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11
.gitignore
vendored
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11
.gitignore
vendored
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#ignore .Rhistory
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.Rhistory
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#ignore all the data files
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data/*
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#ignore the figure files
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figures/*
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#except an example
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!figures/Elwha/ElwhaDischarge_last_6_months.png
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403
USGS_NWIS.R
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403
USGS_NWIS.R
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library(dataRetrieval, quietly = TRUE)
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library(tidyverse, quietly = TRUE)
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library(RColorBrewer, quietly = TRUE)
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library(scales, quietly = TRUE)
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setwd("/home/ben/Documents/dataProjects/USGS_NWIS")
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rivers <- data.frame(names = c("Elwha", "Calawah", "Hoh", "Dungeness", "Duckabush", "Wenatchee", "Snake", "Wisconsin", "Cedar", "Colorado"),
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siteNumber = c("12045500", "12043000", "12041200", "12048000", "12054000", "12462500", "13013650", "05407000", "12119000", "09380000"))
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#rivers <- rivers %>% filter(names %in% c("Elwha"))
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#rivers <- rivers %>% filter(names %in% c("Duckabush"))
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#rivers <- rivers %>% filter(names %in% c("Hoh"))
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ifelse(!dir.exists(file.path(getwd(), "figures")), dir.create(file.path(getwd(), "figures")), FALSE)
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ifelse(!dir.exists(file.path(getwd(), "data")), dir.create(file.path(getwd(), "data")), FALSE)
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for(i in 1:nrow(rivers)){
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rivername <- rivers$names[i]
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message(paste0(i, " of ", nrow(rivers), ": ", rivername, " River - ", Sys.time()))
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ifelse(!dir.exists(file.path(getwd(), paste0("figures/", rivername))), dir.create(file.path(getwd(), paste0("figures/", rivername))), FALSE)
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# this downloads most recent discharge daily value data for the river
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if(sum(list.files(path = "data") %>% match(paste0(rivername,"_discharge_dv.Rda")), na.rm = TRUE) == 0){
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message("downloading all data")
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discharge_dv <- readNWISdv(siteNumber = rivers$siteNumber[i], parameterCd = "00060")
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} else {
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load(paste0("data/",rivername,"_discharge_dv.Rda"))
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message(paste0("downloading new data: previous ", -1 * difftime(max(discharge_dv$Date), Sys.Date()), " days"))
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discharge_dv <- bind_rows(discharge_dv,
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readNWISdv(siteNumber = rivers$siteNumber[i], parameterCd = "00060", startDate = as.Date(max(discharge_dv$Date)) - days(1)) %>%
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filter(Date > max(discharge_dv$Date)))
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}
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save(discharge_dv, file = paste0("data/",rivername,"_discharge_dv.Rda"))
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# this downloads most recent discharge unit value (every 15 min) data for the river
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if(sum(list.files(path = "data") %>% match(paste0(rivername,"_discharge_uv.Rda")), na.rm = TRUE) == 0){
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discharge_uv <- readNWISuv(siteNumber = rivers$siteNumber[i], parameterCd = "00060")
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} else {
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load(paste0("data/",rivername,"_discharge_uv.Rda"))
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discharge_uv <- bind_rows(discharge_uv,
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readNWISuv(siteNumber = rivers$siteNumber[i], parameterCd = "00060", startDate = as.Date(max(discharge_uv$dateTime)) - days(1)) %>%
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filter(dateTime > max(discharge_uv$dateTime)))
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}
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save(discharge_uv, file = paste0("data/",rivername,"_discharge_uv.Rda"))
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message("processing data")
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discharge_dv["daymonth"] <- format(discharge_dv$Date, "%m%d")
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discharge_uv["daymonth"] <- format(discharge_uv$dateTime, "%m%d")
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#removes February 29th leap days from data
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discharge_dv <- discharge_dv %>% filter(daymonth != "0229")
