Merge branch 'dev_add_kill' of git.ufz.de:schuerz/swatdoctr into dev_add_kill

DESCRIPTION

@@ -22,7 +22,8 @@ Imports:
   stringr,
   tibble,
   tidyr,
-  tidyselect
+  tidyselect,
+  plotly
 Suggests:
   datasets,
   stats

NAMESPACE

@@ -2,8 +2,11 @@
 
 export(add_kill_op)
 export(get_hru_id_by_attribute)
+export(plot_basin_var)
 export(plot_climate_annual)
 export(plot_hru_pw_day)
+export(plot_hru_var)
+export(plot_hru_var_aa)
 export(plot_monthly_snow)
 export(plot_variable_at_harvkill)
 export(print_avannual_qtile)
@@ -18,6 +21,7 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_map)
 importFrom(dplyr,group_split)
 importFrom(dplyr,lead)
 importFrom(dplyr,left_join)
@@ -29,7 +33,6 @@ importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,slice_sample)
 importFrom(dplyr,summarise)
-importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_boxplot)
@@ -40,6 +43,7 @@ importFrom(ggplot2,labs)
 importFrom(ggplot2,lims)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_void)
+importFrom(lubridate,floor_date)
 importFrom(lubridate,int_end)
 importFrom(lubridate,int_start)
 importFrom(lubridate,interval)
@@ -47,6 +51,10 @@ importFrom(lubridate,month)
 importFrom(lubridate,yday)
 importFrom(lubridate,year)
 importFrom(lubridate,ymd)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(plotly,plotly_build)
+importFrom(plotly,subplot)
 importFrom(processx,run)
 importFrom(purrr,map)
 importFrom(purrr,map2)

R/globals.R

@@ -5,4 +5,4 @@ utils::globalVariables(c("%&&%", "%//%", ".", "crop", "day", "ecanopy", "eplant"
                          "rhum rm_skp", "schedule", "snofall", "snomlt", "soil", "solarad", "starts_with",
                          "tile", "time_out", "tmn", "tmpav", "tmx", "topo", "val_max", "val_mean",
                          "val_min", "value", "value_sum", "var", "var1", "var2", "var3", "var4", "var5",
-                         "wndspd", "yr", "rhum", "rm_skp"))
+                         "wndspd", "yr", "rhum", "rm_skp", "Date", "Values"))

R/helper.R

@@ -47,3 +47,29 @@ insert_line_at <- function(dat, txt, insert_after){
   post <- dat[(insert_after+1):length(dat)]
   return(c(pre, txt, post))
 }
+
+#' Function to put option remove hide or show all lines in chart and this function also print chart.
+#'
+#' @param graph plotly graph object
+#' @importFrom plotly plotly_build layout
+#' @return plotly graph object with option to remove or show all lines
+#' @keywords internal
+#'
+#' @examples
+#' \dontrun{
+#' hide_show(fig)
+#' }
+
+hide_show <- function(graph){
+  plotly_build(graph) %>%
+    layout(updatemenus = list(
+      list(type = "buttons", direction = "right", xanchor = "center", yanchor = "top",
+           showactive = FALSE, x = 0.3, y = 1.0,
+           buttons = list(
+             list(method = "restyle",
+                  args = list("visible", "all"),
+                  label = "show all"),
+             list(method = "restyle",
+                  args = list("visible", "legendonly"),
+                  label = "hide all")))))
+}

