Nothing
R/write_full_analysis.R
In fasstr: Analyze, Summarize, and Visualize Daily Streamflow Data
Defines functions
write_full_analysis
Documented in
write_full_analysis
# 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 Write a suite of tables and plots from various fasstr functions into a directory
#'
#' @description Calculates and writes tables and plots from a suite of statistics from \code{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 \code{ignore_missing = FALSE} (default) and there is missing data,
#' some tables and plots may be empty and produce warnings. Use \code{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.
#'
#' @inheritParams compute_full_analysis
#' @param 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.
#' @param plot_filetype Image type to write. One of \code{'png'}, \code{'eps'}, \code{'ps'}, \code{'tex'}, \code{'pdf'},
#' \code{'jpeg'}, \code{'tiff'}, \code{'bmp'}, or \code{'svg'}. If not \code{'pdf'} then individual plots will be created instead
#' of a combined PDF. Default \code{'pdf'}.
#'
#' @seealso \code{\link{compute_full_analysis}},
#' \code{\link{screen_flow_data}},
#' \code{\link{plot_data_screening}},
#' \code{\link{plot_missing_dates}},
#' \code{\link{calc_longterm_monthly_stats}},
#' \code{\link{plot_longterm_monthly_stats}},
#' \code{\link{calc_longterm_daily_stats}},
#' \code{\link{plot_longterm_daily_stats}},
#' \code{\link{plot_monthly_means}},
#' \code{\link{plot_flow_duration}},
#' \code{\link{calc_annual_stats}},
#' \code{\link{plot_annual_stats}},
#' \code{\link{calc_annual_cumulative_stats}},
#' \code{\link{plot_annual_cumulative_stats}},
#' \code{\link{calc_annual_flow_timing}},
#' \code{\link{plot_annual_flow_timing}},
#' \code{\link{calc_annual_normal_days}},
#' \code{\link{plot_annual_normal_days}},
#' \code{\link{calc_annual_lowflows}},
#' \code{\link{plot_annual_lowflows}},
#' \code{\link{plot_annual_means}},
#' \code{\link{calc_monthly_stats}},
#' \code{\link{plot_monthly_stats}},
#' \code{\link{calc_monthly_cumulative_stats}},
#' \code{\link{plot_monthly_cumulative_stats}},
#' \code{\link{calc_daily_stats}},
#' \code{\link{plot_daily_stats}},
#' \code{\link{calc_daily_cumulative_stats}},
#' \code{\link{plot_daily_cumulative_stats}},
#' \code{\link{compute_annual_trends}},
#' \code{\link{compute_annual_frequencies}},
#' \code{\link{write_flow_data}},
#' \code{\link{write_plots}}
#'
#' @examples
#' \dontrun{
#'
#' # 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))
#'
#' }
#' @export
write_full_analysis <- function(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'){
## 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
}
if (missing(basin_area)) {
basin_area <- NA
}
if (missing(zyp_alpha)) {
zyp_alpha <- NA
}
water_year_checks(water_year_start)
years_checks(start_year, end_year, exclude_years)
logical_arg_check(ignore_missing)
allowed_missing_checks(allowed_missing_annual, ignore_missing)
allowed_missing_checks(allowed_missing_monthly, ignore_missing)
months_checks(months)
logical_arg_check(complete_years)
if (complete_years) {
if (ignore_missing | allowed_missing_annual > 0 | allowed_missing_monthly > 0) {
ignore_missing <- FALSE
allowed_missing_annual <- 0
allowed_missing_monthly <- 0
message("complete_years argument overrides ignore_missing and allowed_missing_* arguments.")
}
}
if (missing(file_name)) stop("A file name is required with the file_name argument to write all results.", call. = FALSE)
if (!is.numeric(analyses))
stop("analyses argument must be numbers between 1 and 7. See ?write_full_analysis for analysis group numbers.", call. = FALSE)
if (!all(analyses %in% 1:7))
stop("analyses argument must be numbers between 1 and 7. See ?write_full_analysis for analysis group numbers.", call. = FALSE)
if (6 %in% analyses) {
zyp_alpha_checks(zyp_alpha)
zyp_method_checks(zyp_method)
}
# Do this for now, until looping of include_year plots is sorted out
if (length(station_number) > 1) stop("Only one station_number can be listed.", call. = FALSE)
message("* this may take a few moments...")
## FLOW DATA CHECKS AND FORMATTING
## -------------------------------
# Check if data is provided and import it
flow_data_source <- flowdata_import(data = data,
station_number = station_number)
flow_data_raw <- flow_data_source
# Save the original columns (to check for STATION_NUMBER col at end) and ungroup if necessary
orig_cols <- names(flow_data_raw)
flow_data_raw <- dplyr::ungroup(flow_data_raw)
# Check and rename columns
flow_data_raw <- format_all_cols(data = flow_data_raw,
dates = as.character(substitute(dates)),
values = as.character(substitute(values)),
groups = as.character(substitute(groups)),
rm_other_cols = TRUE)
# # Data setup
flow_data_unfiltered <- fill_missing_dates(data = flow_data_raw, water_year_start = water_year_start)
flow_data_unfiltered <- add_date_variables(data = flow_data_unfiltered, water_year_start = water_year_start)
flow_data_unfiltered <- add_rolling_means(data = flow_data_unfiltered)
#
# # Set up basin_area
flow_data_unfiltered <- add_basin_area(flow_data_unfiltered, basin_area = basin_area)
basin_area_stn <- unique(flow_data_unfiltered$Basin_Area_sqkm)[1]
# Get the start and end years of the data to make a list of all included years
flow_data_filtered <- flow_data_unfiltered
flow_data_filtered <- analysis_prep(data = flow_data_filtered,
water_year_start = water_year_start)
if (start_year < min(flow_data_filtered$WaterYear)) {
start_year <- min(flow_data_filtered$WaterYear)
}
if (end_year > max(flow_data_filtered$WaterYear)) {
end_year <- max(flow_data_filtered$WaterYear)
}
# flow_data_plus <- dplyr::filter(flow_data, WaterYear >= start_year - 1 & WaterYear <= end_year + 1)
flow_data_filtered <- dplyr::filter(flow_data_filtered,
WaterYear >= start_year & WaterYear <= end_year,
!(WaterYear %in% exclude_years))
if (any(is.na(flow_data_filtered$Value)) & !ignore_missing) {
message("** warning: selected data contains dates with missing values; some NAs in tables and gaps in plots may be produced")
}
# Create function for condensing consecutive numbers
conseq_fn <- function(s){
dif <- s[seq(length(s))][-1] - s[seq(length(s)-1)]
new <- !c(0, dif == 1)
cs <- cumsum(new)
res <- vector(mode="list", max(cs))
for(i in seq(res)){
s.i <- s[which(cs == i)]
if(length(s.i) > 2){
res[[i]] <- paste(min(s.i), max(s.i), sep=":")
} else {
res[[i]] <- as.character(s.i)
}
}
paste0(ifelse(length(s)==1,paste(s),paste0("c(", paste(unlist(res), collapse=","), ")")))
}
# Create list of all objects
message("** creating data frames and plots")
### Compute results
##########################
results <- suppressMessages(
compute_full_analysis(data = flow_data_raw,
dates = "Date",
values = "Value",
groups = "STATION_NUMBER",
analyses = analyses,
basin_area = basin_area,
water_year_start = water_year_start,
start_year = start_year,
end_year = end_year,
exclude_years = exclude_years,
months = months,
ignore_missing = ignore_missing,
complete_years = complete_years,
allowed_missing_annual = allowed_missing_annual,
allowed_missing_monthly = allowed_missing_monthly,
zyp_method = zyp_method,
zyp_alpha = zyp_alpha)
)
### Writing Functions
##########################
# Create add table function
add_table <- function(wb, sheet, data, title, col, row, comment = NA) {
openxlsx::writeData(wb = wb, sheet = sheet, x = title, startCol = col, startRow = row)
openxlsx::writeData(wb = wb, sheet = sheet, x = data, startCol = col, startRow = row + 1,
headerStyle = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold",
border = "TopBottom",
fgFill = "#add8e6",
halign = "left"))
openxlsx::addStyle(wb = wb, sheet = sheet, cols = col, rows = row,
style = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold"))
if (!is.na(comment)) {
openxlsx::writeComment(wb = wb, sheet = sheet, col = col, row = row,
comment = openxlsx::createComment(comment = comment,
visible = FALSE,
width = 5,
height = 4))
}
}
# Create add plot function
add_plot <- function(wb, sheet, plot, title, col, row, height, width, comment = NA) {
openxlsx::writeData(wb = wb, sheet = sheet, x = title, startCol = col, startRow = row)
print(plot)
openxlsx::insertPlot(wb = wb, sheet = sheet, startCol = col, startRow = row + 1, height = height, width = width)
openxlsx::addStyle(wb = wb, sheet = sheet, cols = col, rows = row,
style = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold"))
if (!is.na(comment)) {
openxlsx::writeComment(wb = wb, sheet = sheet, col = col, row = row,
comment = openxlsx::createComment(comment = comment,
visible = FALSE,
width = 5,
height = 4))
}
}
### Setup dataframe and values for writing the fasstr functions
##########################
fasstr_functions <- data.frame("Worksheet" = character(), "Output" = character(), "Function" = character())
# Create some values for creating character versions of fasstr functions
fn_data <- paste0(ifelse(!is.null(data),
paste0("data = ", as.character(substitute(data)),
ifelse(as.character(substitute(dates)) != "Date",
paste0(", dates = '", as.character(substitute(dates)), "'"), ""),
ifelse(as.character(substitute(values)) != "Value",
paste0(", values = '", as.character(substitute(values)), "'"), ""),
ifelse(as.character(substitute(groups)) != "STATION_NUMBER",
paste0(", groups = '", as.character(substitute(groups)), "'"), "")),
paste0("station_number = '", station_number, "'")))
fn_area <- paste0(ifelse(!is.na(basin_area),
paste0(", basin_area = ", basin_area),
""))
fn_wys <- ifelse(water_year_start != 1, paste0(", water_year_start = ", water_year_start), "")
fn_startend <- paste0(ifelse(start_year != min(flow_data_unfiltered$WaterYear),
paste0(", start_year = ", start_year), ""),
ifelse(end_year != max(flow_data_unfiltered$WaterYear),
paste0(", end_year = ", end_year), ""))
fn_exclude <- paste0(ifelse(!is.null(exclude_years),
paste0(", exclude_years = ", ifelse(length(exclude_years) == 1,
paste(exclude_years),
paste0("c(",paste(exclude_years, collapse = ","),")"))),
""))
fn_months <- ifelse(all(1:12 %in% months),
paste(""),
paste0(", months = ", conseq_fn(months)))
fn_missing <- ifelse(ignore_missing, paste0(", ignore_missing = TRUE"), "")
fn_allowmiss_ann <- ifelse(allowed_missing_annual > 0 , paste0(", allowed_missing = ", allowed_missing_annual), "")
fn_allowmiss_mon <- ifelse(allowed_missing_monthly > 0 , paste0(", allowed_missing = ", allowed_missing_monthly), "")
fn_allowmiss_ann_trend <- ifelse(allowed_missing_annual > 0 , paste0(", allowed_missing_annual = ", allowed_missing_annual), "")
fn_allowmiss_mon_trend <- ifelse(allowed_missing_monthly > 0 , paste0(", allowed_missing_monthly = ", allowed_missing_monthly), "")
fn_complete <- ifelse(complete_years, paste0(", complete_years = TRUE"), "")
fn_zyp <- paste0(", zyp_method = '", zyp_method, "'",
", zyp_alpha = ", ifelse(!is.na(zyp_alpha), zyp_alpha, "NA"))
# Create fasstr function strings for output
analysis_function <- paste0("compute_full_analysis(",
fn_data,
fn_area,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
ifelse(6 %in% analyses, fn_zyp, ""),
ifelse(all(1:7 %in% analyses),
paste(", analyses = c(1:7)"),
paste0(", analyses = ", conseq_fn(analyses))),
")")
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = paste0(file_name,".xlsx"),
"Output" = "Full Analysis Function",
"Function" = analysis_function)
### Excel workbook Setup
##########################
# Create the excel document and first worksheet
output_excel <- openxlsx::createWorkbook()
overview_sheet <- "Analysis Overview"
openxlsx::addWorksheet(wb = output_excel,
sheetName = overview_sheet,
tabColour = "#003e1f") # 73fbd3 44e5e7 59d2fe 4a8fe7 5c7aff
# Add raw data to first worksheet
rawdata_sheet <- "Data Input"
openxlsx::addWorksheet(wb = output_excel,