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discharge_uv <- discharge_uv %>% filter(daymonth != "0229")
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#builds stats
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dayofyear <- unique(discharge_dv %>% arrange(daymonth) %>% pull(daymonth))
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quantiles <- lapply(dayofyear, function(i)
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quantile(discharge_dv %>% filter(daymonth == i, !is.na(X_00060_00003)) %>% pull(X_00060_00003),
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probs = c(seq(0.05, 0.95, 0.1), 0.5)))
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river_stats_dv <- data.frame(dayofyear, bind_rows(quantiles))
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river_stats_dv["Date"] <- ymd(paste0(year(Sys.Date()), river_stats_dv$dayofyear))
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river_stats_dv["dateTime"] <- ymd_h(paste0(year(Sys.Date()), river_stats_dv$dayofyear, 12))
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river_stats_dv <- bind_rows(river_stats_dv, river_stats_dv %>% mutate(Date = Date + years(1), dateTime = dateTime + years(1)), river_stats_dv %>% mutate(Date = Date - years(1), dateTime = dateTime - years(1)))
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river_states_ribbon <- bind_rows(
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data.frame(river_stats_dv %>% mutate(min = X5., max = X95.) %>% select(dayofyear, dateTime, min, max), "median" = 90),
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data.frame(river_stats_dv %>% mutate(min = X15., max = X25.) %>% select(dayofyear, dateTime, min, max), "median" = 70),
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data.frame(river_stats_dv %>% mutate(min = X25., max = X35.) %>% select(dayofyear, dateTime, min, max), "median" = 50),
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data.frame(river_stats_dv %>% mutate(min = X35., max = X45.) %>% select(dayofyear, dateTime, min, max), "median" = 30),
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data.frame(river_stats_dv %>% mutate(min = X45., max = X55.) %>% select(dayofyear, dateTime, min, max), "median" = 10))
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ribbon_colors <- c("#e7f3f9", "#bbddee", "#88c3e1", "#4ba5d1", "#228fc6")
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names(ribbon_colors) <- c("90%", "70%", "50%", "30%", "10%")
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mindvdate <- min(discharge_dv$Date)
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maxdvdate <- max(discharge_dv$Date)
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minuvdate <- min(discharge_uv$dateTime)
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maxuvdate <- max(discharge_uv$dateTime)
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#plots ----
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message("building charts")
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ggplot(data = river_stats_dv %>% filter(Date > Sys.time() - days(61),
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Date < Sys.time() + days(30))) +
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geom_ribbon(aes(x = dateTime,
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ymin = X5.,
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ymax = X95.,
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fill = "90%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X15.,
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ymax = X85.,
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fill = "70%"),
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alpha = 1) +
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geom_ribbon( aes(x = dateTime,
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ymin = X25.,
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ymax = X75.,
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fill = "50%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X35.,
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ymax = X65.,
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fill = "30%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X45.,
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ymax = X55.,
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fill = "10%"),
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alpha = 1) +
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geom_line(data = discharge_uv %>%
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filter(dateTime > floor_date(Sys.time(), "day") - days(60)),
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aes(x = dateTime,
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y = X_00060_00000,
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color = 'current year'),
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linewidth = 0.5) +
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scale_fill_manual(values = ribbon_colors, name = "Median X% of\nhistoric range") +
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scale_x_datetime(date_breaks = "1 week", date_labels = "%b %e", expand = expansion(mult = c(0,0))) +
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scale_y_continuous(label = comma) +
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scale_color_manual(values = "black") +
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theme_bw() +
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theme(axis.text.x = element_text(angle = 60, hjust = 1),
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plot.caption = element_text(color = "grey50"),
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plot.subtitle = element_text(color = "grey50")) +
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guides(fill = guide_legend(label.position = "right",
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nrow = 5),
