R/qc_plant_functions.R

In sapfluxnet/sapfluxnetQC1: Package with functions related to sapfluxnet project data

################################################################################
#' Check plant treatments for misspelling and concordance errors
#'
#' \code{qc_pl_treatments} function looks for spelling errors in treatments
#' provided in the plant metadata.
#'
#' This function summarizes the treatments declared in the plant metadata to
#' look for mispelling and concordance errors. At the moment, function only
#' returns an informative data frame, but the search for spelling errors and
#' fixes must be done at hand, as there is no automatized way of doing it.
#'
#' @family Quality Checks Functions
#'
#' @param plant_md Data frame containing the plant metadata
#'
#' @return A data frame with the information about the different treatments if
#'   any.
#'
#' @export

# START
# Function declaration

qc_pl_treatments <- function(plant_md, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # Is plant_md a data frame and have a pl_treatment variable?
    if (!is.data.frame(plant_md) | is.null(plant_md$pl_treatment)) {
      stop('Data object is not a data frame or it not contains any variable called pl_treatment')
    }

    # STEP 1
    # Check if pl_treatment is a NA vector (there are no treatments), so the
    # treatment comprobation is not necessary
    if (all(is.na(plant_md$pl_treatment))) {
      warning("No treatments found, all values for pl_treatment are NA's")
    }

    # STEP 2
    # Extract the unique treatments and summarise the results
    res <- plant_md %>%
      dplyr::select(pl_treatment) %>%
      dplyr::group_by(pl_treatment) %>%
      dplyr::arrange(pl_treatment) %>%
      dplyr::summarize(n = n())

    # STEP 3
    # Return the results data frame
    return(res)

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger, 'qc_pl_treatments', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger, 'qc_pl_treatments', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger, 'qc_pl_treatments', sep = '.'))})

}