sheetName = rawdata_sheet,
tabColour = "#003e1f")
add_table(wb = output_excel,
sheet = rawdata_sheet,
data = flow_data_source,
title = "Source Daily Data",
col = 1,
row = 1,
comment = NA)
openxlsx::setColWidths(wb = output_excel, sheet = rawdata_sheet,
cols = seq_len(ncol(flow_data_source)), widths = 11)
## Screening
##########################
if (1 %in% analyses) {
# Add worksheet
timeseries_sheet <- "Data Timeseries"
openxlsx::addWorksheet(wb = output_excel,
sheetName = timeseries_sheet,
tabColour = "#73ba9b")
# Create fasstr function strings for output
data_function <- paste0("add_date_variables(",
fn_data,
fn_wys,
") %>% add_rolling_means() %>% add_basin_area(",
paste0(ifelse(!is.na(basin_area),
paste0("basin_area = ", basin_area),
"")),
")")
data_plot_function <- paste0("plot_flow_data(",
fn_data,
fn_wys,
fn_exclude,
")")
# Add data tables
flow_data_out <- flow_data_filtered[,!colnames(flow_data_filtered) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = timeseries_sheet,
data = flow_data_out,
title = paste0("Daily Flows, Dates, Rolling Means (cubic metres per second), and Basin Area (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = data_function)
openxlsx::setColWidths(wb = output_excel, sheet = timeseries_sheet,
cols = seq_len(ncol(flow_data_source)), widths = 12)
# Add plots
add_plot(wb = output_excel,
sheet = timeseries_sheet,
plot = results$Screening$Daily_Flows_Plot[[1]],
title = paste0("Daily Flows (", start_year, "-", end_year, ")"),
col = ncol(flow_data_out) + 2,
row = 2,
height = 5,
width = 20,
comment = data_plot_function)
# Add worksheet
screening_sheet <- "Data Screening"
openxlsx::addWorksheet(wb = output_excel,
sheetName = screening_sheet,
tabColour = "#73ba9b")
# Create fasstr function strings for output
screening_function <- paste0("screen_flow_data(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
screeningplot_function <- paste0("plot_data_screening(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
missingingplot_function <- paste0("plot_missing_dates(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
# Add data tables
flow_screening_out <- results$Screening$Flow_Screening
flow_screening_out <- flow_screening_out[,!colnames(flow_screening_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = screening_sheet,
data = flow_screening_out,
title = paste0("Data Screening: Annual Summary Statistics (cubic metres per second) and Data Availability (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = screening_function)
# Add plots
add_plot(wb = output_excel,
sheet = screening_sheet,
plot = results$Screening$Flow_Screening_Plot[[1]],
title = paste0("Annual Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(flow_screening_out) + 2,
row = 2,
height = 5,
width = 8.5,
comment = screeningplot_function)
add_plot(wb = output_excel,
sheet = screening_sheet,
plot = results$Screening$Missing_Dates_Plot[[1]],
title = paste0("Number of Missing Dates Per Month (", start_year, "-", end_year, ")"),
col = ncol(flow_screening_out) + 2,
row = 29,
height = 4,
width = 8.5,
comment = missingingplot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = timeseries_sheet,
"Output" = "Daily Data Timeseries Table",
"Function" = data_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = timeseries_sheet,
"Output" = "Daily Data Timeseries Plot",
"Function" = data_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Data Screening Table",
"Function" = screening_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Annual Statistics for Screening Plot",
"Function" = screeningplot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Missing Data Plot",
"Function" = missingingplot_function)
}
### Long-term Stats
##########################
if (2 %in% analyses) {
# Add worksheet
lt_sheet <- "Long-term Daily Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = lt_sheet,
tabColour = "#73fbd3")
lt_mon_sheet <- "Long-term Monthly Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = lt_mon_sheet,
tabColour = "#73fbd3")
# Create fasstr function strings for output
longterm_mon_function <- paste0("calc_longterm_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longtermplot_mon_function <- paste0("plot_longterm_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longterm_function <- paste0("calc_longterm_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longtermplot_function <- paste0("plot_longterm_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
durationplot_function <- paste0("plot_flow_duration(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
monthmeanplot_function <- paste0("plot_monthly_means(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
# Add data tables
lt_stats_out <- results$Longterm$Longterm_Daily_Summary_Stats_Percentiles
lt_stats_out <- lt_stats_out[,!colnames(lt_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = lt_sheet,
data = lt_stats_out,
title = paste0("Long-term Summary Statistics of Daily Mean Flows, in cubic metres per second (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = longterm_function)
# Add plots
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Longterm_Daily_Summary_Stats_Plot[[1]],
title = paste0("Long-term Summary Statistics of Daily Mean Flows, in cubic metres per second (",
start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 2,
height = 4,
width = 10,
comment = longtermplot_function)
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Flow_Duration_Curves[[1]],
title = paste0("Flow Duration Curves (", start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 24,
height = 5,
width = 10,
comment = durationplot_function)
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Longterm_Monthly_Means_Plot[[1]],
title = paste0("Long-term Monthly Means (", start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 50,
height = 4,
width = 10,
comment = durationplot_function)
# Add data tables
lt_mon_stats_out <- results$Longterm$Longterm_Monthly_Summary_Stats_Percentiles
lt_mon_stats_out <- lt_mon_stats_out[,!colnames(lt_mon_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = lt_mon_sheet,
data = lt_mon_stats_out,
title = paste0("Long-term Summary Statistics of Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = longterm_function)
# Add plots
add_plot(wb = output_excel,
sheet = lt_mon_sheet,
plot = results$Longterm$Longterm_Monthly_Summary_Stats_Plot[[1]],
title = paste0("Long-term Summary Statistics of Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = ncol(lt_mon_stats_out) + 2,
row = 2,
height = 4,
width = 10,
comment = longtermplot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_mon_sheet,
"Output" = "Long-term Monthly Summary Statistics Table",
"Function" = longterm_mon_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_mon_sheet,
"Output" = "Long-term Monthly Summary Statistics Plot",
"Function" = longtermplot_mon_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Long-term Daily Summary Statistics Table",
"Function" = longterm_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Long-term Daily Summary Statistics Plot",
"Function" = longtermplot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Flow Duration Curves",
"Function" = durationplot_function)
}
### Annual Stats
##########################
if (3 %in% analyses) {
# Add worksheet
ann_stat_sheet <- "Annual Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_stat_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_stats_function <- paste0("calc_annual_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_plot_function <- paste0("plot_annual_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_mean_plot_function <- paste0("plot_annual_means(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
# Add data tables
ann_stats_out <- results$Annual$Annual_Summary_Stats[,!colnames(results$Annual$Annual_Summary_Stats) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_stat_sheet,
data = ann_stats_out,
title = paste0("Annual Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = annual_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = ann_stat_sheet,
plot = results$Annual$Annual_Summary_Stats_Plot[[1]],
title = paste0("Annual Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(ann_stats_out) + 2,
row = 2,
height = 3,
width = 8.5,
comment = annual_plot_function)
add_plot(wb = output_excel,
sheet = ann_stat_sheet,
plot = results$Annual$Annual_Means_Plot[[1]],
title = paste0("Annual Mean Flows In Relation to the Long-term Mean (", start_year, "-", end_year, ")"),
col = ncol(ann_stats_out) + 2,
row = 19,
height = 3,
width = 8.5,
comment = annual_mean_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Summary Statistics Table",
"Function" = annual_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Summary Statistics Plot",
"Function" = annual_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Mean Flows Plot",
"Function" = annual_mean_plot_function)
# Add worksheet
ann_cumul_sheet <- "Annual Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_cumul_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_vol_function <- paste0("calc_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_yield_function <- paste0("calc_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
", use_yield = TRUE",
fn_area,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_vol_plot_function <- paste0("plot_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_yield_plot_function <- paste0("plot_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
", use_yield = TRUE",
fn_area,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
# Add data tables
ann_cumul_out <- dplyr::left_join(results$Annual$Annual_Cumul_Volume_Stats_m3,
results$Annual$Annual_Cumul_Yield_Stats_mm,
by = c("STATION_NUMBER", "Year"))
ann_cumul_out <- ann_cumul_out[,!colnames(ann_cumul_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_cumul_sheet,
data = ann_cumul_out,
title = paste0("Annual Cumulative Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(annual_vol_function, " ", annual_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[1]],
title = paste0("Annual Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 2,
height = 2.2,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[1]],
title = paste0("Annual Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + ifelse(all(1:12 %in% months),8,0),
row = ifelse(all(1:12 %in% months),2,14),
height = 2.2,
width = 6,
comment = annual_yield_plot_function)
if (all(1:12 %in% months)) {
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[2]],
title = paste0("Seasonal (Two Seasons) Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 14,
height = 3,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[3]],
title = paste0("Seasonal (Four Seasons) Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 33,
height = 3,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[2]],
title = paste0("Seasonal (Two Seasons) Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + 8,
row = 14,
height = 3,
width = 6,
comment = annual_yield_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[3]],
title = paste0("Seasonal (Four Seasons) Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + 8,
row = 33,
height = 3,
width = 6,
comment = annual_yield_plot_function)
}
# Add worksheet
ann_oth_sheet <- "Annual Stats Other"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_oth_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_lows_function <- paste0("calc_annual_lowflows(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_lows_plot_function <- paste0("plot_annual_lowflows(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_timing_function <- paste0("calc_annual_flow_timing(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_timing_plot_function <- paste0("plot_annual_flow_timing(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_norm_function <- paste0("calc_annual_normal_days(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_norm_plot_function <- paste0("plot_annual_normal_days(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
