diff --git a/DESCRIPTION b/DESCRIPTION
index de9e7357e88708e4ffacc8b952c9f47217aeac06..6c0292d248a0916ea53ca73c5c75b5c8d0a30d3b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: SWATdoctR
Type: Package
Title: Finding the right diagnoses and treatments for SWAT+ models
-Version: 0.1.12
+Version: 0.1.13
Author: c(person("Svajunas", "Plunge",
email = "svajunas_plunge@sggw.edu.pl",
role = c("aut")),
diff --git a/NAMESPACE b/NAMESPACE
index 07f1319b0f1581ae4fe866fddefb676f0629584c..9a651e517ee4dafb9b8cb11c80220ff09ef71a26 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,7 @@ importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
+importFrom(dplyr,cur_group_id)
importFrom(dplyr,distinct)
importFrom(dplyr,do)
importFrom(dplyr,ends_with)
@@ -67,6 +68,7 @@ importFrom(ggplot2,lims)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
+importFrom(lubridate,ceiling_date)
importFrom(lubridate,floor_date)
importFrom(lubridate,int_end)
importFrom(lubridate,int_start)
@@ -107,9 +109,11 @@ importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_trim)
+importFrom(tibble,add_row)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(tidyselect,all_of)
importFrom(tidyselect,ends_with)
diff --git a/R/plot_hru_pw.R b/R/plot_hru_pw.R
index cac9b1fff58b48f51f62e5b90142ce9cf0213cbc..3cfc9bdd1d6cd5ff67e9bdfeb9e209db61f84317 100644
--- a/R/plot_hru_pw.R
+++ b/R/plot_hru_pw.R
@@ -44,32 +44,48 @@ 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.
+#' @param add_crop TRUE adds subplot with growing periods of crops in plotted HRUs.
#'
-#' @importFrom dplyr filter mutate select %>%
+#' @importFrom dplyr cur_group_id filter group_by group_split mutate rename select %>%
#' @importFrom lubridate ymd
-#' @importFrom tidyr pivot_longer
+#' @importFrom purrr map
+#' @importFrom tibble tibble
+#' @importFrom tidyr pivot_longer pivot_wider
#' @importFrom tidyselect all_of
#' @import ggplot2
+#' @import patchwork
#'
-#' @return Returns a table with hru ids and attributes.
+#' @return Returns a ggplot or patchwork ggplot of daily hru_pw output variables
#'
#' @export
#'
-plot_hru_pw_day <- function(sim_verify, hru_id, var, title = "", years = 1900:2100) {
- .Deprecated("plot_hru_pw")
+#' @examples
+#' \dontrun{
+#' plot_hru_pw_day(sim_nostress, hru_id = 1, var = c('lai', 'bioms'), add_crop = TRUE)
+#' }
+#'
+plot_hru_pw_day <- function(sim_verify, hru_id, var, years = 1900:2100, add_crop = TRUE) {
+ # .Deprecated("plot_hru_pw")
+
+ col_hex <- unname(palette.colors(palette = "Okabe-Ito")[2:(length(hru_id)+1)])
+
plot_data <- sim_verify$hru_pw_day %>%
filter(unit %in% hru_id) %>%
filter(yr %in% years) %>%
mutate(date = ymd(paste(yr, mon, day, sep = '-')),
- unit = paste('hru:', unit)) %>%
+ unit = factor(paste('hru:', unit), levels = paste('hru:', unique(unit)))) %>%
select(date, unit, all_of(var)) %>%
- pivot_longer(., cols = - c(date, unit), names_to = 'var', values_to = 'value')
+ pivot_longer(., cols = - c(date, unit), names_to = 'var', values_to = 'value') %>%
+ rename(hru = unit)
- ggplot(plot_data) +
- geom_line(aes(x = date, y = value, color = unit, lty = unit)) +
- labs(x = 'Date', color = 'HRU', lty = 'HRU', title=title) +
+ var_col_assign <- tibble(hru = unique(plot_data$hru),
+ col = col_hex)
+
+ gg_var <- ggplot(plot_data) +
+ geom_line(aes(x = date, y = value, color = hru, linetype = hru), linewidth = 0.75) +
+ scale_color_manual(values = var_col_assign$col) +
+ labs(x = 'Date', color = 'HRU', lty = 'HRU') +
scale_x_date(date_labels = '%Y-%m-%d') +
facet_grid(rows = vars(all_of(var)), scales = 'free_y', switch = 'y') +
theme_bw() +
@@ -78,6 +94,96 @@ plot_hru_pw_day <- function(sim_verify, hru_id, var, title = "", years = 1900:21
strip.placement = 'outside',
strip.text = element_text(face = 'bold'),
axis.title.y = element_blank())
+
+ if (add_crop) {
+ crop_dates <- sim_verify$mgt_out %>%
+ filter(hru %in% hru_id) %>%
+ filter(year %in% unique(year(plot_data$date))) %>%
+ filter(operation %in% c('PLANT', 'KILL', 'HARV/KILL'))
+
+ if(nrow(crop_dates) > 0) {
+ crop_dates <- crop_dates %>%
+ mutate(date = ymd(paste(year, mon, day, sep = '-')),
+ operation = ifelse(operation == 'PLANT', 'start', 'end')) %>%
+ select(hru, date, op_typ, operation) %>%
+ group_by(hru) %>%
+ group_split() %>%
+ map(., ~ add_start_end(.x)) %>%
+ bind_rows() %>%
+ mutate(id = ifelse(operation == 'start', 1, 0),
+ id = cumsum(id)) %>%
+ pivot_wider(.,
+ names_from = operation,
+ values_from = date,
