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,
ignore_missing = FALSE,
zyp_method = "yuepilon",
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 if using station_number argument. Name of column in data that contains dates formatted YYYY-MM-DD. Only required if dates column name is not 'Date' (default). Leave blank if using station_number argument. 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. 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. 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. 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 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. Numeric value indicating the month (1 through 12) of the start of water year for analysis. Default 1. Numeric value of the first year to consider for analysis. Leave blank to use the first year of the source data. Numeric value of the last year to consider for analysis. Leave blank to use the last year of the source data. Numeric vector of years to exclude from analysis. Leave blank to include all years. 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. Character string identifying the prewhitened trend method to use from 'zyp', either 'zhang' or 'yuepilon'. Only required if analysis group 6 is included. Default 'yuepilon'. Numeric value of the significance level (ex. 0.05) of when to plot a trend line. Leave blank for no line. Character string of the name of the Excel Workbook (and folder for plots if necessary) to create on drive to write all results. 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'.

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_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_outside_normal, plot_annual_outside_normal, 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))

}