# Add data tables
ann_other_out <- dplyr::left_join(results$Annual$Annual_Low_Flows,
results$Annual$Annual_Flow_Timing,
by = c("STATION_NUMBER", "Year"))
ann_other_out <- dplyr::left_join(ann_other_out,
results$Annual$Annual_Normal_Days,
by = c("STATION_NUMBER", "Year"))
ann_other_out <- ann_other_out[,!colnames(ann_other_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_oth_sheet,
data = ann_other_out,
title = paste0("Annual Low-flow Values (cubic metres per second) and Dates, Timing of Flows",
" (day of year), and Number Days Normal and Above/Below Normal (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(annual_lows_function, " ", annual_timing_function,
" ", annual_norm_function))
# Add plots
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Low_Flows_Plot[[1]],
title = paste0("Annual Low-flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2,
row = 2,
height = 5.5,
width = 6,
comment = annual_lows_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Low_Flows_Plot[[2]],
title = paste0("Day of Annual Low-flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2,
row = 31,
height = 5.5,
width = 6,
comment = annual_lows_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Flow_Timing_Plot[[1]],
title = paste0("Annual Timing of Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2 + 8,
row = 2,
height = 5.5,
width = 6,
comment = annual_timing_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Normal_Days_Plot[[1]],
title = paste0("Annual Days Per Year Above, Below, and Outside Normal (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2 + 8,
row = 31,
height = 3.5,
width = 7,
comment = annual_norm_plot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Volumes Table",
"Function" = annual_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Yields Table",
"Function" = annual_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Volumes Plots",
"Function" = annual_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Yields Plots",
"Function" = annual_yield_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Low-Flows Table",
"Function" = annual_lows_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Low-Flows Plot",
"Function" = annual_lows_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Timing-of-Flows Table",
"Function" = annual_timing_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Timing-of-Flows Plot",
"Function" = annual_timing_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Days Outside Normal Table",
"Function" = annual_norm_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Days Outside Normal Plot",
"Function" = annual_norm_plot_function)
}
### Monthly Stats
##########################
if (4 %in% analyses) {
# Add worksheet
month_stat_sheet <- "Monthly Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = month_stat_sheet,
tabColour = "#59d2fe")
# Create fasstr function strings for output
month_stats_function <- paste0("calc_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_mon,
fn_complete,
")")
month_stats_plot_function <- paste0("plot_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_mon,
fn_complete,
")")
# Add data tables
mon_stats_out <- suppressWarnings(calc_monthly_stats(data = flow_data_raw,
start_year = start_year,
end_year = end_year,
exclude_years = exclude_years,
water_year_start = water_year_start,
ignore_missing = ignore_missing,
complete_years = complete_years,
spread = TRUE))
mon_stats_out <- mon_stats_out[,!colnames(mon_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = month_stat_sheet,
data = mon_stats_out,
title = paste0("Monthly Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = month_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[1]],
title = paste0("Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2,
row = 2,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[2]],
title = paste0("Monthly Median Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2,
row = 29,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[3]],
title = paste0("Monthly Maximum Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2 + 12,
row = 2,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[4]],
title = paste0("Monthly Minimum Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2 + 12,
row = 29,
height = 5,
width = 9,
comment = month_stats_plot_function)
# Add worksheet
month_cumul_sheet <- "Monthly Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = month_cumul_sheet,
tabColour = "#59d2fe")
# Create fasstr function strings for output
month_vol_function <- paste0("calc_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
month_vol_plot_function <- paste0("plot_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
month_yield_function <- paste0("calc_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
month_yield_plot_function <- paste0("plot_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
# Add data tables
mon_vol_out <- results$Monthly$Monthly_Total_Cumul_Volume_m3[,!colnames(results$Monthly$Monthly_Total_Cumul_Volume_m3) %in% "STATION_NUMBER"]
mon_vol_out <- mon_vol_out[,!colnames(mon_vol_out) %in% "STATION_NUMBER"]
mon_vol_out <- tidyr::gather(mon_vol_out, Statistic, Value, -1)
mon_vol_out <- dplyr::mutate(mon_vol_out,
Statistic = paste0(Statistic, "_Volume_m3"),
Statistic = factor(Statistic, levels = unique(Statistic)))
mon_vol_out <- tidyr::spread(mon_vol_out, Month, Value)
mon_yield_out <- results$Monthly$Monthly_Total_Cumul_Yield_mm[,!colnames(results$Monthly$Monthly_Total_Cumul_Yield_mm) %in% "STATION_NUMBER"]
mon_yield_out <- mon_yield_out[,!colnames(mon_yield_out) %in% "STATION_NUMBER"]
mon_yield_out <- tidyr::gather(mon_yield_out, Statistic, Value, -1)
mon_yield_out <- dplyr::mutate(mon_yield_out,
Statistic = paste0(Statistic, "_Yield_mm"),
Statistic = factor(Statistic, levels = unique(Statistic)))
mon_yield_out <- tidyr::spread(mon_yield_out, Month, Value)
mon_cumul_out <- suppressWarnings(dplyr::bind_rows(mon_vol_out, mon_yield_out))
add_table(wb = output_excel,
sheet = month_cumul_sheet,
data = mon_cumul_out,
title = paste0("Annual Cumulative Monthly Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(month_vol_function, " ", month_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = month_cumul_sheet,
plot = results$Monthly$Monthly_Total_Cumul_Volume_m3_Plot[[1]],
title = paste0("Annual Cumulative Monthly Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_cumul_out) + 2,
row = 2,
height = 4,
width = 9,
comment = month_vol_plot_function)
add_plot(wb = output_excel,
sheet = month_cumul_sheet,
plot = results$Monthly$Monthly_Total_Cumul_Yield_mm_Plot[[1]],
title = paste0("Annual Cumulative Monthly Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(mon_cumul_out) + 2,
row = 24,
height = 4,
width = 9,
comment = month_yield_plot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_stat_sheet,
"Output" = "Monthly Summary Statistics Table",
"Function" = month_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_stat_sheet,
"Output" = "Monthly Summary Statistics Plot",
"Function" = month_stats_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Volumes Table",
"Function" = month_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Volumes Plot",
"Function" = month_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Yields Table",
"Function" = month_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Yields Plot",
"Function" = month_yield_plot_function)
}
### Daily Stats
##########################
if (5 %in% analyses) {
# Create folder for plots if it doesn't exist
plot_dir <- paste0(file_name, " Plots/")
if (!dir.exists(plot_dir)) {
message(paste0("** creating folder '", plot_dir ,"' for additional plots"))
}
dir.create(path = plot_dir, showWarnings = FALSE)
# Add worksheet
day_stats_sheet <- "Daily Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = day_stats_sheet,
tabColour = "#4a8fe7")
# Create fasstr function strings for output
daily_stats_function <- paste0("calc_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
daily_stats_plot_function <- paste0("plot_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
# Add data tables
day_stats_out <- results$Daily$Daily_Summary_Stats[,!colnames(results$Daily$Daily_Summary_Stats) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = day_stats_sheet,
data = day_stats_out,
title = paste0("Daily Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = daily_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = day_stats_sheet,
plot = results$Daily$Daily_Summary_Stats_Plot[[1]],
title = paste0("Daily Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(day_stats_out) + 2,
row = 2,
height = 5,
width = 10,
comment = daily_stats_plot_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Daily_Statistics_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Statistics_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Summary_Stats_with_Years,
folder_name = paste0(plot_dir, "Daily_Statistics_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
# Add worksheet
day_cumul_sheet <- "Daily Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = day_cumul_sheet,
tabColour = "#4a8fe7")
# Create fasstr function strings for output
daily_vol_function <- paste0("calc_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
daily_vol_plot_function <- paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
daily_yield_function <- paste0("calc_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
daily_yield_plot_function <- paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
# Add data tables
day_vol_out <- results$Daily$Daily_Total_Cumul_Volume_m3[,!colnames(results$Daily$Daily_Total_Cumul_Volume_m3) %in% "STATION_NUMBER"]
day_vol_out <- day_vol_out[,!colnames(day_vol_out) %in% "STATION_NUMBER"]
day_vol_out <- tidyr::gather(day_vol_out, Statistic, Value, -(1:2))
day_vol_out <- dplyr::mutate(day_vol_out, Statistic = paste0(Statistic, "_Volume_m3"))
order <- unique(day_vol_out$Statistic)
day_vol_out <- tidyr::spread(day_vol_out, Statistic, Value)
day_vol_out <- dplyr::select(day_vol_out, Date, DayofYear, order)
day_vol_out <- dplyr::arrange(day_vol_out, DayofYear)
day_yield_out <- results$Daily$Daily_Total_Cumul_Yield_mm[,!colnames(results$Daily$Daily_Total_Cumul_Yield_mm) %in% "STATION_NUMBER"]
day_yield_out <- day_yield_out[,!colnames(day_yield_out) %in% "STATION_NUMBER"]
day_yield_out <- tidyr::gather(day_yield_out, Statistic, Value, -(1:2))
day_yield_out <- dplyr::mutate(day_yield_out, Statistic = paste0(Statistic, "_Yield_mm"))
order <- unique(day_yield_out$Statistic)
day_yield_out <- tidyr::spread(day_yield_out, Statistic, Value)
day_yield_out <- dplyr::select(day_yield_out, Date, DayofYear, order)
day_yield_out <- dplyr::arrange(day_yield_out, DayofYear)
day_cumul_out <- dplyr::left_join(day_vol_out, day_yield_out, by = c("Date", "DayofYear"))
add_table(wb = output_excel,
sheet = day_cumul_sheet,
data = day_cumul_out,
title = paste0("Annual Cumulative Daily Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(daily_vol_function, " ", daily_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = day_cumul_sheet,
plot = results$Daily$Daily_Total_Cumul_Volume_m3_Plot[[1]],
title = paste0("Annual Cumulative Daily Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(day_cumul_out) + 2,
row = 2,
height = 4,
width = 9,
comment = daily_vol_plot_function)
add_plot(wb = output_excel,
