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# updated to NASIS 6.2
# convenience function for loading most commonly used vegplot information from local NASIS database
#' Get vegetation plot data from local NASIS database
#' @aliases get_vegplot_from_NASIS_db
#' get_vegplot_location_from_NASIS_db get_vegplot_species_from_NASIS_db
#' get_vegplot_textnote_from_NASIS_db get_vegplot_transect_from_NASIS_db
#' get_vegplot_transpecies_from_NASIS_db
#' get_vegplot_tree_si_details_from_NASIS_db
#' get_vegplot_tree_si_summary_from_NASIS_db get_vegplot_trhi_from_NASIS_db
#'
#' @param SS fetch data from the currently loaded selected set in NASIS or from the entire local database (default: `TRUE`)
#' @param stringsAsFactors deprecated
#' @param dsn Optional: path to local SQLite database containing NASIS
#' table structure; default: `NULL`
#'
#' @return A named list containing: "vegplot", "vegplotlocation", "vegplotrhi", "vegplotspecies", "vegtransect", "vegtransplantsum", 'vegsiteindexsum', "vegsiteindexdet", and "vegplottext" tables
#'
#' @export
#'
fetchVegdata <- function(SS=TRUE, stringsAsFactors = NULL, dsn = NULL) {
if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
.Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
NASISDomainsAsFactor(stringsAsFactors)
}
# check if NASIS local DB instance/ODBC data source is available
.soilDB_test_NASIS_connection(dsn = dsn)
# 1. load data in pieces
site <- get_site_data_from_NASIS_db(SS = SS, dsn = dsn)
vegplot <- get_vegplot_from_NASIS_db(SS = SS, dsn = dsn)
vegplotlocation <- get_vegplot_location_from_NASIS_db(SS = SS, dsn = dsn)
vegplotrhi <- get_vegplot_trhi_from_NASIS_db(SS = SS, dsn = dsn)
vegplotspecies <- get_vegplot_species_from_NASIS_db(SS = SS, dsn = dsn)
vegtransect <- get_vegplot_transect_from_NASIS_db(SS = SS, dsn = dsn)
vegtransplantsum <- get_vegplot_transpecies_from_NASIS_db(SS = SS, dsn = dsn)
vegtranspoint <- get_vegplot_transpoints_from_NASIS_db(SS = SS, dsn = dsn)
vegprodquadrat <- get_vegplot_prodquadrats_from_NASIS_db(SS = SS, dsn = dsn)
vegsiteindexsum <- get_vegplot_tree_si_summary_from_NASIS_db(SS = SS, dsn = dsn)
vegsiteindexdet <- get_vegplot_tree_si_details_from_NASIS_db(SS = SS, dsn = dsn)
vegplottext <- get_vegplot_textnote_from_NASIS_db(SS = SS, fixLineEndings = TRUE, dsn = dsn)
# test to see if the selected set is loaded
if (nrow(site) == 0 || nrow(vegplot) == 0) {
message('Selected set is missing either the vegplot, pedon or site table, please load and try again :)')
}
# add ecosite id, corrdate, selection method to vegplot
vegplot <- merge(site[,c("siteiid", "ecositeid", "ecositecorrdate", "siteecositehistory.classifier", "es_selection_method")],
vegplot, by = "siteiid", all.x = TRUE, sort = FALSE)
# done
return(list(
vegplot = vegplot,
vegplotlocation = vegplotlocation,
vegplotrhi = vegplotrhi,
vegplotspecies = vegplotspecies,
vegtransect = vegtransect,
vegtransplantsum = vegtransplantsum,
vegtranspoint = vegtranspoint,
vegprodquadrat = vegprodquadrat,
vegsiteindexsum = vegsiteindexsum,
vegsiteindexdet = vegsiteindexdet,
vegplottext = vegplottext,
site = site
))
}
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