+ id_cols = c(id, hru, op_typ)) %>%
+ mutate(mid = start + (end - start)/2,
+ hru = factor(paste('hru:', hru), levels = paste('hru:', unique(hru)))) %>%
+ group_by(hru) %>%
+ mutate(id = cur_group_id()) %>%
+ ungroup()
+
+ y_labels <- crop_dates %>%
+ distinct(id, hru)
+
+ crop_col_assign <- tibble(hru = unique(crop_dates$hru)) %>%
+ left_join(., var_col_assign, by = 'hru')
+
+ gg_crop <- ggplot(crop_dates) +
+ geom_rect(aes(xmin = start, xmax = end, ymin = id- 0.35, ymax = id + 0.35, fill = hru)) +
+ geom_text(aes(x = mid, y = id, label = op_typ)) +
+ scale_y_continuous(breaks = y_labels$id, labels = y_labels$hru) +
+ scale_fill_manual(values = crop_col_assign$col) +
+ labs(y = 'hru') +
+ facet_grid(rows = vars(hru), scales = 'free_y', switch = 'y') +
+ theme_bw() +
+ theme(axis.text = element_blank(),
+ axis.title = element_blank(),
+ axis.ticks.y = element_blank(),
+ strip.background = element_blank(),
+ legend.position = 'none',
+ # strip.placement = 'outside',
+ strip.text.y.left = element_text(face = 'bold', angle = 0))
+
+ hru_plot <- gg_crop / gg_var + plot_layout(heights = c(0.05*length(unique(crop_dates$hru)), 1))
+ } else {
+ message('Adding crop plot omitted, as selected HRUs do not have plant and harvest operations.')
+ hru_plot <- gg_var
+ }
+ } else {
+ hru_plot <- gg_var
+ }
+
+ return(hru_plot)
+}
+
+#' Add start and end of a crop planting period at beginning and end of year for
+#' winter crops. This is required to correctly display crops in plot_hru_pw_day
+#'
+#' @param tbl Table with crops and plant and harvest dates
+#'
+#' @importFrom lubridate ceiling_date floor_date
+#' @importFrom tibble add_row
+#'
+#' @keywords internal
+#'
+add_start_end <- function(tbl) {
+ if(tbl$operation[1] == 'end') {
+ tbl <- add_row(tbl,
+ hru = tbl$hru[1],
+ date = floor_date(tbl$date[1], unit = 'year'),
+ op_typ = tbl$op_typ[1],
+ operation = 'start',
+ .before = 1)
+ }
+
+ if(tbl$operation[nrow(tbl)] == 'start') {
+ tbl <- add_row(tbl,
+ hru = tbl$hru[1],
+ date = ceiling_date(tbl$date[nrow(tbl)], unit = 'year'),
+ op_typ = tbl$op_typ[nrow(tbl)],
+ operation = 'end')
+ }
+ return(tbl)
}
diff --git a/R/run_swat_verify.R b/R/run_swat_verify.R
index 78634bc4b84d4664cdf3d5d5057b9a7ba8c4f960..4b6173cddc22d2c0ca8fc67904d3fd933c11138c 100644
--- a/R/run_swat_verify.R
+++ b/R/run_swat_verify.R
@@ -123,7 +123,7 @@ run_swat_verification <- function(project_path, outputs = c('wb', 'mgt', 'plt'),
read_tbl <- function(file, run_path, n_skip) {
file_path <- paste0(run_path, '/', file)
- col_names <- read_lines(file = file_path, skip = 1, n_max = 1) %>%
+ col_names <- read_lines(file = file_path, skip = 1, n_max = 1, lazy = FALSE) %>%
str_trim(.) %>%
str_split(., '[:space:]+') %>%
unlist()
diff --git a/man/add_start_end.Rd b/man/add_start_end.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..e9711ec88fab20f2adb4624d0b4eb799f072f937
--- /dev/null
+++ b/man/add_start_end.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_hru_pw.R
+\name{add_start_end}
+\alias{add_start_end}
+\title{Add start and end of a crop planting period at beginning and end of year for
+winter crops. This is required to correctly display crops in plot_hru_pw_day}
+\usage{
+add_start_end(tbl)
+}
+\arguments{
+\item{tbl}{Table with crops and plant and harvest dates}
+}
+\description{
+Add start and end of a crop planting period at beginning and end of year for
+winter crops. This is required to correctly display crops in plot_hru_pw_day
+}
+\keyword{internal}
diff --git a/man/plot_hru_pw_day.Rd b/man/plot_hru_pw_day.Rd
index c10d6f9befa2fd96bd577877159ddcddf6778ffc..f40583ac0396ed621541b1d1bbe9a5af1f93a962 100644
--- a/man/plot_hru_pw_day.Rd
+++ b/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, title = "", years = 1900:2100)
+plot_hru_pw_day(sim_verify, hru_id, var, years = 1900:2100, add_crop = TRUE)
}
\arguments{
\item{sim_verify}{Simulation output of the function \code{run_swat_verification()}.
@@ -15,13 +15,19 @@ 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.}
+
+\item{add_crop}{TRUE adds subplot with growing periods of crops in plotted HRUs.}
}
\value{
-Returns a table with hru ids and attributes.
+Returns a ggplot or patchwork ggplot of daily hru_pw output variables
}
\description{
plot_hru_pw_day plots daily time series of variables from the output file hru_pw_day
}
+\examples{
+\dontrun{
+plot_hru_pw_day(sim_nostress, hru_id = 1, var = c('lai', 'bioms'), add_crop = TRUE)
+}
+
+}