R/joinTreeNotes.R

In KateMMiller/forestNETN: Package for importing, joining and querying NETN forest database tables

#' @include joinLocEvent.R
#'
#' @title joinTreeNotes: compiles tree notes
#'
#' @importFrom dplyr filter inner_join mutate select
#' @importFrom magrittr %>%
#'
#' @description This function combines all tree-level notes recorded in a given visit. N
#'
#' @param park Combine data from all parks or one or more parks at a time. Valid inputs:
#' \describe{
#' \item{"all"}{Includes all parks in the network}
#' \item{"ACAD"}{Acadia NP only}
#' \item{"MABI"}{Marsh-Billings-Rockefeller NHP only}
#' \item{"MIMA"}{Minute Man NHP only}
#' \item{"MORR"}{Morristown NHP only}
#' \item{"ROVA"}{Roosevelt-Vanderbilt NHS only}
#' \item{"SAGA"}{Saint-Gaudens NHS only}
#' \item{"SARA"}{Saratoga NHP only}
#' \item{"WEFA"}{Weir Farm NHS only}}
#'
#' @param from Year to start analysis, ranging from 2006 to current year
#' @param to Year to stop analysis, ranging from 2006 to current year
#'
#' @param QAQC Allows you to remove or include QAQC events.
#' \describe{
#' \item{FALSE}{Default. Only returns visits that are not QAQC visits}
#' \item{TRUE}{Returns all visits, including QAQC visits}}
#'
#' @param locType Allows you to only include plots that are part of the GRTS sample design or
#' include all plots, such as deer exclosures.
#' \describe{
#' \item{"VS"}{Only include plots that are part of the Vital Signs GRTS sample design}
#' \item{"all"}{Include all plots, such as plots in deer exclosures or test plots.}}
#'
#' @param eventType Allows you to include only complete sampling events or all sampling events
#' \describe{
#' \item{"complete"}{Default. Only include sampling events for a plot that are complete.}
#' \item{"all}{Include all plot events with a record in tblCOMN.Event, including plots missing most of the data
#' associated with that event (eg ACAD-029.2010). This feature is currently hard-coded in the function.}}
#'
#' @param panels Allows you to select individual panels from 1 to 4. Default is all 4 panels (1:4).
#' If more than one panel is selected, specify by c(1, 3), for example.
#'
#' @param ... Other arguments passed to function.
#'
#' @return Returns a dataframe with all tree-related notes. Only returns records with notes.
#'
#' @examples
#' \dontrun{
#' importData()
#' # compile quadrat data for invasive species in SARA for 2018
#' SARA_tree_notes <- joinTreeNotes(park = 'SARA', from = 2018, to = 2018)
#' }
#'
#' @export
#'

joinTreeNotes <- function(park = 'all', from = 2006, to = as.numeric(format(Sys.Date(), "%Y")),
                          QAQC = FALSE, panels = 1:4,
                          locType = c('VS', 'all'), eventType = c('complete', 'all'), ...){

  # Match args and class
  park <- match.arg(park, several.ok = TRUE,
                    c("all", "ACAD", "MABI", "MIMA", "MORR", "ROVA", "SAGA", "SARA", "WEFA"))
  stopifnot(class(from) == "numeric", from >= 2006)
  stopifnot(class(to) == "numeric", to >= 2006)
  stopifnot(class(QAQC) == 'logical')
  stopifnot(panels %in% c(1, 2, 3, 4))
  locType <- match.arg(locType)
  eventType <- match.arg(eventType)

  options(scipen = 100)
  env <- if(exists("VIEWS_NETN")){VIEWS_NETN} else {.GlobalEnv}

  tryCatch(tree_vw <- get("TreesByEvent_NETN", envir = env) %>%
                      select(PlotID, EventID, TagCode, TreeEventNote) %>%
                      filter(!is.na(TreeEventNote)),
           error = function(e){stop("TreesByEvent_NETN view not found. Please import view.")}
  )

  plot_events <- joinLocEvent(park = park, from = from, to = to, QAQC = QAQC, panels = panels,
                              locType = locType, eventType = eventType, output = 'verbose', ...) %>%
                 select(Plot_Name, PlotID, EventID, Network, ParkUnit, ParkSubUnit,
                        SampleDate, SampleYear, cycle, IsQAQC)

  if(nrow(plot_events) == 0){stop("Function returned 0 rows. Check that park and years specified contain visits.")}

  tree_evs <- inner_join(plot_events, tree_vw, by = intersect(names(plot_events), names(tree_vw))) %>%
              mutate(Sample_Info = paste0("Tree Tag: ", TagCode),
                     Note_Type = "Tree_Notes",
                     Notes = TreeEventNote) %>%
              select(Plot_Name, PlotID, EventID, EventID, Network, ParkUnit, ParkSubUnit,
                     SampleDate, SampleYear, IsQAQC, Note_Type, Sample_Info, Notes)

  return(tree_evs)

  }