R/summary.R

In jentjr/manager: Tools for plotting and analyzing environmental data

#' Summary function
#'
#' @param df dataframe of groundwater data in tidy format
#' @param location_id column of sample locations
#' @param param_name column of constituents
#' @param lt_measure column of less than symbols for non-detect data
#' @param analysis_result column for numerical result
#' @param default_unit column of units
#' @param combine_locations logical. Summarize by individual sample location
#' or by grouping all sample locations. Default is FALSE.
#' @param na.rm TRUE/FALSE for missing values
#'
#' @export

summary <- function(df,
                    location_id = "location_id",
                    param_name = "param_name",
                    lt_measure = "lt_measure",
                    analysis_result = "analysis_result",
                    default_unit = "default_unit",
                    combine_locations = FALSE,
                    na.rm = TRUE) {

  if (!combine_locations) {
    df %>%
      group_by(location_id, param_name, default_unit) %>%
      summarise(n = n(),
                percent_lt = sum(lt_measure == "<", na.rm = na.rm) / n() * 100,
                mean = mean(analysis_result, na.rm = na.rm),
                median = median(analysis_result, na.rm = na.rm),
                sd = sd(analysis_result, na.rm = na.rm),
                var = var(analysis_result, na.rm = na.rm),
                min = min(analysis_result, na.rm = na.rm),
                max = max(analysis_result, na.rm = na.rm),
                cv = cv(analysis_result, na.rm = na.rm),
                `25%` = quantile(analysis_result, na.rm = na.rm)[2][[1]],
                `75%` = quantile(analysis_result, na.rm = na.rm)[4][[1]],
                IQR = IQR(analysis_result, na.rm = na.rm),
                mad = mad(analysis_result, na.rm = na.rm)
      )
  } else {
    df %>%
      group_by(param_name, default_unit) %>%
      summarise(n = n(),
                percent_lt = sum(lt_measure == "<", na.rm = na.rm) / n() * 100,
                mean = mean(analysis_result, na.rm = na.rm),
                median = median(analysis_result, na.rm = na.rm),
                sd = sd(analysis_result, na.rm = na.rm),
                var = var(analysis_result, na.rm = na.rm),
                min = min(analysis_result, na.rm = na.rm),
                max = max(analysis_result, na.rm = na.rm),
                cv = cv(analysis_result, na.rm = na.rm),
                `25%` = quantile(analysis_result, na.rm = na.rm)[2][[1]],
                `75%` = quantile(analysis_result, na.rm = na.rm)[4][[1]],
                IQR = IQR(analysis_result, na.rm = na.rm),
                mad = mad(analysis_result, na.rm = na.rm)
      )
  }

}