Question

Here is my function:

# Purpose: Scrape Floraweb.de for plant species data (photograph, sociology, ecology, anatomy)
# Author: Kay Cichini
# Date: 2012-06-10
# Output: PDF saved to created folder .~/FLORAWEB
# Packages: XML, jpeg, 
# Licence: cc by-nc-sa

floraweb_scraper <- function(input) {

    # I didn't get around this encoding issue other than with gsub..
    spch_sub <- function(x) {
        x <- gsub("ü", "ü", x)
        x <- gsub("ä", "ä", x)
        x <- gsub("ö", "ö", x)
        x <- gsub("Ä", "Ä", x)
        x <- gsub("Ãoe", "Ü", x)
        x <- gsub("ü", "Ä", x)
        x <- gsub("Ö", "Ö", x)
        x <- gsub("ß", "ß", x)
        x <- gsub("é", "é", x)
        x <- gsub("Ã-", "í", x)
        x <- gsub("á", "á", x)
        x <- gsub("±", "~", x)
        x <- gsub(" ", "", x)  # pattern for backspaces
    }

    # automated package installation:
    pkgs <- c("XML", "jpeg")

    pkgs_miss <- pkgs[which(!pkgs %in% installed.packages()[, 1])]
    if (length(pkgs_miss) > 0) {
        install.packages(pkgs_miss)
    }

    # load packages:
    require(XML)
    require(jpeg)


    # prepare input and get parsed script:
    input1 <- gsub("[[:space:]]", "+", input)
    URL <- paste("http://www.floraweb.de/pflanzenarten/taxoquery.xsql?taxname=", 
                 input1, sep = "")
    doc <- htmlParse(URL)

    # get returned species names (dismiss last row with additional info):
    sp <- xpathSApply(doc, "//div[@id='contentblock']//a", xmlValue)
    sp <- sp[1:length(sp)-1]

    # get species ids from contentblock:
    con <- getNodeSet(doc, "//div[@id='contentblock']//a")[1:len]
    urls <- sapply(con, xmlGetAttr, "href")
    id_1 <- gsub("[^0-9]", "", urls)

    # check matching and assign to resulting dataframe:
    match <- numeric()
    for (i in 1:len) {
        match[i] <- sum(unlist(strsplit(tolower(sp), " ")[i]) %in% unlist(strsplit(input, 
            " ")) == 0)
    }
    df <- data.frame(sp, id_1, match)

    # select the one with best match:
    sel <- id_1[rank(df$match)][1]

    # build urls for retrieving species data
    url <- paste("http://www.floraweb.de/pflanzenarten/druck.xsql?suchnr=", sel, sep = "")

    doc <- htmlParse(url)
    img_src <- xpathSApply(doc, '//*/p[@class="centeredcontent"]/img/@src')
    img_url <- gsub("../", "http://www.floraweb.de/", img_src, fixed = T)

    # get infos:
    infos <- xpathSApply(doc, "//div[@id='content']//p", xmlValue)[c(2, 7, 22, 33, 35, 14)]

    # replace special characters:
    infos <- spch_sub(infos)

    # make dir to save data:
    dir.create(path.expand("~/FLORAWEB/"), showWarnings = F)
    setwd(path.expand("~/FLORAWEB/"))

    # download image:
    download.file(img_url, "floraweb.jpg", mode = "wb")

    # open device:
    pdf(paste(spch_sub(df$sp[df$id_1 == sel]), ".FloraWeb.pdf", sep = ""), paper = "a4")

    # read image:
    img <- readJPEG("floraweb.jpg")
    w <- dim(img)[2]
    h <- dim(img)[1]

    # print img to plot region:
    par(mar = rep(0, 4), oma = rep(0, 4), mfrow = c(2, 1))
    plot(NA, xlim = c(0, w), ylim = c(0, h), xlab = "", ylab = "", axes = F, 
    type = "n", yaxs = "i", xaxs = "i", asp = 1)
    rasterImage(img, 0, 0, w, h)

    # print text:
    plot(NA, xlim = c(0, 1), ylim = c(0, 1), xlab = "", ylab = "", axes = F, type = "n", 
        yaxs = "i", xaxs = "i")
    # text left intendent and center adjustment:
    l <- 0.5
    c_adj <- c(0.5, 0.5)

    # plot text:
    text(l, 0.95, paste("Eingabe = ", input, " / Gefunden = ", infos[1], sep = ""), font = 2, adj = c_adj, cex = 0.7)
    text(l, 0.5, paste(strwrap(infos[-1], width = 112), collapse = "\n"), adj = c_adj, cex = 0.7)

    # Credit:
    text(l, 0.05, "Die hier verwendeten Daten sind der Internet-Seite FloraWeb.de entnommen.", 
        adj = c_adj, cex = 0.4, font = 3)

    graphics.off()
    message(paste(sp_name, "PDF wurde erzeugt\n\n", sep = "\n -- "))

    # remove jpegs:
    unlink(dir(pattern = ".jpg"))
}

# Examples:
floraweb_scraper("Poa alp")

pfl_liste <- c("leuc alp", "Poa badensis", "Poa alp")
lapply(pfl_liste, FUN = floraweb_scraper)

It works well in the first example but throws error when used with lapply –
does anyone have a clue?

Answer 1

object len is undefined

for (i in 1:len) {
        match[i] <- sum(unlist(strsplit(tolower(sp), " ")[i]) %in% unlist(strsplit(input, 
            " ")) == 0)
    }

you probably have it defined in your workspace. When you call the first function everything is ok. Maybe you have problems with scope when using lapply. Defining len in your function may resolve matters