R/calc_monthly_stats.R

In fasstr: Analyze, Summarize, and Visualize Daily Streamflow Data

# Copyright 2019 Province of British Columbia
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
# http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and limitations under the License.

#' @title Calculate monthly summary statistics
#'
#' @description Calculates means, medians, maximums, minimums, and percentiles for each month of all years of flow values 
#'    from a daily streamflow data set. Calculates statistics from all values, unless specified. Returns a tibble with statistics.
#'
#' @inheritParams calc_annual_stats
#' @param transpose Logical value indicating if each month statistic should be individual rows. Default \code{FALSE}.
#' @param spread Logical value indicating if each month statistic should be the column name. Default \code{FALSE}.
#' 
#' @return A tibble data frame with the following columns:
#'   \item{Year}{calendar or water year selected}
#'   \item{Month}{month of the year}
#'   \item{Mean}{mean of all daily flows for a given month and year}
#'   \item{Median}{median of all daily flows for a given month and year}
#'   \item{Maximum}{maximum of all daily flows for a given month and year}
#'   \item{Minimum}{minimum of all daily flows for a given month and year}
#'   \item{P'n'}{each n-th percentile selected for a given month and year}
#'   Default percentile columns:
#'   \item{P10}{10th percentile of all daily flows for a given month and year}
#'   \item{P90}{90th percentile of all daily flows for a given month and year}
#'   Transposing data creates a column of 'Statistics' for each month, labeled as 'Month-Statistic' (ex "Jan-Mean"),
#'   and subsequent columns for each year selected.
#'   Spreading data creates columns of Year and subsequent columns of Month-Statistics  (ex 'Jan-Mean').
#'   
#' @examples
#' # Run if HYDAT database has been downloaded (using tidyhydat::download_hydat())
#' if (file.exists(tidyhydat::hy_downloaded_db())) {
#' 
#' # Calculate statistics using a data frame and data argument with defaults
#' flow_data <- tidyhydat::hy_daily_flows(station_number = "08NM116")
#' calc_monthly_stats(data = flow_data,
#'                    start_year = 1980)
#' 
#' # Calculate statistics using station_number argument with defaults
#' calc_monthly_stats(station_number = "08NM116",
#'                    start_year = 1980)
#' 
#' # Calculate statistics regardless if there is missing data for a given year
#' calc_monthly_stats(station_number = "08NM116",
#'                    ignore_missing = TRUE)
#'                   
#' # Calculate statistics for water years starting in October
#' calc_monthly_stats(station_number = "08NM116",
#'                    start_year = 1980,
#'                    water_year_start = 10)
#'                   
#' # Calculate statistics with custom years and percentiles
#' calc_monthly_stats(station_number = "08NM116",
#'                    start_year = 1981,
#'                    end_year = 2010,
#'                    exclude_years = c(1991,1993:1995),
#'                    percentiles = c(25,75))
#'                    
#' }
#' @export


calc_monthly_stats <- function(data,
                               dates = Date,
                               values = Value,
                               groups = STATION_NUMBER,
                               station_number,
                               percentiles = c(10,90),
                               roll_days = 1,
                               roll_align = "right",
                               water_year_start = 1,
                               start_year,
                               end_year,
                               exclude_years,
                               months = 1:12,
                               transpose = FALSE,
                               spread = FALSE,
                               complete_years = FALSE,
                               ignore_missing = FALSE,
                               allowed_missing = ifelse(ignore_missing,100,0)){
  
  
  ## ARGUMENT CHECKS
  ## ---------------
  
  if (missing(data)) {
    data <- NULL
  }
  if (missing(station_number)) {
    station_number <- NULL
  }
  if (missing(start_year)) {
    start_year <- 0
  }
  if (missing(end_year)) {
    end_year <- 9999
  }
  if (missing(exclude_years)) {
    exclude_years <- NULL
  }
  
  rolling_days_checks(roll_days, roll_align, multiple = FALSE)
  water_year_checks(water_year_start)
  years_checks(start_year, end_year, exclude_years)
  months_checks(months)
  logical_arg_check(ignore_missing)
  allowed_missing_checks(allowed_missing, ignore_missing)
  logical_arg_check(transpose)
  logical_arg_check(spread)
  if(transpose & spread) stop("Both spread and transpose arguments cannot be TRUE.", call. = FALSE)
  
  logical_arg_check(complete_years)
  if (complete_years) {
    if (ignore_missing | allowed_missing > 0) {
      ignore_missing <- FALSE
      allowed_missing <- 0
      message("complete_years argument overrides ignore_missing and allowed_missing arguments.")
    }
  }
  
  
  ## FLOW DATA CHECKS AND FORMATTING
  ## -------------------------------
  
  # Check if data is provided and import it
  flow_data <- flowdata_import(data = data, 
                               station_number = station_number)
  
  # Save the original columns (to check for STATION_NUMBER col at end) and ungroup if necessary
  orig_cols <- names(flow_data)
  flow_data <- dplyr::ungroup(flow_data)
  
  # Check and rename columns
  flow_data <- format_all_cols(data = flow_data,
                               dates = as.character(substitute(dates)),
                               values = as.character(substitute(values)),
                               groups = as.character(substitute(groups)),
                               rm_other_cols = TRUE)
  
  
  ## PREPARE FLOW DATA
  ## -----------------
  
  # Fill missing dates, add date variables, and add WaterYear
  flow_data <- analysis_prep(data = flow_data, 
                             water_year_start = water_year_start)
  
  # Add rolling means to end of dataframe
  flow_data <- add_rolling_means(data = flow_data, roll_days = roll_days, roll_align = roll_align)
  colnames(flow_data)[ncol(flow_data)] <- "RollingValue"
  