R/plot_climate.R

@@ -237,3 +237,44 @@ plot_monthly_snow <- function(sim_verify) {
     facet_wrap(.~process, ncol = 1) +
     theme_bw()
 }
+
+#' Plot selected basin variable aggregated by defined time step
+#'
+#' @param sim_verify Simulation output of the function \code{run_swat_verification()}.
+#'   To plot the climate outputs at least the output option \code{outputs = 'wb'} must
+#'   be set in  \code{run_swat_verification()}.
+#' @param var Character which defines the variable to be printed
+#' @param period (optional) character describing, which time interval to display (default is "day",
+#' other examples are "week", "month", etc). \code{Default = "day"}
+#' @param fn_summarize (optional) function to recalculate to time interval (default is "mean", other examples
+#' are "median", "sum", etc). \code{Default = "mean"}
+#' @importFrom lubridate floor_date
+#' @importFrom plotly plot_ly layout
+#' @importFrom dplyr %>% rename summarize mutate group_by arrange
+#' @return plotly figure object
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' plot_basin_var(sim_nostress, "percn")
+#' }
+
+plot_basin_var <- function(sim_verify, var, period = "day", fn_summarize = "mean"){
+  if(var %in% names(sim_verify$basin_wb_day)){
+    df <- sim_verify$basin_wb_day[,c("yr","mon","day",var)]
+  } else if (var %in% names(sim_verify$basin_pw_day)){
+    df <- sim_verify$basin_pw_day[,c("yr","mon","day",var)]
+  }
+  ##Aggregating data by time step
+  df$Date<- floor_date(ISOdate(df$yr, df$mon, df$day), period)
+  df <- df[c("Date", var)] %>%
+    rename(Values = 2) %>%
+    group_by(Date) %>%
+    summarize(Values = get(fn_summarize)(Values))
+  ##Plotting
+  plot_ly(df %>% arrange(Date), x=~Date, y=~Values, name = var, type = 'scatter', mode = 'lines',
+          connectgaps = FALSE) %>% layout(showlegend = FALSE) %>%
+    layout(title = paste(var, "variable"), yaxis = list(title = "Values"))
+}
+
+

R/plot_hru_pw.R

@@ -44,6 +44,7 @@ get_hru_id_by_attribute <- function(sim_verify, lum = NULL, mgt = NULL, soil = N
 #'   be set in  \code{run_swat_verification()}
 #' @param hru_id Numeric vector with HRU ids for which variables should be plotted
 #' @param var Character vector that defines the variable names that are plotted
+#' @param title Character for title to be put in the figure.
 #' @param years Years of the simulated data for which varaibles are plotted.
 #'
 #' @importFrom dplyr filter mutate select %>%
@@ -56,7 +57,7 @@ get_hru_id_by_attribute <- function(sim_verify, lum = NULL, mgt = NULL, soil = N
 #'
 #' @export
 #'
-plot_hru_pw_day <- function(sim_verify, hru_id, var, years = 1900:2100) {
+plot_hru_pw_day <- function(sim_verify, hru_id, var, title = "", years = 1900:2100) {
   plot_data <- sim_verify$hru_pw_day %>%
     filter(unit %in% hru_id) %>%
     filter(yr %in% years) %>%
@@ -67,7 +68,7 @@ plot_hru_pw_day <- function(sim_verify, hru_id, var, years = 1900:2100) {
 
   ggplot(plot_data) +
     geom_line(aes(x = date, y = value, color = unit, lty = unit)) +
-    labs(x = 'Date', color = 'HRU', lty = 'HRU') +
+    labs(x = 'Date', color = 'HRU', lty = 'HRU', title=title) +
     scale_x_date(date_labels = '%Y-%m-%d') +
     facet_grid(rows = vars(all_of(var)), scales = 'free_y', switch = 'y') +
     theme_bw() +
@@ -78,7 +79,6 @@ plot_hru_pw_day <- function(sim_verify, hru_id, var, years = 1900:2100) {
           axis.title.y = element_blank())
 }
 
-
 #' Print the average annual qtile for HRUs
 #'
 #' print_avannual_qtile prints a table with the average annual qtile in mm
@@ -112,3 +112,77 @@ print_avannual_qtile <- function(sim_verify,
     arrange(qtile, id)
 }
 
