", N))
        if(i == 1) write.csv(dbaseTaxa[1,], file = "dbaseCheck.csv", append = F, row.names = F) 
        else write.table(dbaseTaxa[i,], file = "dbaseRunning.csv", append = T, col.names = F, row.names = F, sep = ",")
    }
    for (i in seq(length(dbase))) write.csv(dbase[i], paste("dbaseFile", 
        i, ".", Sys.Date(), ".csv", sep = ""))
    write.csv(dbaseTaxa, paste("dbaseTaxaAnalyzed.", Sys.Date(), 
        ".csv", sep = ""))
    write.csv(usda, paste("usda.", Sys.Date(), ".csv", sep = ""))
    write.csv(ed, paste("ed.", Sys.Date(), ".csv", sep = ""))
    write.csv(oracle, paste("oracle.", Sys.Date(), ".csv", sep = ""))
    return(list(dbaseTaxa = dbaseTaxa, dbase = dbase, oracle = oracle, 
        ed = ed, usda = usda))
}