sheet = day_cumul_sheet,
plot = results$Daily$Daily_Total_Cumul_Yield_mm_Plot[[1]],
title = paste0("Annual Cumulative Daily Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(day_cumul_out) + 2,
row = 24,
height = 4,
width = 9,
comment = daily_yield_plot_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Daily_Cumulative_Volume_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Cumulative_Volume_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Total_Cumul_Volume_m3_with_Years,
folder_name = paste0(plot_dir, "Daily_Cumulative_Volume_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
if (plot_filetype == "pdf") {
message("** writing 'Daily_Cumulative_Yield_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Cumulative_Yield_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Total_Cumul_Yield_mm_with_Years,
folder_name = paste0(plot_dir, "Daily_Cumulative_Yield_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Table",
"Function" = daily_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Plot",
"Function" = daily_stats_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Plot with Year",
"Function" = paste0("plot_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
", include_year = ", start_year,
")"))
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Table",
"Function" = daily_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Plot",
"Function" = daily_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Plot with Year",
"Function" = paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", include_year = ", start_year,
")"))
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Table",
"Function" = daily_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Plot",
"Function" = daily_yield_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Plot with Year",
"Function" = paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
", include_year = ", start_year,
")"))
}
# ### Annual Trending
##########################
if (6 %in% analyses) {
# Create folder for plots if it doesn't exist
plot_dir <- paste0(file_name, " Plots/")
if (!dir.exists(plot_dir)) {
message(paste0("** creating folder '", plot_dir ,"' for additional plots"))
}
dir.create(path = plot_dir, showWarnings = FALSE)
# Add worksheet
trends_sheet <- "Annual Trends"
openxlsx::addWorksheet(wb = output_excel,
sheetName = trends_sheet,
tabColour = "#5c7aff")
# Create fasstr function strings for output
trends_function <- paste0("compute_annual_trends(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_area,
", zyp_method = '", zyp_method, "'",
", zyp_alpha = ", zyp_alpha,
fn_missing,
fn_allowmiss_ann_trend,
fn_allowmiss_mon_trend,
fn_complete,
")")
# Add data tables
trends_out <- dplyr::left_join(results$Trending$Annual_Trends_Results,
results$Trending$Annual_Trends_Data,
by = c("STATION_NUMBER", "Statistic"))
trends_out <- trends_out[,!colnames(trends_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = trends_sheet,
data = trends_out,
title = paste0("Annual Trending Statistics Results using '", zyp_method,
"' Prewhitening Method, and Annual Values (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = trends_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Annual_Trends_Results_Plots.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Annual_Trends_Results_Plots' folder"))
}
suppressMessages(
write_plots(plots = results$Trending$Annual_Trends_Plots,
folder_name = paste0(plot_dir , "Annual_Trends_Results_Plots"),
plot_filetype = plot_filetype,
width = 8.5,
height = 3,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = trends_sheet,
"Output" = "Annual Trends Tables and Plots",
"Function" = trends_function)
}
### Low Flow Frequency
##########################
if (7 %in% analyses) {
# Check if there is sufficient data for frequency analysis
data_check <- suppressWarnings(
calc_annual_lowflows(data = flow_data_raw,
start_year = start_year, end_year = end_year, exclude_years = exclude_years,
water_year_start = water_year_start,
ignore_missing = ignore_missing,
complete_years = complete_years,
allowed_missing = allowed_missing_annual)
)
data_check <- dplyr::select(data_check, Min_1_Day, Min_3_Day, Min_7_Day, Min_30_Day)
if (any(as.numeric(colSums(!is.na(data_check))) < 3)) {
warning("Not enough annual data (3 years) for frequency analysis. Consider filtering for appropriate years or use ignore_missing = TRUE,",
call. = FALSE)
} else {
# Add worksheet
freq_sheet <- "Low-flow Frequencies"
openxlsx::addWorksheet(wb = output_excel,
sheetName = freq_sheet,
tabColour = "#5c7aff")
# Create fasstr function strings for output
frequency_function <- paste0("compute_annual_frequencies(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", roll_days = c(1,3,7,30,60)",
", prob_plot_position = 'weibull'",
", fit_distr = 'PIII'",
", fit_distr_method = 'MOM'",
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
# Add data tables
freq_ann_data_out <- tidyr::spread(results$Lowflow_Frequencies$Freq_Analysis_Data, Measure, Value)
freq_ann_data_out <- freq_ann_data_out[,!colnames(freq_ann_data_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_ann_data_out,
title = paste0("Annual Low-flow Values (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(frequency_function, "[[1]]"))
freq_plot_data_out <- results$Lowflow_Frequencies$Freq_Plot_Data[,!colnames(results$Lowflow_Frequencies$Freq_Plot_Data) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_plot_data_out,
title = paste0("Annual Low-flow Value Probabilities for Plotting using 'weibull' Plotting Positions (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2,
row = 1,
comment = paste0(frequency_function, "[[2]]"))
freq_quantiles_out <- results$Lowflow_Frequencies$Freq_Fitted_Quantiles[,!colnames(results$Lowflow_Frequencies$Freq_Fitted_Quantiles) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_quantiles_out,
title = paste0("Fitted Flow Quantiles using a logPIII Distribution with Method of Moments Fitting (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2 + ncol(freq_plot_data_out) + 1 + 11,
row = 1,
comment = paste0(frequency_function, "[[5]]"))
# Add plots
add_plot(wb = output_excel,
sheet = freq_sheet,
plot = results$Lowflow_Frequencies$Freq_Plot,
title = paste0("Annual Low-flow Value Probabilities and Return Periods using 'weibull' Plotting Positions (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2 + ncol(freq_plot_data_out) + 1,
row = 1,
height = 5,
width = 7,
comment = paste0(frequency_function, "[[3]]"))
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = freq_sheet,
"Output" = "Low-Flow Frequency Analysis Tables and Plots",
"Function" = frequency_function)
}
}
# Write the analysis information
##########################
## Create a meta data file of the analysis arguments
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "fasstr Full Analysis Results",
startCol = 1, startRow = 1)
openxlsx::addStyle(wb = output_excel, sheet = overview_sheet, cols = 1, rows = 1,
style = openxlsx::createStyle(fontSize = 12,
textDecoration = "bold"))
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = paste0("Analysis Date: ",as.character(Sys.time())),
startCol = 1, startRow = 2)
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "fasstr 0.3.0",
startCol = 1, startRow = 3)
metadata <- list(data = ifelse(!is.null(data), as.character(substitute(data)), ""),
dates = as.character(substitute(Date)),
values = as.character(substitute(Value)),
groups = as.character(substitute(STATION_NUMBER)),
station_number = ifelse(!is.null(station_number), toupper(station_number), ""),
basin_area = basin_area_stn,
water_year_start = water_year_start,
start_year = start_year,
end_year = end_year,
exclude_years = paste0(ifelse(!is.null(exclude_years),
paste0(ifelse(length(exclude_years) == 1,
paste(exclude_years),
paste(exclude_years, collapse = ", "))),
"")),
ignore_missing = ignore_missing,
zyp_method = zyp_method,
zyp_alpha = ifelse(!is.na(zyp_alpha), zyp_alpha, ""),
analyses = analyses,
file_name = paste0(file_name, ".xlsx"),
plot_filetype = plot_filetype,
analysis_function = analysis_function)
metadata <- data.frame("Argument" = names(metadata),
"Option" = as.character(unname(metadata)))
metadata <- metadata[c(1,5,2:4,6:nrow(metadata)),]
add_table(wb = output_excel,
sheet = overview_sheet,
data = metadata,
title = paste0("Analysis Overview"),
col = 1,
row = 5)
if (5 %in% analyses | 6 %in% analyses) {
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "Click for additional plots:",
startCol = 1, startRow = 25)
link <- normalizePath(plot_dir)
class(link) <- "hyperlink"
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = link,
startCol = 1, startRow = 26)
}
if (!is.null(station_number)) {
hydat_info <- dplyr::left_join(tidyhydat::hy_stations(station_number),
tidyhydat::hy_stn_regulation(station_number),
by = "STATION_NUMBER")
hydat_info <- dplyr::select(hydat_info, STATION_NUMBER, STATION_NAME, PROV_TERR_STATE_LOC, HYD_STATUS,
LATITUDE, LONGITUDE, DRAINAGE_AREA_GROSS, REGULATED, RHBN, REAL_TIME)
hydat_info <- dplyr::mutate(hydat_info, HYDAT_VERSION = as.character(dplyr::pull(tidyhydat::hy_version()[,2])))
hydat_info <- tidyr::gather(hydat_info, "Station Attribute", Info)
add_table(wb = output_excel,
sheet = overview_sheet,
data = hydat_info,
title = paste0("HYDAT Station Information"),
col = 5,
row = 5)
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = c(5,6), widths = "auto")
}
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = 1, widths = 31)
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = 2, widths = 17)
# Write the fasstr functions
##########################
fasstr_sheet <- "fasstr Functions"
openxlsx::addWorksheet(wb = output_excel,
sheetName = fasstr_sheet,
tabColour = "#003e1f")
add_table(wb = output_excel,
sheet = fasstr_sheet,
data = fasstr_functions,
title = paste0("fasstr Functions"),
col = 1,
row = 1,
comment = "Copy and paste a function into R to reproduce or further customize results")
openxlsx::setColWidths(wb = output_excel, sheet = fasstr_sheet, cols = 1:3, widths = "auto")
# Save the workbook
##########################
message(paste0("** writing analysis results in '", file_name, ".xlsx'"))
openxlsx::saveWorkbook(wb = output_excel,
file = paste0(file_name, ".xlsx"),
overwrite = TRUE)
if (5 %in% analyses | 6 %in% analyses) {
message(paste0("* DONE. For analysis results go to: '", normalizePath(paste0(file_name, ".xlsx")),
"' and '", normalizePath(plot_dir), "' folder"))
} else {
message(paste0("* DONE. For analysis results go to: '", normalizePath(paste0(file_name, ".xlsx"))))
}
}
Try the fasstr package in your browser
Any scripts or data that you put into this service are public.
fasstr documentation built on March 31, 2023, 10:25 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions write_full_analysis
Documented in write_full_analysis
# 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 Write a suite of tables and plots from various fasstr functions into a directory
#'
#' @description Calculates and writes tables and plots from a suite of statistics from \code{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 \code{ignore_missing = FALSE} (default) and there is missing data,
#' some tables and plots may be empty and produce warnings. Use \code{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.
#'
#' @inheritParams compute_full_analysis
#' @param 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.
#' @param plot_filetype Image type to write. One of \code{'png'}, \code{'eps'}, \code{'ps'}, \code{'tex'}, \code{'pdf'},
#' \code{'jpeg'}, \code{'tiff'}, \code{'bmp'}, or \code{'svg'}. If not \code{'pdf'} then individual plots will be created instead
#' of a combined PDF. Default \code{'pdf'}.
