R/leda_download.R

In GioBo/TR8: A Tool for Downloading Functional Traits Data for Plant Species

##'  Allows the user to retrieve the data files from the LEDA
##'  Traitbase website, merge them in a single \code{R} dataset and store
##'  the result in a local file; this file could be then used whenever the
##'  \code{tr8()} function is used in order to speed up the process of
##'  retrieving traits data.
##'
##'   The function uses a GUI created via the \code{gWidgets} package, to
##'   let the user select a folder where the datasets has to be stored.
##' @title A utility to download a local copy of the LEDA data files.
##' @param directory    is the directory where the downloaded data will be
##' stored (in order  to be used in future R sessions); default is NULL.
##' @return   The function save a local copy of LEDA data in a file called
##' \code{leda_database.Rda}
##' @references Kleyer, M., Bekker, R.M., Knevel, I.C., Bakker, J.P,
##' Thompson, K., Sonnenschein, M., Poschlod, P., Van
##' Groenendael, J.M., Klimes, L., Klimesova, J., Klotz, S.,
##' Rusch, G.M., Hermy, M., Adriaens, D., Boedeltje, G.,
##' Bossuyt, B., Dannemann, A., Endels, P., Götzenberger, L.,
##' Hodgson, J.G., Jackel, A-K., Kühn, I., Kunzmann, D.,
##' Ozinga, W.A., Römermann, C., Stadler, M., Schlegelmilch,
##' J., Steendam, H.J., Tackenberg, O., Wilmann, B.,
##' Corneliss
##' n, J.H.C., Eriksson, O., Garnier, E., Peco, B.
##' (2008): The LEDA Traitbase: A database of life-history
##' traits of Northwest European flora. Journal of Ecology 96:1266-1274. \samp{  http://www.leda-traitbase.org/LEDAportal/data_files.jsp}
##' @author   Gionata Bocci <boccigionata@@gmail.com>
leda_download_to_local_directory<-function(directory){
  ## gmessage(title="","Downloading LEDA files is a time-consuming activity, \nthus you are suggested to download the dataset once\nand store them in a local directory.\n\nYou will now be asked to choose such a directory.")
  ##directory<-gfile(type="selectdir")
  ## load the list containing the data (url, names, etc..) of the txt files
  ## data(leda_lookup)
  ## convert it to a dframe
  env<-new.env(parent = parent.frame())
  data(leda_lookup,envir=env)
  leda_lookup<-get("leda_lookup",envir=env)
  ## DF<-ldply(leda_lookup)
  ## ## build the first dataframe
  ## first<-leda_download(url=DF[1,2],skip_row=DF[1,3],column=DF[1,4],out_name=DF[1,5])
  ## rearranged<-first
  ## ## download all the other txt files and merge each one to the
  ## ## previous one
  ## for(i in 2:nrow(DF)){
  ##   temp<-leda_download(url=DF[i,2],skip_row=DF[i,3],column=DF[i,4],out_name=DF[i,5])
  ##   rearranged<-merge(rearranged,temp,by.x=0,by.y=0,all.x=TRUE,all.y=TRUE)
  ##   row.names(rearranged)<-rearranged$Row.names
  ##   rearranged<-rearranged[,2:ncol(rearranged)]
  ## }

  ## create a list of dataframes, one for each LEDA file;
  ## each dataframe has 2 columns: one called "Species" and a second
  ## one with the code name of the trait
  tmp_leda <- lapply(leda_lookup, function(x){
    ## print(x)
    a<-leda_download(
      URL=x[1],
      skip_row=x[2],
      column=x[3],
      out_name=x[4]
    )
    return(a)
  })
  ## merge all dataframes in a single one
  RES <- Reduce(function(dtf1, dtf2) merge(dtf1, dtf2, by = "Species", all.x = TRUE),
                tmp_leda)

  ## save the complete dataset in a file called "leda_database.Rda"
  ## in the directory chosen by the user
  remove(list=c("leda_lookup"), envir = env)    
                                        #save(file=file.path(directory,"leda_database.Rda"),rearranged)
  save(file=file.path(directory,"leda_database.Rda"),RES)
}