Write a suite of tables and plots from various fasstr functions into a directory

Calculates and writes tables and plots from a suite of statistics from fasstr functions into an Excel workbook, and accompanying plot files for certain analyses. Due to the number of tables and plots to be made, this function may take several minutes to complete. If ignore_missing = FALSE (default) and there is missing data, some tables and plots may be empty and produce warnings. Use ignore_missing = TRUE to ignore the missing values or filter your data to complete years. Calculates statistics from all values, unless specified. Returns a list of tibbles and plots, along with saving the Excel and image files in a directory.

write_full_analysis(
  data,
  dates = Date,
  values = Value,
  groups = STATION_NUMBER,
  station_number,
  analyses = 1:7,
  basin_area,
  water_year_start = 1,
  start_year,
  end_year,
  exclude_years,
  months = 1:12,
  ignore_missing = FALSE,
  complete_years = FALSE,
  allowed_missing_annual = ifelse(ignore_missing, 100, 0),
  allowed_missing_monthly = ifelse(ignore_missing, 100, 0),
  zyp_method = "zhang",
  zyp_alpha,
  file_name,
  plot_filetype = "pdf"
)

Arguments

data

Data frame of daily data that contains columns of dates, flow values, and (optional) groups (e.g. station numbers). Leave blank or set to NULL if using station_number argument.

dates

Name of column in data that contains dates formatted YYYY-MM-DD. Only required if dates column name is not 'Date' (default). Leave blank or set to NULL if using station_number argument.

values

Name of column in data that contains numeric flow values, in units of cubic metres per second. Only required if values column name is not 'Value' (default). Leave blank if using station_number argument.

groups

Name of column in data that contains unique identifiers for different data sets, if applicable. Only required if groups column name is not 'STATION_NUMBER'. Function will automatically group by a column named 'STATION_NUMBER' if present. Remove the 'STATION_NUMBER' column beforehand to remove this grouping. Leave blank if using station_number argument.

station_number

Character string vector of seven digit Water Survey of Canada station numbers (e.g. "08NM116") of which to extract daily streamflow data from a HYDAT database. Requires tidyhydat package and a HYDAT database. Leave blank if using data argument.

analyses

Numeric vector of analyses to run (default is all (1:7)):

• 1: Screening

• 2: Long-term

• 3: Annual

• 4: Monthly

• 5: Daily

• 6: Annual Trends

• 7: Low-flow Frequencies

basin_area

Upstream drainage basin area, in square kilometres, to apply to observations. Three options:

(1) Leave blank if groups is STATION_NUMBER with HYDAT station numbers to extract basin areas from HYDAT.

(2) A single numeric value to apply to all observations.

(3) List each basin area for each group/station in groups (can override HYDAT value if listed) as such c("08NM116" = 795, "08NM242" = 10). If group is not listed the HYDAT area will be applied if it exists, otherwise it will be NA.

water_year_start

Numeric value indicating the month (1 through 12) of the start of water year for analysis. Default 1.

start_year

Numeric value of the first year to consider for analysis. Leave blank or set well before start date (i.e. 1800) to use from the first year of the source data.

end_year

Numeric value of the last year to consider for analysis. Leave blank or set well after end date (i.e. 2100) to use up to the last year of the source data.

exclude_years

Numeric vector of years to exclude from analysis. Leave blank or set to NULL to include all years.

months

Numeric vector of months to include in analysis. For example, 3 for March, 6:8 for Jun-Aug or c(10:12,1) for first four months (Oct-Jan) when water_year_start = 10 (Oct). Default summarizes all months (1:12). If not all months, seasonal total yield and volumetric flows will not be included.

ignore_missing

Logical value indicating whether dates with missing values should be included in the calculation. If TRUE then a statistic will be calculated regardless of missing dates. If FALSE then only those statistics from time periods with no missing dates will be returned. Default FALSE.

complete_years

Logical values indicating whether to include only years with complete data in analysis. Default FALSE.

allowed_missing_annual

Numeric value between 0 and 100 indicating the percentage of missing dates allowed to be included to calculate an annual statistic (0 to 100 percent). If 'ignore_missing = FALSE' then it defaults to 0 (zero missing dates allowed), if 'ignore_missing = TRUE' then it defaults to 100 (any missing dates allowed); consistent with ignore_missing usage. Supersedes ignore_missing when used. Only for annual means, percentiles, minimums, and maximums.

allowed_missing_monthly

Numeric value between 0 and 100 indicating the percentage of missing dates allowed to be included to calculate a monthly statistic (0 to 100 percent). If 'ignore_missing = FALSE' then it defaults to 0 (zero missing dates allowed), if 'ignore_missing = TRUE' then it defaults to 100 (any missing dates allowed); consistent with ignore_missing usage. Supersedes ignore_missing when used.Only for monthly means, percentiles, minimums, and maximums.

zyp_method

Character string identifying the prewhitened trend method to use from 'zyp', either 'zhang' or 'yuepilon'. 'zhang' is recommended over 'yuepilon' for hydrologic applications (see compute_annual_trends(); Bürger 2017; Zhang and Zwiers 2004). Only required if analysis group 6 is included. Default 'zhang'.

zyp_alpha

Numeric value of the significance level (ex. 0.05) of when to plot a trend line. Leave blank for no line.

file_name

Character string of the name of the Excel Workbook (and folder for plots if necessary) to create on drive to write all results.

plot_filetype

Image type to write. One of 'png', 'eps', 'ps', 'tex', 'pdf', 'jpeg', 'tiff', 'bmp', or 'svg'. If not 'pdf' then individual plots will be created instead of a combined PDF. Default 'pdf'.

See also

compute_full_analysis, screen_flow_data, plot_data_screening, plot_missing_dates, calc_longterm_monthly_stats, plot_longterm_monthly_stats, calc_longterm_daily_stats, plot_longterm_daily_stats, plot_monthly_means, plot_flow_duration, calc_annual_stats, plot_annual_stats, calc_annual_cumulative_stats, plot_annual_cumulative_stats, calc_annual_flow_timing, plot_annual_flow_timing, calc_annual_normal_days, plot_annual_normal_days, calc_annual_lowflows, plot_annual_lowflows, plot_annual_means, calc_monthly_stats, plot_monthly_stats, calc_monthly_cumulative_stats, plot_monthly_cumulative_stats, calc_daily_stats, plot_daily_stats, calc_daily_cumulative_stats, plot_daily_cumulative_stats, compute_annual_trends, compute_annual_frequencies, write_flow_data, write_plots

Examples

if (FALSE) {

# Working examples:

# Save a full analysis will all the analyses
write_full_analysis(station_number = "08NM116",
                    file_name = "Mission Creek",
                    start_year = 1980,
                    end_year = 2010)

# Save a full analysis with only Annual and Daily analyses
write_full_analysis(station_number = "08NM116",
                    file_name = "Mission Creek",
                    start_year = 1980,
                    end_year = 2010,
                    analyses = c(3,5))
                    
}