#'
#' @seealso \code{\link{compute_full_analysis}},
#' \code{\link{screen_flow_data}},
#' \code{\link{plot_data_screening}},
#' \code{\link{plot_missing_dates}},
#' \code{\link{calc_longterm_monthly_stats}},
#' \code{\link{plot_longterm_monthly_stats}},
#' \code{\link{calc_longterm_daily_stats}},
#' \code{\link{plot_longterm_daily_stats}},
#' \code{\link{plot_monthly_means}},
#' \code{\link{plot_flow_duration}},
#' \code{\link{calc_annual_stats}},
#' \code{\link{plot_annual_stats}},
#' \code{\link{calc_annual_cumulative_stats}},
#' \code{\link{plot_annual_cumulative_stats}},
#' \code{\link{calc_annual_flow_timing}},
#' \code{\link{plot_annual_flow_timing}},
#' \code{\link{calc_annual_normal_days}},
#' \code{\link{plot_annual_normal_days}},
#' \code{\link{calc_annual_lowflows}},
#' \code{\link{plot_annual_lowflows}},
#' \code{\link{plot_annual_means}},
#' \code{\link{calc_monthly_stats}},
#' \code{\link{plot_monthly_stats}},
#' \code{\link{calc_monthly_cumulative_stats}},
#' \code{\link{plot_monthly_cumulative_stats}},
#' \code{\link{calc_daily_stats}},
#' \code{\link{plot_daily_stats}},
#' \code{\link{calc_daily_cumulative_stats}},
#' \code{\link{plot_daily_cumulative_stats}},
#' \code{\link{compute_annual_trends}},
#' \code{\link{compute_annual_frequencies}},
#' \code{\link{write_flow_data}},
#' \code{\link{write_plots}}
#'
#' @examples
#' \dontrun{
#'
#' # 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))
#'
#' }
#' @export
write_full_analysis <- function(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'){
## 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
}
if (missing(basin_area)) {
basin_area <- NA
}
if (missing(zyp_alpha)) {
zyp_alpha <- NA
}
water_year_checks(water_year_start)
years_checks(start_year, end_year, exclude_years)
logical_arg_check(ignore_missing)
allowed_missing_checks(allowed_missing_annual, ignore_missing)
allowed_missing_checks(allowed_missing_monthly, ignore_missing)
months_checks(months)
logical_arg_check(complete_years)
if (complete_years) {
if (ignore_missing | allowed_missing_annual > 0 | allowed_missing_monthly > 0) {
ignore_missing <- FALSE
allowed_missing_annual <- 0
allowed_missing_monthly <- 0
message("complete_years argument overrides ignore_missing and allowed_missing_* arguments.")
}
}
if (missing(file_name)) stop("A file name is required with the file_name argument to write all results.", call. = FALSE)
if (!is.numeric(analyses))
stop("analyses argument must be numbers between 1 and 7. See ?write_full_analysis for analysis group numbers.", call. = FALSE)
if (!all(analyses %in% 1:7))
stop("analyses argument must be numbers between 1 and 7. See ?write_full_analysis for analysis group numbers.", call. = FALSE)
if (6 %in% analyses) {
zyp_alpha_checks(zyp_alpha)
zyp_method_checks(zyp_method)
}
# Do this for now, until looping of include_year plots is sorted out
if (length(station_number) > 1) stop("Only one station_number can be listed.", call. = FALSE)
message("* this may take a few moments...")
## FLOW DATA CHECKS AND FORMATTING
## -------------------------------
# Check if data is provided and import it
flow_data_source <- flowdata_import(data = data,
station_number = station_number)
flow_data_raw <- flow_data_source
# Save the original columns (to check for STATION_NUMBER col at end) and ungroup if necessary
orig_cols <- names(flow_data_raw)
flow_data_raw <- dplyr::ungroup(flow_data_raw)
# Check and rename columns
flow_data_raw <- format_all_cols(data = flow_data_raw,
dates = as.character(substitute(dates)),
values = as.character(substitute(values)),
groups = as.character(substitute(groups)),
rm_other_cols = TRUE)
# # Data setup
flow_data_unfiltered <- fill_missing_dates(data = flow_data_raw, water_year_start = water_year_start)
flow_data_unfiltered <- add_date_variables(data = flow_data_unfiltered, water_year_start = water_year_start)
flow_data_unfiltered <- add_rolling_means(data = flow_data_unfiltered)
#
# # Set up basin_area
flow_data_unfiltered <- add_basin_area(flow_data_unfiltered, basin_area = basin_area)
basin_area_stn <- unique(flow_data_unfiltered$Basin_Area_sqkm)[1]
# Get the start and end years of the data to make a list of all included years
flow_data_filtered <- flow_data_unfiltered
flow_data_filtered <- analysis_prep(data = flow_data_filtered,
water_year_start = water_year_start)
if (start_year < min(flow_data_filtered$WaterYear)) {
start_year <- min(flow_data_filtered$WaterYear)
}
if (end_year > max(flow_data_filtered$WaterYear)) {
end_year <- max(flow_data_filtered$WaterYear)
}
# flow_data_plus <- dplyr::filter(flow_data, WaterYear >= start_year - 1 & WaterYear <= end_year + 1)
flow_data_filtered <- dplyr::filter(flow_data_filtered,
WaterYear >= start_year & WaterYear <= end_year,
!(WaterYear %in% exclude_years))
if (any(is.na(flow_data_filtered$Value)) & !ignore_missing) {
message("** warning: selected data contains dates with missing values; some NAs in tables and gaps in plots may be produced")
}
# Create function for condensing consecutive numbers
conseq_fn <- function(s){
dif <- s[seq(length(s))][-1] - s[seq(length(s)-1)]
new <- !c(0, dif == 1)
cs <- cumsum(new)
res <- vector(mode="list", max(cs))
for(i in seq(res)){
s.i <- s[which(cs == i)]
if(length(s.i) > 2){
res[[i]] <- paste(min(s.i), max(s.i), sep=":")
} else {
res[[i]] <- as.character(s.i)
}
}
paste0(ifelse(length(s)==1,paste(s),paste0("c(", paste(unlist(res), collapse=","), ")")))
}
# Create list of all objects
message("** creating data frames and plots")
### Compute results
##########################
results <- suppressMessages(
compute_full_analysis(data = flow_data_raw,
dates = "Date",
values = "Value",
groups = "STATION_NUMBER",
analyses = analyses,
basin_area = basin_area,
water_year_start = water_year_start,
start_year = start_year,
end_year = end_year,
exclude_years = exclude_years,
months = months,
ignore_missing = ignore_missing,
complete_years = complete_years,
allowed_missing_annual = allowed_missing_annual,
allowed_missing_monthly = allowed_missing_monthly,
zyp_method = zyp_method,
zyp_alpha = zyp_alpha)
)
### Writing Functions
##########################
# Create add table function
add_table <- function(wb, sheet, data, title, col, row, comment = NA) {
openxlsx::writeData(wb = wb, sheet = sheet, x = title, startCol = col, startRow = row)
openxlsx::writeData(wb = wb, sheet = sheet, x = data, startCol = col, startRow = row + 1,
headerStyle = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold",
border = "TopBottom",
fgFill = "#add8e6",
halign = "left"))
openxlsx::addStyle(wb = wb, sheet = sheet, cols = col, rows = row,
style = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold"))
if (!is.na(comment)) {
openxlsx::writeComment(wb = wb, sheet = sheet, col = col, row = row,
comment = openxlsx::createComment(comment = comment,
visible = FALSE,
width = 5,
height = 4))
}
}
# Create add plot function
add_plot <- function(wb, sheet, plot, title, col, row, height, width, comment = NA) {
openxlsx::writeData(wb = wb, sheet = sheet, x = title, startCol = col, startRow = row)
print(plot)
openxlsx::insertPlot(wb = wb, sheet = sheet, startCol = col, startRow = row + 1, height = height, width = width)
openxlsx::addStyle(wb = wb, sheet = sheet, cols = col, rows = row,
style = openxlsx::createStyle(fontSize = 11,
textDecoration = "bold"))
if (!is.na(comment)) {
openxlsx::writeComment(wb = wb, sheet = sheet, col = col, row = row,
comment = openxlsx::createComment(comment = comment,
visible = FALSE,
width = 5,
height = 4))
}
}
### Setup dataframe and values for writing the fasstr functions
##########################
fasstr_functions <- data.frame("Worksheet" = character(), "Output" = character(), "Function" = character())
# Create some values for creating character versions of fasstr functions
fn_data <- paste0(ifelse(!is.null(data),
paste0("data = ", as.character(substitute(data)),
ifelse(as.character(substitute(dates)) != "Date",
paste0(", dates = '", as.character(substitute(dates)), "'"), ""),
ifelse(as.character(substitute(values)) != "Value",
paste0(", values = '", as.character(substitute(values)), "'"), ""),
ifelse(as.character(substitute(groups)) != "STATION_NUMBER",
paste0(", groups = '", as.character(substitute(groups)), "'"), "")),
paste0("station_number = '", station_number, "'")))
fn_area <- paste0(ifelse(!is.na(basin_area),
paste0(", basin_area = ", basin_area),
""))
fn_wys <- ifelse(water_year_start != 1, paste0(", water_year_start = ", water_year_start), "")
fn_startend <- paste0(ifelse(start_year != min(flow_data_unfiltered$WaterYear),
paste0(", start_year = ", start_year), ""),
ifelse(end_year != max(flow_data_unfiltered$WaterYear),
paste0(", end_year = ", end_year), ""))
fn_exclude <- paste0(ifelse(!is.null(exclude_years),
paste0(", exclude_years = ", ifelse(length(exclude_years) == 1,
paste(exclude_years),
paste0("c(",paste(exclude_years, collapse = ","),")"))),
""))
fn_months <- ifelse(all(1:12 %in% months),
paste(""),
paste0(", months = ", conseq_fn(months)))
fn_missing <- ifelse(ignore_missing, paste0(", ignore_missing = TRUE"), "")
fn_allowmiss_ann <- ifelse(allowed_missing_annual > 0 , paste0(", allowed_missing = ", allowed_missing_annual), "")
fn_allowmiss_mon <- ifelse(allowed_missing_monthly > 0 , paste0(", allowed_missing = ", allowed_missing_monthly), "")
fn_allowmiss_ann_trend <- ifelse(allowed_missing_annual > 0 , paste0(", allowed_missing_annual = ", allowed_missing_annual), "")
fn_allowmiss_mon_trend <- ifelse(allowed_missing_monthly > 0 , paste0(", allowed_missing_monthly = ", allowed_missing_monthly), "")
fn_complete <- ifelse(complete_years, paste0(", complete_years = TRUE"), "")
fn_zyp <- paste0(", zyp_method = '", zyp_method, "'",
", zyp_alpha = ", ifelse(!is.na(zyp_alpha), zyp_alpha, "NA"))
# Create fasstr function strings for output
analysis_function <- paste0("compute_full_analysis(",
fn_data,
fn_area,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
ifelse(6 %in% analyses, fn_zyp, ""),
ifelse(all(1:7 %in% analyses),
paste(", analyses = c(1:7)"),
paste0(", analyses = ", conseq_fn(analyses))),
")")
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = paste0(file_name,".xlsx"),
"Output" = "Full Analysis Function",
"Function" = analysis_function)
### Excel workbook Setup
##########################
# Create the excel document and first worksheet
output_excel <- openxlsx::createWorkbook()
overview_sheet <- "Analysis Overview"
openxlsx::addWorksheet(wb = output_excel,
sheetName = overview_sheet,
tabColour = "#003e1f") # 73fbd3 44e5e7 59d2fe 4a8fe7 5c7aff
# Add raw data to first worksheet
rawdata_sheet <- "Data Input"
openxlsx::addWorksheet(wb = output_excel,
sheetName = rawdata_sheet,
tabColour = "#003e1f")
add_table(wb = output_excel,
sheet = rawdata_sheet,
data = flow_data_source,
title = "Source Daily Data",
col = 1,
row = 1,
comment = NA)
openxlsx::setColWidths(wb = output_excel, sheet = rawdata_sheet,
cols = seq_len(ncol(flow_data_source)), widths = 11)
## Screening
##########################
if (1 %in% analyses) {
# Add worksheet
timeseries_sheet <- "Data Timeseries"
openxlsx::addWorksheet(wb = output_excel,
sheetName = timeseries_sheet,
tabColour = "#73ba9b")
# Create fasstr function strings for output
data_function <- paste0("add_date_variables(",
fn_data,
fn_wys,
") %>% add_rolling_means() %>% add_basin_area(",
paste0(ifelse(!is.na(basin_area),
paste0("basin_area = ", basin_area),
"")),
")")
data_plot_function <- paste0("plot_flow_data(",
fn_data,
fn_wys,
fn_exclude,
")")
# Add data tables
flow_data_out <- flow_data_filtered[,!colnames(flow_data_filtered) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = timeseries_sheet,
