R/TPL.R

In plantlist: Looking Up the Status of Plant Scientific Names based on The Plant List Database

TPL <- function (plant.names = NULL) {    
    options(stringsAsFactors = FALSE)
    if (is.null(plant.names)) {
        stop("At least one plant species or genus should be provided.")
    }
    get.genus <- function(x) {
        Cap <- function(x) {
            paste(toupper(substring(x, 1, 1)), tolower(substring(x, 
                2)), sep = "")
        }
        if (is.data.frame(x)) {
            x <- as.vector(x)
        }
        x <- gsub("^[[:space:]]+|[[:space:]]+$", "", x)
        x <- Cap(x)
        first <- substr(x, 1, 1)
        start.point <- 2
        if (min(regexpr(" ", x)) > 1) {
            end.point <- regexpr(" ", x)
            second <- substr(x, start.point, end.point - 1)
        }
        else {
            x <- paste(x, " ")
            end.point <- regexpr(" ", x)
            second <- substr(x, start.point, end.point - 1)
        }
        return(paste(first, second, sep = ""))
    }
    
    genera_dat <- plantlist::genera_dat
    orders_dat <- plantlist::orders_dat
    
    genus <- get.genus(plant.names)
    genus <- data.frame(YOUR_SPECIES = plant.names, YOUR_GENUS = genus)
    
    res1 <- merge(x = genus, y = genera_dat, by.x = "YOUR_GENUS", 
        by.y = "GENUS", sort = FALSE, all.x = TRUE)

    res <- merge(x = res1, y = orders_dat, by = "FAMILY",  
        sort = FALSE, all.x = TRUE)
    
    return(data.frame(YOUR_SEARCH = res$YOUR_SPECIES, POSSIBLE_GENUS = res$YOUR_GENUS, 
        FAMILY = res$FAMILY, FAMILY_NUMBER = res$FAMILY_NUMBER, ORDER = res$ORDER,  
        GROUP = res$GROUP))
}