+#' Aggregate and plot simulated variables saved in hru_pw_day
+#'
+#' @param sim_verify Simulation output of the function \code{run_swat_verification()}.
+#'   To plot the heat units at least the output option \code{outputs = 'mgt'} must
+#'   be set in  \code{run_swat_verification()}.
+#' @param hru_id Numeric vector with HRU ids for which variables should be plotted.
+#' @param var Character vector that defines the variable names that are plotted.
+#' @param period (optional) character describing, which time interval to display (default is "day",
+#' other examples are "week", "month", etc). \code{Default = "day"}
+#' @param fn_summarize (optional) function to recalculate to time interval (default is "mean", other examples
+#' are "median", "sum", etc). \code{Default = "mean"}
+#' @return plotly figure object
+#' @importFrom lubridate floor_date
+#' @importFrom plotly plot_ly layout
+#' @importFrom dplyr %>% rename summarize mutate group_by arrange
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' id <- get_hru_id_by_attribute(sim_nostress, "wwht_lum")
+#' plot_hru_var(sim_nostress, sample(id$id, 10), "lai")
+#' }
+
+plot_hru_var <- function(sim_verify, hru_id, var, period = "day", fn_summarize = "mean"){
+  options(dplyr.summarise.inform = FALSE)
+  df <- sim_verify$hru_pw_day[sim_verify$hru_pw_day$unit %in% hru_id, c("unit", "yr", "mon", "day", var)]
+  ##Aggregating data by time step
+  df$Date<- floor_date(ISOdate(df$yr, df$mon, df$day), period)
+  df <- df[c("Date", "unit", var)] %>%
+    rename(Values = 3) %>%
+    mutate(unit = paste('hru:', unit)) %>%
+    group_by(unit, Date) %>%
+    summarize(Values = get(fn_summarize)(Values))
+
+  ##Plotting
+  plot_ly(df %>% arrange(Date), x=~Date, y=~Values,  color = ~factor(unit), colors = "Set2", type = 'scatter', mode = 'lines',
+          connectgaps = FALSE) %>% layout(showlegend = TRUE) %>%
+    layout(title = paste(var, "parameter"), xaxis = list(title = "Date"), yaxis = list(title = "Values")) %>%
+    hide_show()
+}
+
+#' Plot simulated variables of filtered HRUs saved in hru_wb_aa with boxplots
+#'
+#' @param sim_verify Simulation output of the function \code{run_swat_verification()}.
+#'   To plot the heat units at least the output option \code{outputs = 'wb'} must
+#'   be set in  \code{run_swat_verification()}
+#' @param lum Optional character vector with landuse.lum labels
+#' @param mgt Optional character vector with management labels as defined in management.sch.
+#' @param soil Optional character vector with soil type labels as defined in the soil data.
+#' @return plot_ly multi boxplot figure for all available variables, which are not 0.
+#' @importFrom dplyr %>% mutate group_by group_map
+#' @importFrom tidyr pivot_longer
+#' @importFrom plotly plot_ly layout subplot
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' plot_hru_var_aa(sim_nostress, "wwht_lum")
+#' }
+
+plot_hru_var_aa <- function(sim_verify, lum = NULL, mgt = NULL, soil = NULL){
+  p <- paste(lum, mgt, soil)
+  id <- get_hru_id_by_attribute(sim_verify, lum, mgt, soil)
+  fig <- sim_verify$hru_wb_aa[sim_verify$hru_wb_aa$unit %in% id$id, -c(1:7)] %>%
+    .[, colSums(.!= 0) > 0] %>%
+    mutate(p = p) %>%
+    pivot_longer(-p,names_to = 'var', values_to = 'Values') %>%
+    group_by(p, var) %>%
+    group_map(~plot_ly(., y=~Values, color = ~var, colors = "cyan4", type = 'box'), keep = TRUE) %>%
+    subplot(nrows = 5) %>%
+    layout(title = paste("HRUs selected by", p))
+  return(fig)
+}
+

man/hide_show.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helper.R
+\name{hide_show}
+\alias{hide_show}
+\title{Function to put option remove hide or show all lines in chart and this function also print chart.}
+\usage{
+hide_show(graph)
+}
+\arguments{
+\item{graph}{plotly graph object}
+}
+\value{
+plotly graph object with option to remove or show all lines
+}
+\description{
+Function to put option remove hide or show all lines in chart and this function also print chart.
+}
+\examples{
+\dontrun{
+hide_show(fig)
+}
+}
+\keyword{internal}