data = flow_data_out,
title = paste0("Daily Flows, Dates, Rolling Means (cubic metres per second), and Basin Area (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = data_function)
openxlsx::setColWidths(wb = output_excel, sheet = timeseries_sheet,
cols = seq_len(ncol(flow_data_source)), widths = 12)
# Add plots
add_plot(wb = output_excel,
sheet = timeseries_sheet,
plot = results$Screening$Daily_Flows_Plot[[1]],
title = paste0("Daily Flows (", start_year, "-", end_year, ")"),
col = ncol(flow_data_out) + 2,
row = 2,
height = 5,
width = 20,
comment = data_plot_function)
# Add worksheet
screening_sheet <- "Data Screening"
openxlsx::addWorksheet(wb = output_excel,
sheetName = screening_sheet,
tabColour = "#73ba9b")
# Create fasstr function strings for output
screening_function <- paste0("screen_flow_data(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
screeningplot_function <- paste0("plot_data_screening(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
missingingplot_function <- paste0("plot_missing_dates(",
fn_data,
fn_wys,
fn_startend,
fn_months,
")")
# Add data tables
flow_screening_out <- results$Screening$Flow_Screening
flow_screening_out <- flow_screening_out[,!colnames(flow_screening_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = screening_sheet,
data = flow_screening_out,
title = paste0("Data Screening: Annual Summary Statistics (cubic metres per second) and Data Availability (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = screening_function)
# Add plots
add_plot(wb = output_excel,
sheet = screening_sheet,
plot = results$Screening$Flow_Screening_Plot[[1]],
title = paste0("Annual Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(flow_screening_out) + 2,
row = 2,
height = 5,
width = 8.5,
comment = screeningplot_function)
add_plot(wb = output_excel,
sheet = screening_sheet,
plot = results$Screening$Missing_Dates_Plot[[1]],
title = paste0("Number of Missing Dates Per Month (", start_year, "-", end_year, ")"),
col = ncol(flow_screening_out) + 2,
row = 29,
height = 4,
width = 8.5,
comment = missingingplot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = timeseries_sheet,
"Output" = "Daily Data Timeseries Table",
"Function" = data_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = timeseries_sheet,
"Output" = "Daily Data Timeseries Plot",
"Function" = data_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Data Screening Table",
"Function" = screening_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Annual Statistics for Screening Plot",
"Function" = screeningplot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = screening_sheet,
"Output" = "Missing Data Plot",
"Function" = missingingplot_function)
}
### Long-term Stats
##########################
if (2 %in% analyses) {
# Add worksheet
lt_sheet <- "Long-term Daily Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = lt_sheet,
tabColour = "#73fbd3")
lt_mon_sheet <- "Long-term Monthly Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = lt_mon_sheet,
tabColour = "#73fbd3")
# Create fasstr function strings for output
longterm_mon_function <- paste0("calc_longterm_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longtermplot_mon_function <- paste0("plot_longterm_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longterm_function <- paste0("calc_longterm_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
longtermplot_function <- paste0("plot_longterm_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
durationplot_function <- paste0("plot_flow_duration(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
monthmeanplot_function <- paste0("plot_monthly_means(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
# Add data tables
lt_stats_out <- results$Longterm$Longterm_Daily_Summary_Stats_Percentiles
lt_stats_out <- lt_stats_out[,!colnames(lt_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = lt_sheet,
data = lt_stats_out,
title = paste0("Long-term Summary Statistics of Daily Mean Flows, in cubic metres per second (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = longterm_function)
# Add plots
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Longterm_Daily_Summary_Stats_Plot[[1]],
title = paste0("Long-term Summary Statistics of Daily Mean Flows, in cubic metres per second (",
start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 2,
height = 4,
width = 10,
comment = longtermplot_function)
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Flow_Duration_Curves[[1]],
title = paste0("Flow Duration Curves (", start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 24,
height = 5,
width = 10,
comment = durationplot_function)
add_plot(wb = output_excel,
sheet = lt_sheet,
plot = results$Longterm$Longterm_Monthly_Means_Plot[[1]],
title = paste0("Long-term Monthly Means (", start_year, "-", end_year, ")"),
col = ncol(lt_stats_out) + 2,
row = 50,
height = 4,
width = 10,
comment = durationplot_function)
# Add data tables
lt_mon_stats_out <- results$Longterm$Longterm_Monthly_Summary_Stats_Percentiles
lt_mon_stats_out <- lt_mon_stats_out[,!colnames(lt_mon_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = lt_mon_sheet,
data = lt_mon_stats_out,
title = paste0("Long-term Summary Statistics of Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = longterm_function)
# Add plots
add_plot(wb = output_excel,
sheet = lt_mon_sheet,
plot = results$Longterm$Longterm_Monthly_Summary_Stats_Plot[[1]],
title = paste0("Long-term Summary Statistics of Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = ncol(lt_mon_stats_out) + 2,
row = 2,
height = 4,
width = 10,
comment = longtermplot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_mon_sheet,
"Output" = "Long-term Monthly Summary Statistics Table",
"Function" = longterm_mon_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_mon_sheet,
"Output" = "Long-term Monthly Summary Statistics Plot",
"Function" = longtermplot_mon_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Long-term Daily Summary Statistics Table",
"Function" = longterm_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Long-term Daily Summary Statistics Plot",
"Function" = longtermplot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = lt_sheet,
"Output" = "Flow Duration Curves",
"Function" = durationplot_function)
}
### Annual Stats
##########################
if (3 %in% analyses) {
# Add worksheet
ann_stat_sheet <- "Annual Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_stat_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_stats_function <- paste0("calc_annual_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_plot_function <- paste0("plot_annual_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_mean_plot_function <- paste0("plot_annual_means(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
# Add data tables
ann_stats_out <- results$Annual$Annual_Summary_Stats[,!colnames(results$Annual$Annual_Summary_Stats) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_stat_sheet,
data = ann_stats_out,
title = paste0("Annual Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = annual_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = ann_stat_sheet,
plot = results$Annual$Annual_Summary_Stats_Plot[[1]],
title = paste0("Annual Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(ann_stats_out) + 2,
row = 2,
height = 3,
width = 8.5,
comment = annual_plot_function)
add_plot(wb = output_excel,
sheet = ann_stat_sheet,
plot = results$Annual$Annual_Means_Plot[[1]],
title = paste0("Annual Mean Flows In Relation to the Long-term Mean (", start_year, "-", end_year, ")"),
col = ncol(ann_stats_out) + 2,
row = 19,
height = 3,
width = 8.5,
comment = annual_mean_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Summary Statistics Table",
"Function" = annual_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Summary Statistics Plot",
"Function" = annual_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_stat_sheet,
"Output" = "Annual Mean Flows Plot",
"Function" = annual_mean_plot_function)
# Add worksheet
ann_cumul_sheet <- "Annual Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_cumul_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_vol_function <- paste0("calc_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_yield_function <- paste0("calc_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
", use_yield = TRUE",
fn_area,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_vol_plot_function <- paste0("plot_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
annual_yield_plot_function <- paste0("plot_annual_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
", use_yield = TRUE",
fn_area,
ifelse(all(1:12 %in% months),", include_seasons = TRUE)",")"))
# Add data tables
ann_cumul_out <- dplyr::left_join(results$Annual$Annual_Cumul_Volume_Stats_m3,
results$Annual$Annual_Cumul_Yield_Stats_mm,
by = c("STATION_NUMBER", "Year"))
ann_cumul_out <- ann_cumul_out[,!colnames(ann_cumul_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_cumul_sheet,
data = ann_cumul_out,
title = paste0("Annual Cumulative Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (",
start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(annual_vol_function, " ", annual_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[1]],
title = paste0("Annual Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 2,
height = 2.2,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[1]],
title = paste0("Annual Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + ifelse(all(1:12 %in% months),8,0),
row = ifelse(all(1:12 %in% months),2,14),
height = 2.2,
width = 6,
comment = annual_yield_plot_function)
if (all(1:12 %in% months)) {
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[2]],
title = paste0("Seasonal (Two Seasons) Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 14,
height = 3,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Volume_Stats_m3_Plot[[3]],
title = paste0("Seasonal (Four Seasons) Total Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2,
row = 33,
height = 3,
width = 6,
comment = annual_vol_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[2]],
title = paste0("Seasonal (Two Seasons) Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + 8,
row = 14,
height = 3,
width = 6,
comment = annual_yield_plot_function)
add_plot(wb = output_excel,
sheet = ann_cumul_sheet,
plot = results$Annual$Annual_Cumul_Yield_Stats_mm_Plot[[3]],
title = paste0("Seasonal (Four Seasons) Total Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(ann_cumul_out) + 2 + 8,
row = 33,
height = 3,
width = 6,
comment = annual_yield_plot_function)
}
# Add worksheet
ann_oth_sheet <- "Annual Stats Other"
openxlsx::addWorksheet(wb = output_excel,
sheetName = ann_oth_sheet,
tabColour = "#44e5e7")
# Create fasstr function strings for output
annual_lows_function <- paste0("calc_annual_lowflows(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_lows_plot_function <- paste0("plot_annual_lowflows(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
annual_timing_function <- paste0("calc_annual_flow_timing(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_timing_plot_function <- paste0("plot_annual_flow_timing(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_norm_function <- paste0("calc_annual_normal_days(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
annual_norm_plot_function <- paste0("plot_annual_normal_days(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_complete,
fn_months,
")")
# Add data tables
ann_other_out <- dplyr::left_join(results$Annual$Annual_Low_Flows,