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color = guide_legend(title = NULL,
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label.position = "bottom",
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nrow = 1)) +
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labs(title = paste0(rivername, " River discharge - last two months (",format(Sys.time() - days(61), "%B %e"), " - ", format(Sys.time(), "%B %e, %Y"), ")"),
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subtitle = paste("historical data", format(mindvdate, "%Y"), "-", format(maxdvdate, "%Y")),
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caption = "data: USGS",
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x = NULL,
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y = "Discharge (cubic feet per second)")
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ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_last_two_months.png"),
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device = "png",
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height = 11,
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width = 17,
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units = "in")
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ggplot(data = river_stats_dv %>% filter(Date > Sys.time() - months(6) - days(1),
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Date < Sys.time() + months(3))
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) +
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geom_ribbon(aes(x = dateTime,
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ymin = X5.,
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ymax = X95.,
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fill = "90%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X15.,
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ymax = X85.,
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fill = "70%"),
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alpha = 1) +
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geom_ribbon( aes(x = dateTime,
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ymin = X25.,
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ymax = X75.,
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fill = "50%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X35.,
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ymax = X65.,
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fill = "30%"),
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alpha = 1) +
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geom_ribbon(aes(x = dateTime,
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ymin = X45.,
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ymax = X55.,
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fill = "10%"),
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alpha = 1) +
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geom_line(data = discharge_uv %>%
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filter(dateTime > floor_date(Sys.time(), "day") - months(6)),
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aes(x = dateTime,
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y = X_00060_00000,
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color = "current year"),
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linewidth = 0.5) +
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scale_fill_manual(values = ribbon_colors, name = "Median X% of\nhistoric range") +
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scale_x_datetime(date_breaks = "1 month", date_labels = "%b", expand = expansion(mult = c(0,0))) +
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scale_y_continuous(label = comma, expand = expansion(mult = c(0, 0.1)), limits = c(0, NA)) +
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scale_color_manual(values = "black") +
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theme_bw() +
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theme(axis.text.x = element_text(hjust = -1),
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panel.grid.minor = element_blank(),
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plot.caption = element_text(color = "grey50"),
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plot.subtitle = element_text(color = "grey50")) +
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guides(fill = guide_legend(label.position = "right",
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nrow = 5),
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color = guide_legend(title = NULL,
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label.position = "bottom",
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nrow = 1)) +
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labs(title = paste0(rivername, " River discharge - last 6 months (",format(Sys.time() - months(6), "%B %e, %Y"), " - ", format(Sys.time(), "%B %e, %Y"), ")"),
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subtitle = paste("historical data", format(mindvdate, "%Y"), "-", format(maxdvdate, "%Y")),
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caption = "data: USGS",
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x = NULL,
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y = "Discharge (cubic feet per second)")
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ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_last_6_months.png"),
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device = "png",
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height = 11,
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width = 17,
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units = "in")
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ggplot(data = river_stats_dv %>% filter(year(Date) %in% year(Sys.Date()))) +