man/plot_basin_var.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_climate.R
+\name{plot_basin_var}
+\alias{plot_basin_var}
+\title{Plot selected basin variable aggregated by defined time step}
+\usage{
+plot_basin_var(sim_verify, var, period = "day", fn_summarize = "mean")
+}
+\arguments{
+\item{sim_verify}{Simulation output of the function \code{run_swat_verification()}.
+To plot the climate outputs at least the output option \code{outputs = 'wb'} must
+be set in  \code{run_swat_verification()}.}
+
+\item{var}{Character which defines the variable to be printed}
+
+\item{period}{(optional) character describing, which time interval to display (default is "day",
+other examples are "week", "month", etc). \code{Default = "day"}}
+
+\item{fn_summarize}{(optional) function to recalculate to time interval (default is "mean", other examples
+are "median", "sum", etc). \code{Default = "mean"}}
+}
+\value{
+plotly figure object
+}
+\description{
+Plot selected basin variable aggregated by defined time step
+}
+\examples{
+\dontrun{
+plot_basin_var(sim_nostress, "percn")
+}
+}

man/plot_hru_pw_day.Rd

@@ -4,7 +4,7 @@
 \alias{plot_hru_pw_day}
 \title{Plot daily simulated variables which are saved in hru_pw_day}
 \usage{
-plot_hru_pw_day(sim_verify, hru_id, var, years = 1900:2100)
+plot_hru_pw_day(sim_verify, hru_id, var, title = "", years = 1900:2100)
 }
 \arguments{
 \item{sim_verify}{Simulation output of the function \code{run_swat_verification()}.
@@ -15,6 +15,8 @@ be set in  \code{run_swat_verification()}}
 
 \item{var}{Character vector that defines the variable names that are plotted}
 
+\item{title}{Character for title to be put in the figure.}
+
 \item{years}{Years of the simulated data for which varaibles are plotted.}
 }
 \value{

man/plot_hru_var.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_hru_pw.R
+\name{plot_hru_var}
+\alias{plot_hru_var}
+\title{Aggregate and plot simulated variables saved in hru_pw_day}
+\usage{
+plot_hru_var(sim_verify, hru_id, var, period = "day", fn_summarize = "mean")
+}
+\arguments{
+\item{sim_verify}{Simulation output of the function \code{run_swat_verification()}.
+To plot the heat units at least the output option \code{outputs = 'mgt'} must
+be set in  \code{run_swat_verification()}.}
+
+\item{hru_id}{Numeric vector with HRU ids for which variables should be plotted.}
+
+\item{var}{Character vector that defines the variable names that are plotted.}
+
+\item{period}{(optional) character describing, which time interval to display (default is "day",
+other examples are "week", "month", etc). \code{Default = "day"}}
+
+\item{fn_summarize}{(optional) function to recalculate to time interval (default is "mean", other examples
+are "median", "sum", etc). \code{Default = "mean"}}
+}
+\value{
+plotly figure object
+}
+\description{
+Aggregate and plot simulated variables saved in hru_pw_day
+}
+\examples{
+\dontrun{
+id <- get_hru_id_by_attribute(sim_nostress, "wwht_lum")
+plot_hru_var(sim_nostress, sample(id$id, 10), "lai")
+}
+}

man/plot_hru_var_aa.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_hru_pw.R
+\name{plot_hru_var_aa}
+\alias{plot_hru_var_aa}
+\title{Plot simulated variables of filtered HRUs saved in hru_wb_aa with boxplots}
+\usage{
+plot_hru_var_aa(sim_verify, lum = NULL, mgt = NULL, soil = NULL)
+}
+\arguments{
+\item{sim_verify}{Simulation output of the function \code{run_swat_verification()}.
+To plot the heat units at least the output option \code{outputs = 'wb'} must
+be set in  \code{run_swat_verification()}}
+
+\item{lum}{Optional character vector with landuse.lum labels}
+
+\item{mgt}{Optional character vector with management labels as defined in management.sch.}
+
+\item{soil}{Optional character vector with soil type labels as defined in the soil data.}
+}
+\value{
+plot_ly multi boxplot figure for all available variables, which are not 0.
+}
+\description{
+Plot simulated variables of filtered HRUs saved in hru_wb_aa with boxplots
+}
+\examples{
+\dontrun{
+plot_hru_var_aa(sim_nostress, "wwht_lum")
+}
+}