results$Annual$Annual_Flow_Timing,
by = c("STATION_NUMBER", "Year"))
ann_other_out <- dplyr::left_join(ann_other_out,
results$Annual$Annual_Normal_Days,
by = c("STATION_NUMBER", "Year"))
ann_other_out <- ann_other_out[,!colnames(ann_other_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = ann_oth_sheet,
data = ann_other_out,
title = paste0("Annual Low-flow Values (cubic metres per second) and Dates, Timing of Flows",
" (day of year), and Number Days Normal and Above/Below Normal (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(annual_lows_function, " ", annual_timing_function,
" ", annual_norm_function))
# Add plots
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Low_Flows_Plot[[1]],
title = paste0("Annual Low-flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2,
row = 2,
height = 5.5,
width = 6,
comment = annual_lows_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Low_Flows_Plot[[2]],
title = paste0("Day of Annual Low-flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2,
row = 31,
height = 5.5,
width = 6,
comment = annual_lows_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Flow_Timing_Plot[[1]],
title = paste0("Annual Timing of Flows (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2 + 8,
row = 2,
height = 5.5,
width = 6,
comment = annual_timing_plot_function)
add_plot(wb = output_excel,
sheet = ann_oth_sheet,
plot = results$Annual$Annual_Normal_Days_Plot[[1]],
title = paste0("Annual Days Per Year Above, Below, and Outside Normal (", start_year, "-", end_year, ")"),
col = ncol(ann_other_out) + 2 + 8,
row = 31,
height = 3.5,
width = 7,
comment = annual_norm_plot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Volumes Table",
"Function" = annual_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Yields Table",
"Function" = annual_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Volumes Plots",
"Function" = annual_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_cumul_sheet,
"Output" = "Annual Cumulative Yields Plots",
"Function" = annual_yield_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Low-Flows Table",
"Function" = annual_lows_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Low-Flows Plot",
"Function" = annual_lows_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Timing-of-Flows Table",
"Function" = annual_timing_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Timing-of-Flows Plot",
"Function" = annual_timing_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Days Outside Normal Table",
"Function" = annual_norm_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = ann_oth_sheet,
"Output" = "Annual Days Outside Normal Plot",
"Function" = annual_norm_plot_function)
}
### Monthly Stats
##########################
if (4 %in% analyses) {
# Add worksheet
month_stat_sheet <- "Monthly Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = month_stat_sheet,
tabColour = "#59d2fe")
# Create fasstr function strings for output
month_stats_function <- paste0("calc_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_mon,
fn_complete,
")")
month_stats_plot_function <- paste0("plot_monthly_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_allowmiss_mon,
fn_complete,
")")
# Add data tables
mon_stats_out <- suppressWarnings(calc_monthly_stats(data = flow_data_raw,
start_year = start_year,
end_year = end_year,
exclude_years = exclude_years,
water_year_start = water_year_start,
ignore_missing = ignore_missing,
complete_years = complete_years,
spread = TRUE))
mon_stats_out <- mon_stats_out[,!colnames(mon_stats_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = month_stat_sheet,
data = mon_stats_out,
title = paste0("Monthly Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = month_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[1]],
title = paste0("Monthly Mean Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2,
row = 2,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[2]],
title = paste0("Monthly Median Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2,
row = 29,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[3]],
title = paste0("Monthly Maximum Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2 + 12,
row = 2,
height = 5,
width = 9,
comment = month_stats_plot_function)
add_plot(wb = output_excel,
sheet = month_stat_sheet,
plot = results$Monthly$Monthly_Summary_Stats_Plot[[4]],
title = paste0("Monthly Minimum Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_stats_out) + 2 + 12,
row = 29,
height = 5,
width = 9,
comment = month_stats_plot_function)
# Add worksheet
month_cumul_sheet <- "Monthly Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = month_cumul_sheet,
tabColour = "#59d2fe")
# Create fasstr function strings for output
month_vol_function <- paste0("calc_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
month_vol_plot_function <- paste0("plot_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
month_yield_function <- paste0("calc_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
month_yield_plot_function <- paste0("plot_monthly_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
# Add data tables
mon_vol_out <- results$Monthly$Monthly_Total_Cumul_Volume_m3[,!colnames(results$Monthly$Monthly_Total_Cumul_Volume_m3) %in% "STATION_NUMBER"]
mon_vol_out <- mon_vol_out[,!colnames(mon_vol_out) %in% "STATION_NUMBER"]
mon_vol_out <- tidyr::gather(mon_vol_out, Statistic, Value, -1)
mon_vol_out <- dplyr::mutate(mon_vol_out,
Statistic = paste0(Statistic, "_Volume_m3"),
Statistic = factor(Statistic, levels = unique(Statistic)))
mon_vol_out <- tidyr::spread(mon_vol_out, Month, Value)
mon_yield_out <- results$Monthly$Monthly_Total_Cumul_Yield_mm[,!colnames(results$Monthly$Monthly_Total_Cumul_Yield_mm) %in% "STATION_NUMBER"]
mon_yield_out <- mon_yield_out[,!colnames(mon_yield_out) %in% "STATION_NUMBER"]
mon_yield_out <- tidyr::gather(mon_yield_out, Statistic, Value, -1)
mon_yield_out <- dplyr::mutate(mon_yield_out,
Statistic = paste0(Statistic, "_Yield_mm"),
Statistic = factor(Statistic, levels = unique(Statistic)))
mon_yield_out <- tidyr::spread(mon_yield_out, Month, Value)
mon_cumul_out <- suppressWarnings(dplyr::bind_rows(mon_vol_out, mon_yield_out))
add_table(wb = output_excel,
sheet = month_cumul_sheet,
data = mon_cumul_out,
title = paste0("Annual Cumulative Monthly Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(month_vol_function, " ", month_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = month_cumul_sheet,
plot = results$Monthly$Monthly_Total_Cumul_Volume_m3_Plot[[1]],
title = paste0("Annual Cumulative Monthly Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(mon_cumul_out) + 2,
row = 2,
height = 4,
width = 9,
comment = month_vol_plot_function)
add_plot(wb = output_excel,
sheet = month_cumul_sheet,
plot = results$Monthly$Monthly_Total_Cumul_Yield_mm_Plot[[1]],
title = paste0("Annual Cumulative Monthly Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(mon_cumul_out) + 2,
row = 24,
height = 4,
width = 9,
comment = month_yield_plot_function)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_stat_sheet,
"Output" = "Monthly Summary Statistics Table",
"Function" = month_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_stat_sheet,
"Output" = "Monthly Summary Statistics Plot",
"Function" = month_stats_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Volumes Table",
"Function" = month_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Volumes Plot",
"Function" = month_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Yields Table",
"Function" = month_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = month_cumul_sheet,
"Output" = "Monthly Cumulative Yields Plot",
"Function" = month_yield_plot_function)
}
### Daily Stats
##########################
if (5 %in% analyses) {
# Create folder for plots if it doesn't exist
plot_dir <- paste0(file_name, " Plots/")
if (!dir.exists(plot_dir)) {
message(paste0("** creating folder '", plot_dir ,"' for additional plots"))
}
dir.create(path = plot_dir, showWarnings = FALSE)
# Add worksheet
day_stats_sheet <- "Daily Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = day_stats_sheet,
tabColour = "#4a8fe7")
# Create fasstr function strings for output
daily_stats_function <- paste0("calc_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
daily_stats_plot_function <- paste0("plot_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
fn_complete,
")")
# Add data tables
day_stats_out <- results$Daily$Daily_Summary_Stats[,!colnames(results$Daily$Daily_Summary_Stats) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = day_stats_sheet,
data = day_stats_out,
title = paste0("Daily Summary Statistics, in cubic metres per second (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = daily_stats_function)
# Add plots
add_plot(wb = output_excel,
sheet = day_stats_sheet,
plot = results$Daily$Daily_Summary_Stats_Plot[[1]],
title = paste0("Daily Summary Statistics (", start_year, "-", end_year, ")"),
col = ncol(day_stats_out) + 2,
row = 2,
height = 5,
width = 10,
comment = daily_stats_plot_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Daily_Statistics_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Statistics_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Summary_Stats_with_Years,
folder_name = paste0(plot_dir, "Daily_Statistics_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
# Add worksheet
day_cumul_sheet <- "Daily Cumulative Stats"
openxlsx::addWorksheet(wb = output_excel,
sheetName = day_cumul_sheet,
tabColour = "#4a8fe7")
# Create fasstr function strings for output
daily_vol_function <- paste0("calc_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
daily_vol_plot_function <- paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
")")
daily_yield_function <- paste0("calc_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
daily_yield_plot_function <- paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
")")
# Add data tables
day_vol_out <- results$Daily$Daily_Total_Cumul_Volume_m3[,!colnames(results$Daily$Daily_Total_Cumul_Volume_m3) %in% "STATION_NUMBER"]
day_vol_out <- day_vol_out[,!colnames(day_vol_out) %in% "STATION_NUMBER"]
day_vol_out <- tidyr::gather(day_vol_out, Statistic, Value, -(1:2))
day_vol_out <- dplyr::mutate(day_vol_out, Statistic = paste0(Statistic, "_Volume_m3"))
order <- unique(day_vol_out$Statistic)
day_vol_out <- tidyr::spread(day_vol_out, Statistic, Value)
day_vol_out <- dplyr::select(day_vol_out, Date, DayofYear, order)
day_vol_out <- dplyr::arrange(day_vol_out, DayofYear)
day_yield_out <- results$Daily$Daily_Total_Cumul_Yield_mm[,!colnames(results$Daily$Daily_Total_Cumul_Yield_mm) %in% "STATION_NUMBER"]
day_yield_out <- day_yield_out[,!colnames(day_yield_out) %in% "STATION_NUMBER"]
day_yield_out <- tidyr::gather(day_yield_out, Statistic, Value, -(1:2))
day_yield_out <- dplyr::mutate(day_yield_out, Statistic = paste0(Statistic, "_Yield_mm"))
order <- unique(day_yield_out$Statistic)
day_yield_out <- tidyr::spread(day_yield_out, Statistic, Value)
day_yield_out <- dplyr::select(day_yield_out, Date, DayofYear, order)
day_yield_out <- dplyr::arrange(day_yield_out, DayofYear)
day_cumul_out <- dplyr::left_join(day_vol_out, day_yield_out, by = c("Date", "DayofYear"))
add_table(wb = output_excel,
sheet = day_cumul_sheet,
data = day_cumul_out,
title = paste0("Annual Cumulative Daily Volumetric (cubic metres) and Yield (millimetres) Summary Statistics (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(daily_vol_function, " ", daily_yield_function))
# Add plots
add_plot(wb = output_excel,
sheet = day_cumul_sheet,