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geom_ribbon(aes(x = Date,
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ymin = X5.,
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ymax = X95.,
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fill = "90%"),
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alpha = 1) +
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geom_ribbon(aes(x = Date,
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ymin = X15.,
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ymax = X85.,
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fill = "70%"),
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alpha = 1) +
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geom_ribbon( aes(x = Date,
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ymin = X25.,
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ymax = X75.,
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fill = "50%"),
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alpha = 1) +
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geom_ribbon(aes(x = Date,
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|
ymin = X35.,
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|
ymax = X65.,
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|
fill = "30%"),
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|
alpha = 1) +
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geom_ribbon(aes(x = Date,
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|
ymin = X45.,
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|
ymax = X55.,
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|
fill = "10%"),
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|
alpha = 1) +
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geom_line(data = discharge_dv %>%
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|
filter(Date > ymd(paste(year(Sys.Date()) - 5, 1, 1))) %>%
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|
mutate(years = year(Date)),
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|
aes(x = ymd(paste(year(Sys.Date()), daymonth)),
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|
y = X_00060_00003,
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|
color = "Daily Value"),
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|
linewidth = 0.5) +
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|
facet_grid(years ~ ., scales = "free_x", space = "free_x") +
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|
scale_fill_manual(values = ribbon_colors, name = "Median X% of\nhistoric range") +
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|
scale_color_manual(values = "black") +
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|
scale_x_date(date_breaks = "1 month", date_labels = "%b", expand = expansion(mult = c(0,0))) +
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|
scale_y_continuous(label = comma) +
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|
theme_bw() +
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|
theme(axis.text.x = element_text(hjust = -2.5),
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|
plot.caption = element_text(color = "grey50"),
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|
plot.subtitle = element_text(color = "grey50")) +
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|
guides(fill = guide_legend(label.position = "right",
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|
nrow = 5),
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|
color = guide_legend(title = NULL,
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|
label.position = "bottom",
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|
nrow = 1)) +
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|
coord_cartesian(ylim = c(0, max(river_stats_dv$X95.))) +
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|
labs(title = paste(rivername, "River discharge - last 5 years"),
|
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|
subtitle = paste(format(ymd(paste(year(Sys.Date()) - 5, 1, 1)), "%B %e, %Y"), "-", format(Sys.Date(), "%B %e, %Y")),
|
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|
caption = "data: USGS",
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|
x = NULL,
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|
y = "Discharge (cubic feet per second)")
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|
ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_last5years.png"),
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|
device = "png",
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|
height = 11,
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|
width = 17,
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units = "in")
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|
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|
ggplot() +
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|
geom_line(data = discharge_dv %>%
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filter(Date > ymd(paste(year(Sys.Date()) - 5, 1, 1))) %>%
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|
mutate(years = year(Date)),
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|
aes(x = ymd(paste(year(Sys.Date()), daymonth)),
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|
y = X_00060_00003,
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color = as.factor(years)),
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|
linewidth = 1,
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||||||
|
alpha = 0.5) +
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|
scale_color_brewer(palette = "Set3") +
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|
scale_x_date(date_breaks = "1 month", date_labels = "%b", expand = expansion(mult = c(0.001,0))) +
|
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|
scale_y_continuous(label = comma) +
|