  # Filter for the selected year (remove excluded years after)
  flow_data <- dplyr::filter(flow_data, WaterYear >= start_year & WaterYear <= end_year)
  flow_data <- dplyr::filter(flow_data, Month %in% months)
  
  # Stop if all data is NA
  no_values_error(flow_data$RollingValue)
  
  flow_data <- filter_complete_yrs(complete_years, flow_data, keep_all = TRUE)
  
  ## CALCULATE STATISTICS
  ## --------------------
  
  # Calculate basic stats
  monthly_stats <- dplyr::summarize(dplyr::group_by(flow_data, STATION_NUMBER, WaterYear, MonthName),
                                    Mean = mean(RollingValue, na.rm = allowed_narm(RollingValue, allowed_missing)),  
                                    Median = stats::median(RollingValue, na.rm = allowed_narm(RollingValue, allowed_missing)), 
                                    Maximum = suppressWarnings(max(RollingValue, na.rm = allowed_narm(RollingValue, allowed_missing))),    
                                    Minimum = suppressWarnings(min(RollingValue, na.rm = allowed_narm(RollingValue, allowed_missing))))
  monthly_stats <- dplyr::ungroup(monthly_stats)
  
  # Calculate annual percentiles
  if(!all(is.na(percentiles))) {
    for (ptile in unique(percentiles)) {
      monthly_stats_ptile <- dplyr::summarise(dplyr::group_by(flow_data, STATION_NUMBER, WaterYear, MonthName),
                                              Percentile = stats::quantile(RollingValue, ptile / 100, na.rm = TRUE))
      monthly_stats_ptile <- dplyr::ungroup(monthly_stats_ptile)
      
      names(monthly_stats_ptile)[names(monthly_stats_ptile) == "Percentile"] <- paste0("P", ptile)
      
      # Merge with monthly_stats
      monthly_stats <- merge(monthly_stats, monthly_stats_ptile, by = c("STATION_NUMBER", "WaterYear", "MonthName"))
      
      # Remove percentile if mean is NA (workaround for na.rm=FALSE in quantile)
      monthly_stats[, ncol(monthly_stats)] <- ifelse(is.na(monthly_stats$Mean), NA, monthly_stats[, ncol(monthly_stats)])
    }
  }
  
  #Remove Nans and Infs
  monthly_stats$Mean[is.nan(monthly_stats$Mean)] <- NA
  monthly_stats$Maximum[is.infinite(monthly_stats$Maximum)] <- NA
  monthly_stats$Minimum[is.infinite(monthly_stats$Minimum)] <- NA
  
  # Rename year column
  monthly_stats <- dplyr::rename(monthly_stats, Year = WaterYear, Month = MonthName)
  monthly_stats$Month <- factor(monthly_stats$Month, levels = month.abb[c(water_year_start:12, 1:water_year_start-1)])
  
  
  # Reorder months and row.names
  monthly_stats <- with(monthly_stats, monthly_stats[order(Year, Month),])
  
  
  # Make excluded years data NA
  if(as.character(substitute(groups)) %in% orig_cols) {
    monthly_stats[monthly_stats$Year %in% exclude_years,-(1:3)] <- NA
  } else {
    monthly_stats[monthly_stats$Year %in% exclude_years,-(1:2)] <- NA
  }
  
  
  # Transform data to chosen format
  # Spread data if selected
  if (spread | transpose) {
    monthly_stats_spread <- dplyr::summarise(dplyr::group_by(monthly_stats, STATION_NUMBER, Year))
    monthly_stats_spread <- dplyr::ungroup(monthly_stats_spread)
    for (mnth in unique(monthly_stats$Month)) {
      monthly_stats_month <- dplyr::filter(monthly_stats, Month == mnth)
      monthly_stats_month <- tidyr::gather(monthly_stats_month, Statistic, Value, 4:ncol(monthly_stats_month))
      monthly_stats_month <- dplyr::mutate(monthly_stats_month, StatMonth = paste0(Month, "_", Statistic))
      monthly_stats_month <- dplyr::select(monthly_stats_month, -Statistic, -Month)
      stat_order <- unique(monthly_stats_month$StatMonth)
      monthly_stats_month <- tidyr::spread(monthly_stats_month, StatMonth, Value)
      monthly_stats_month <-  monthly_stats_month[, c("STATION_NUMBER", "Year", stat_order)]
      monthly_stats_spread <- merge(monthly_stats_spread, monthly_stats_month, by = c("STATION_NUMBER", "Year"), all = TRUE)
    }
    monthly_stats <- monthly_stats_spread
    
    if(transpose){
      monthly_stats <- tidyr::gather(monthly_stats, Statistic, Value, -(1:2))
    }
  }
  
  monthly_stats <- with(monthly_stats, monthly_stats[order(STATION_NUMBER, Year),])
  
  # Give warning if any NA values
  missing_test <- dplyr::filter(monthly_stats, !(Year %in% exclude_years))
  if (ignore_missing){
    if (anyNA(missing_test[, 4:ncol(missing_test)])) 
      warning("One or more calculations included missing values and NA's were produced. Some months in some years have no data to summarize.", call. = FALSE)
  } else {
    missing_values_warning(missing_test[, 4:ncol(missing_test)])
  }
  
  
  # Recheck if station_number/grouping was in original flow_data and rename or remove as necessary
  if(as.character(substitute(groups)) %in% orig_cols) {
    names(monthly_stats)[names(monthly_stats) == "STATION_NUMBER"] <- as.character(substitute(groups))
  } else {
    monthly_stats <- dplyr::select(monthly_stats, -STATION_NUMBER)
  }
  
  
  
  dplyr::as_tibble(monthly_stats)
  
}