plot = results$Daily$Daily_Total_Cumul_Volume_m3_Plot[[1]],
title = paste0("Annual Cumulative Daily Volumetric Flows (", start_year, "-", end_year, ")"),
col = ncol(day_cumul_out) + 2,
row = 2,
height = 4,
width = 9,
comment = daily_vol_plot_function)
add_plot(wb = output_excel,
sheet = day_cumul_sheet,
plot = results$Daily$Daily_Total_Cumul_Yield_mm_Plot[[1]],
title = paste0("Annual Cumulative Daily Yield Runoff (", start_year, "-", end_year, ")"),
col = ncol(day_cumul_out) + 2,
row = 24,
height = 4,
width = 9,
comment = daily_yield_plot_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Daily_Cumulative_Volume_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Cumulative_Volume_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Total_Cumul_Volume_m3_with_Years,
folder_name = paste0(plot_dir, "Daily_Cumulative_Volume_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
if (plot_filetype == "pdf") {
message("** writing 'Daily_Cumulative_Yield_with_Years.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Daily_Cumulative_Yield_with_Years' folder"))
}
suppressWarnings(
suppressMessages(
write_plots(plots = results$Daily$Daily_Total_Cumul_Yield_mm_with_Years,
folder_name = paste0(plot_dir, "Daily_Cumulative_Yield_with_Years"),
plot_filetype = plot_filetype,
width = 8.5,
height = 4,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
))
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Table",
"Function" = daily_stats_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Plot",
"Function" = daily_stats_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_stats_sheet,
"Output" = "Daily Summary Statistics Plot with Year",
"Function" = paste0("plot_daily_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_missing,
", include_year = ", start_year,
")"))
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Table",
"Function" = daily_vol_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Plot",
"Function" = daily_vol_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Volumes Plot with Year",
"Function" = paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", include_year = ", start_year,
")"))
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Table",
"Function" = daily_yield_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Plot",
"Function" = daily_yield_plot_function)
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = day_cumul_sheet,
"Output" = "Daily Cumulative Yields Plot with Year",
"Function" = paste0("plot_daily_cumulative_stats(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", use_yield = TRUE",
fn_area,
", include_year = ", start_year,
")"))
}
# ### Annual Trending
##########################
if (6 %in% analyses) {
# Create folder for plots if it doesn't exist
plot_dir <- paste0(file_name, " Plots/")
if (!dir.exists(plot_dir)) {
message(paste0("** creating folder '", plot_dir ,"' for additional plots"))
}
dir.create(path = plot_dir, showWarnings = FALSE)
# Add worksheet
trends_sheet <- "Annual Trends"
openxlsx::addWorksheet(wb = output_excel,
sheetName = trends_sheet,
tabColour = "#5c7aff")
# Create fasstr function strings for output
trends_function <- paste0("compute_annual_trends(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
fn_area,
", zyp_method = '", zyp_method, "'",
", zyp_alpha = ", zyp_alpha,
fn_missing,
fn_allowmiss_ann_trend,
fn_allowmiss_mon_trend,
fn_complete,
")")
# Add data tables
trends_out <- dplyr::left_join(results$Trending$Annual_Trends_Results,
results$Trending$Annual_Trends_Data,
by = c("STATION_NUMBER", "Statistic"))
trends_out <- trends_out[,!colnames(trends_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = trends_sheet,
data = trends_out,
title = paste0("Annual Trending Statistics Results using '", zyp_method,
"' Prewhitening Method, and Annual Values (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = trends_function)
# Write plots
if (plot_filetype == "pdf") {
message("** writing 'Annual_Trends_Results_Plots.pdf'")
} else {
message(paste0("** writing .", plot_filetype, " plots in 'Annual_Trends_Results_Plots' folder"))
}
suppressMessages(
write_plots(plots = results$Trending$Annual_Trends_Plots,
folder_name = paste0(plot_dir , "Annual_Trends_Results_Plots"),
plot_filetype = plot_filetype,
width = 8.5,
height = 3,
combined_pdf = ifelse(plot_filetype == "pdf", TRUE, FALSE))
)
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = trends_sheet,
"Output" = "Annual Trends Tables and Plots",
"Function" = trends_function)
}
### Low Flow Frequency
##########################
if (7 %in% analyses) {
# Check if there is sufficient data for frequency analysis
data_check <- suppressWarnings(
calc_annual_lowflows(data = flow_data_raw,
start_year = start_year, end_year = end_year, exclude_years = exclude_years,
water_year_start = water_year_start,
ignore_missing = ignore_missing,
complete_years = complete_years,
allowed_missing = allowed_missing_annual)
)
data_check <- dplyr::select(data_check, Min_1_Day, Min_3_Day, Min_7_Day, Min_30_Day)
if (any(as.numeric(colSums(!is.na(data_check))) < 3)) {
warning("Not enough annual data (3 years) for frequency analysis. Consider filtering for appropriate years or use ignore_missing = TRUE,",
call. = FALSE)
} else {
# Add worksheet
freq_sheet <- "Low-flow Frequencies"
openxlsx::addWorksheet(wb = output_excel,
sheetName = freq_sheet,
tabColour = "#5c7aff")
# Create fasstr function strings for output
frequency_function <- paste0("compute_annual_frequencies(",
fn_data,
fn_wys,
fn_startend,
fn_exclude,
fn_months,
", roll_days = c(1,3,7,30,60)",
", prob_plot_position = 'weibull'",
", fit_distr = 'PIII'",
", fit_distr_method = 'MOM'",
fn_missing,
fn_allowmiss_ann,
fn_complete,
")")
# Add data tables
freq_ann_data_out <- tidyr::spread(results$Lowflow_Frequencies$Freq_Analysis_Data, Measure, Value)
freq_ann_data_out <- freq_ann_data_out[,!colnames(freq_ann_data_out) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_ann_data_out,
title = paste0("Annual Low-flow Values (", start_year, "-", end_year, ")"),
col = 1,
row = 1,
comment = paste0(frequency_function, "[[1]]"))
freq_plot_data_out <- results$Lowflow_Frequencies$Freq_Plot_Data[,!colnames(results$Lowflow_Frequencies$Freq_Plot_Data) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_plot_data_out,
title = paste0("Annual Low-flow Value Probabilities for Plotting using 'weibull' Plotting Positions (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2,
row = 1,
comment = paste0(frequency_function, "[[2]]"))
freq_quantiles_out <- results$Lowflow_Frequencies$Freq_Fitted_Quantiles[,!colnames(results$Lowflow_Frequencies$Freq_Fitted_Quantiles) %in% "STATION_NUMBER"]
add_table(wb = output_excel,
sheet = freq_sheet,
data = freq_quantiles_out,
title = paste0("Fitted Flow Quantiles using a logPIII Distribution with Method of Moments Fitting (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2 + ncol(freq_plot_data_out) + 1 + 11,
row = 1,
comment = paste0(frequency_function, "[[5]]"))
# Add plots
add_plot(wb = output_excel,
sheet = freq_sheet,
plot = results$Lowflow_Frequencies$Freq_Plot,
title = paste0("Annual Low-flow Value Probabilities and Return Periods using 'weibull' Plotting Positions (", start_year, "-", end_year, ")"),
col = ncol(freq_ann_data_out) + 2 + ncol(freq_plot_data_out) + 1,
row = 1,
height = 5,
width = 7,
comment = paste0(frequency_function, "[[3]]"))
# Add fasstr functions to table
fasstr_functions <- dplyr::add_row(fasstr_functions,
"Worksheet" = freq_sheet,
"Output" = "Low-Flow Frequency Analysis Tables and Plots",
"Function" = frequency_function)
}
}
# Write the analysis information
##########################
## Create a meta data file of the analysis arguments
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "fasstr Full Analysis Results",
startCol = 1, startRow = 1)
openxlsx::addStyle(wb = output_excel, sheet = overview_sheet, cols = 1, rows = 1,
style = openxlsx::createStyle(fontSize = 12,
textDecoration = "bold"))
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = paste0("Analysis Date: ",as.character(Sys.time())),
startCol = 1, startRow = 2)
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "fasstr 0.3.0",
startCol = 1, startRow = 3)
metadata <- list(data = ifelse(!is.null(data), as.character(substitute(data)), ""),
dates = as.character(substitute(Date)),
values = as.character(substitute(Value)),
groups = as.character(substitute(STATION_NUMBER)),
station_number = ifelse(!is.null(station_number), toupper(station_number), ""),
basin_area = basin_area_stn,
water_year_start = water_year_start,
start_year = start_year,
end_year = end_year,
exclude_years = paste0(ifelse(!is.null(exclude_years),
paste0(ifelse(length(exclude_years) == 1,
paste(exclude_years),
paste(exclude_years, collapse = ", "))),
"")),
ignore_missing = ignore_missing,
zyp_method = zyp_method,
zyp_alpha = ifelse(!is.na(zyp_alpha), zyp_alpha, ""),
analyses = analyses,
file_name = paste0(file_name, ".xlsx"),
plot_filetype = plot_filetype,
analysis_function = analysis_function)
metadata <- data.frame("Argument" = names(metadata),
"Option" = as.character(unname(metadata)))
metadata <- metadata[c(1,5,2:4,6:nrow(metadata)),]
add_table(wb = output_excel,
sheet = overview_sheet,
data = metadata,
title = paste0("Analysis Overview"),
col = 1,
row = 5)
if (5 %in% analyses | 6 %in% analyses) {
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = "Click for additional plots:",
startCol = 1, startRow = 25)
link <- normalizePath(plot_dir)
class(link) <- "hyperlink"
openxlsx::writeData(wb = output_excel, sheet = overview_sheet,
x = link,
startCol = 1, startRow = 26)
}
if (!is.null(station_number)) {
hydat_info <- dplyr::left_join(tidyhydat::hy_stations(station_number),
tidyhydat::hy_stn_regulation(station_number),
by = "STATION_NUMBER")
hydat_info <- dplyr::select(hydat_info, STATION_NUMBER, STATION_NAME, PROV_TERR_STATE_LOC, HYD_STATUS,
LATITUDE, LONGITUDE, DRAINAGE_AREA_GROSS, REGULATED, RHBN, REAL_TIME)
hydat_info <- dplyr::mutate(hydat_info, HYDAT_VERSION = as.character(dplyr::pull(tidyhydat::hy_version()[,2])))
hydat_info <- tidyr::gather(hydat_info, "Station Attribute", Info)
add_table(wb = output_excel,
sheet = overview_sheet,
data = hydat_info,
title = paste0("HYDAT Station Information"),
col = 5,
row = 5)
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = c(5,6), widths = "auto")
}
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = 1, widths = 31)
openxlsx::setColWidths(wb = output_excel, sheet = overview_sheet, cols = 2, widths = 17)
# Write the fasstr functions
##########################
fasstr_sheet <- "fasstr Functions"
openxlsx::addWorksheet(wb = output_excel,
sheetName = fasstr_sheet,
tabColour = "#003e1f")
add_table(wb = output_excel,
sheet = fasstr_sheet,
data = fasstr_functions,
title = paste0("fasstr Functions"),
col = 1,
row = 1,
comment = "Copy and paste a function into R to reproduce or further customize results")
openxlsx::setColWidths(wb = output_excel, sheet = fasstr_sheet, cols = 1:3, widths = "auto")
# Save the workbook
##########################
message(paste0("** writing analysis results in '", file_name, ".xlsx'"))
openxlsx::saveWorkbook(wb = output_excel,
file = paste0(file_name, ".xlsx"),
overwrite = TRUE)
if (5 %in% analyses | 6 %in% analyses) {
message(paste0("* DONE. For analysis results go to: '", normalizePath(paste0(file_name, ".xlsx")),
"' and '", normalizePath(plot_dir), "' folder"))
} else {
message(paste0("* DONE. For analysis results go to: '", normalizePath(paste0(file_name, ".xlsx"))))
}
}
Try the fasstr package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.