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|
theme_bw() +
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|
theme(axis.text.x = element_text(hjust = -1),
|
||||||
|
plot.caption = element_text(color = "grey50"),
|
||||||
|
plot.subtitle = element_text(color = "grey50")) +
|
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|
labs(title = paste(rivername, "River discharge - last 5 years"),
|
||||||
|
subtitle = paste(format(ymd(paste(year(Sys.Date()) - 5, 1, 1)), "%B %e, %Y"), "-", format(Sys.Date(), "%B %e, %Y")),
|
||||||
|
caption = "USGS data",
|
||||||
|
x = NULL,
|
||||||
|
y = "Discharge (cubic feet per second)") +
|
||||||
|
guides(color = guide_legend(title = NULL,
|
||||||
|
label.position = "right",
|
||||||
|
legend.key.size = unit(3,"line")))
|
||||||
|
ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_last5years_comb.png"),
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||||||
|
device = "png",
|
||||||
|
height = 11,
|
||||||
|
width = 17,
|
||||||
|
units = "in")
|
||||||
|
|
||||||
|
ggplot() +
|
||||||
|
geom_boxplot(data = discharge_uv %>%
|
||||||
|
filter(dateTime > ymd(paste(year(Sys.Date()) - 5, 1, 1))) %>%
|
||||||
|
mutate(year = year(dateTime),
|
||||||
|
month = month(dateTime, label = TRUE)),
|
||||||
|
aes(x = as.factor(month),
|
||||||
|
y = X_00060_00000,
|
||||||
|
fill = as.factor(year)),
|
||||||
|
outlier.shape=NA,
|
||||||
|
size = 0.1) +
|
||||||
|
geom_vline(xintercept=c(seq(1.5, 11.5, 1)), colour='black', linewidth = 0.3, linetype = "dotted") +
|
||||||
|
scale_fill_brewer(palette = "Set3") +
|
||||||
|
scale_y_continuous(label = comma) +
|
||||||
|
coord_cartesian(ylim = c(0, max(river_stats_dv$X95.))) +
|
||||||
|
theme_bw() +
|
||||||
|
theme(panel.grid.major = element_blank(),
|
||||||
|
panel.grid.minor.y = element_blank(),
|
||||||
|
panel.grid.minor.x = element_line(),
|
||||||
|
axis.ticks.x = element_blank(),
|
||||||
|
plot.caption = element_text(color = "grey50"),
|
||||||
|
plot.subtitle = element_text(color = "grey50")) +
|
||||||
|
guides(fill = guide_legend(title = NULL,
|
||||||
|
label.position = "right")) +
|
||||||
|
labs(title = paste(rivername, "River discharge - last 5 years"),
|
||||||
|
subtitle = paste(format(ymd(paste(year(Sys.Date()) - 5, 1, 1)), "%B %e, %Y"), "-", format(Sys.Date(), "%B %e, %Y")),
|
||||||
|
caption = "data: USGS",
|
||||||
|
x = NULL,
|
||||||
|
y = "Discharge (cubic feet per second)")
|
||||||
|
ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_boxplot.png"),
|
||||||
|
device = "png",
|
||||||
|
height = 11,
|
||||||
|
width = 17,
|
||||||
|
units = "in")
|
||||||
|
|
||||||
|
ggplot(data = river_stats_dv %>% filter(year(Date) %in% year(Sys.Date()))) +
|
||||||
|
geom_ribbon(aes(x = Date,
|
||||||
|
ymin = X5.,
|
||||||
|
ymax = X95.,
|
||||||
|
fill = "90%"),
|
||||||
|
alpha = 0.5) +
|
||||||
|
geom_ribbon(aes(x = Date,
|
||||||
|
ymin = X15.,
|
||||||
|
ymax = X85.,
|
||||||
|
fill = "70%"),
|
||||||
|
alpha = 0.5) +
|
||||||
|
geom_ribbon( aes(x = Date,
|
||||||
|
ymin = X25.,
|
||||||
|
ymax = X75.,
|
||||||
|
fill = "50%"),
|
||||||
|
alpha = 0.5) +
|
||||||
|
geom_ribbon(aes(x = Date,
|
||||||
|
ymin = X35.,
|
||||||
|
ymax = X65.,
|
||||||
|
fill = "30%"),
|
||||||
|
alpha = 0.5) +
|
||||||
|
geom_ribbon(aes(x = Date,
|
||||||
|
ymin = X45.,
|
||||||
|
ymax = X55.,
|
||||||
|
fill = "10%"),
|
||||||
|
alpha = 0.5) +
|
||||||
|
geom_line(data = discharge_dv %>%
|
||||||
|
filter(Date > ymd(paste(year(Sys.Date()), 1, 1))),
|
||||||
|
aes(x = Date,
|
||||||
|
y = X_00060_00003,
|
||||||
|
color = "current year"),
|
||||||
|
linewidth = 0.7) +
|
||||||
|
scale_x_date(date_breaks = "1 month", date_labels = "%b", expand = expansion(mult = c(0.001,0))) +
|
||||||
|
scale_y_continuous(label = comma, expand = expansion(mult = c(0, NA))) +
|
||||||
|
scale_fill_manual(values = ribbon_colors, name = "Median X% of\nhistoric range") +
|
||||||
|
scale_color_manual(values = "black") +
|
||||||
|
coord_cartesian(ylim = c(0, max(river_stats_dv$X95.))) +
|
||||||
|
theme_bw() +
|
||||||
|
theme(axis.text.x = element_text(hjust = -1),
|
||||||
|
plot.caption = element_text(color = "grey50"),
|
||||||
|
plot.subtitle = element_text(color = "grey50")) +
|
||||||
|
guides(fill = guide_legend(label.position = "right",
|
||||||
|
nrow = 5),
|
||||||
|
color = guide_legend(label.position = "bottom",
|
||||||
|
nrow = 1)) +
|
||||||
|
labs(title = paste(rivername, "River discharge - current year compared to historical"),
|
||||||
|
subtitle = paste("historical data", format(mindvdate, "%Y"), "-", format(maxdvdate, "%Y")),
|
||||||
|
caption = "data: USGS",
|
||||||
|
x = NULL,
|
||||||
|
y = "Discharge (cubic feet per second)",
|
||||||
|
color = NULL)
|
||||||
|
ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_current_compared.png"),
|
||||||
|
device = "png",
|
||||||
|
height = 11,
|
||||||
|
width = 17,
|
||||||
|
units = "in")
|
||||||
|
|
||||||
|
ggplot(data = discharge_dv %>%
|
||||||
|
mutate(decade = floor(year(Date)/10)*10)) +
|
||||||
|
geom_boxplot(aes(x = Date,
|
||||||
|
y = X_00060_00003,
|
||||||
|
group = decade),
|
||||||
|
outlier.shape = NA) +
|
||||||
|
theme(plot.caption = element_text(color = "grey50"),
|
||||||
|
plot.subtitle = element_text(color = "grey50")) +
|
||||||
|
coord_cartesian(ylim = c(0, max(river_stats_dv$X85.))) +
|
||||||
|
labs(title = paste(rivername, "River - discharge by decade"),
|
||||||
|
subtitle = paste(format(mindvdate, "%Y"), "-", format(maxdvdate, "%Y")),
|
||||||
|
caption = "data: USGS",
|
||||||
|
x = "Decade",
|
||||||
|
y = "Discharge (cubic feet per second)")
|
||||||
|
ggsave(file = paste0("figures/",rivername, "/", rivername, "Discharge_decades.png"),
|
||||||
|
device = "png",
|
||||||
|
height = 11,
|
||||||
|
width = 17,
|
||||||
|
units = "in")
|
||||||
|
}
|
||||||
|
message(paste0("Finished - ", Sys.time()))
|
||||||
Loading…
Add table
Add a link
Reference in a new issue