---
title: "wxgenR - GHCN CONUS evaluation - in sample"
author: "Subhrendu Gangopadhyay, Lindsay Bearup, David Woodson, Andrew Verdin, Eylon Shamir, Eve Halper, Marketa McGuire"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{wxgenR - GHCN CONUS evaluation - in sample}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

A weather generator is a numerical tool that resamples a daily time series of precipitation, temperature, and season many times, while
preserving observed or projected characteristics of importance, such as the statistics of the
transition between wet and dry days. The resulting large group, or ensemble, of likely rainfall
and temperature time series represents a range of possible amounts, daily patterns, and
seasonality. This weather generator is, to our knowledge, novel in that it includes *seasons* (up to 26) in training the simulation algorithm.  

The goal of `wxgenR` is to provide users a tool that can simulate, with fidelity, an ensemble of precipitation and temperature based on training data that could include, for example, station based point measurements, grid cell values derived from models or remotely sensed data, or basin averages. The incorporation of seasonality as a covariate in the training algorithm allows users to examine the effects of shifts in seasonality due to climate warming (e.g., earlier snowmelt seasons or prolonged summer dry periods). `wxgenR` is an effective and robust scenario planning tool for a wide variety of potential futures. 

## Running `wxgenR`

All that is needed to run `wxgenR` is a single time series of precipitation, temperature, and season. Up to 20 seasons may be defined, but most users will likely only need two to four based on their study region. For example, `wxgenR` is provided with basin-average data from nine different GHCN gauges within the conterminous United States. Within the data used to train the weather generator, four standard seasons are set (spring, summer, autumn, winter) for each day in the time series. The varying statistics of each season will impact the resulting simulations.

## Tutorial

For example, using the GHCN precipitation, temperature, and season data, we can generate simulated precipitation and temperature for any desired time length and ensemble size. Your variables *must* be named as the following: 'year', 'month', 'day', 'prcp', 'temp', 'season', whether they are input as a dataframe or a text file. All input variables must be contained within the same dataframe or text file. If inputting a text file, it must be comma separated (.csv). The weather generator can handle NA values for precipitation or temperature, but all other variables should be numeric values.

### Step 1: Load your data
```{r}
library(wxgenR)
library(tidyr)
library(reshape2)
library(ggpubr)
library(lubridate)
library(dplyr)
# library(data.table)
library(moments)
library(seas)
library(padr)
library(hydroGOF)
library(SpecsVerification)
# library(sm)
library(ggridges)

```
### Step 2: Select your run settings and run the weather generator

Use the variables within the wx() function like `syr` and `eyr` (start and end year) to set the temporal boundaries from which to sample, otherwise, if left empty the start and end years will default to the beginning and end of your training data. Use `nsim` to set the length (in years) of your simulated weather, and `nrealz` to set the ensemble size (number of traces). 

The variable `wwidth` will set the sampling window for each day of year (Jan. 1 through Dec. 31) for every year in the simulation. The sampling window for each day of year is +/- `wwidth` + 1, effectively sampling `wwidth` number of days before and after each day of year, including that day of year. A lower value for `wwidth` will sample fewer surrounding days and a higher value will sample more days, resulting in dampened and heightened variability, respectively. Typical setting of `wwidth` is between 1 and 15, resulting in a daily sampling window of 3 days and 31 days, respectively. Generally, higher and lower values of `wwidth` result in higher and lower variance, respectively, in the simulated data. 

For example, to simulate precipitation on day 1 of the simulation (Jan. 1 of year 1), with `wwidth` = 1 (a 3-day window), the algorithm will sample days in the training record between (and including) December 31 and January 2 (for all years in the training record). For day 2 of the simulation (Jan. 2 of year 1), the algorithm will sample days in the training record between January 1 and January 3. Simulation day 3 (Jan. 3) will sample between January 2 and January 4, and so on. Increasing `wwidth` to 2 (a 5-day window) will sample between December 30 and January 3 for Jan. 1 simulations, December 31 to January 4 for Jan. 2, and January 1 to January 5 for Jan. 3, and so on.    

In some cases, the `wwidth` will be automatically increased through an adaptive window width if precipitation occurred on a given day but there were less than two daily precipitation values over 0.01 inches during the window for that day. `wwidth` will adaptively increase by 1 until two or more daily precipitation values over 0.01 inches are in each window. Adaptive window width is most likely to occur in regions with high aridity, dry seasons, a small initial value of `wwidth` is used, or if the number of years in the training data is relatively short (e.g., less than 30 years). To display the results of the adaptive window width, set `awinFlag = T`.

Here, our training data spans January 1, 2000 through the end of the GHCN record so `syr` is set to be 2000 or greater. We want a simulation length of 23-years (`nsim`) in order to match the length of the historical record and 2 traces in our ensemble (`nrealz = 2`) for brevity. Sampling for each day of the year will sample from the preceding 3-days, the day of, and the following 3-days (`wwidth = 3`) for a total window size of 7-days.

We may also want to increase the variability of our simulated precipitation by sampling outside the historical envelope with an Epanechnikov Kernel (`ekflag = T`). For more details on the Epanechnikov kernel and its use in a weather generator, see Rajagopalan et al. (1996). Setting `tempPerturb = T` will increase the variability of the simulated temperature by adding random noise from a normal distribution fit using a mean of zero and a standard deviation equal to the monthly standard deviation of simulated temperature residuals. Given that simulated daily temperature at time t is a function of temperature(t-1), cosine(t), sine(t), precipitation occurrence(t), and monthly mean temperature(t), the standard deviation of daily residuals from this model is calculated for each month and used to add random noise to the simulated temperature. The temperature simulation approach is inspired by- and adapted from- Verdin et al. (2015, 2018).

Since the training data has units of inches and degrees Fahrenheit for precipitation and temperature, respectively, we must set `unitSystem = "U.S. Customary"`.

### Pre-processing was done on the GHCN station data using the following code (not run here):
```{r, eval = FALSE}
# path = ".../path to GHCN station data/"
# files = list.files(path, full.names = T)

# n = length(files)
# 
# fileList = vector("list", n)
# 
# i = 1
# for(i in 1:n){
#   
#   fi = read.csv(files[i])
#   
#   staNum = fi$STATION[1]
#   staNam = fi$NAME[1]
#   
#   fi.p = fi %>%
#   dplyr::select(DATE, PRCP, TMAX, TMIN) %>% 
#   mutate(DATE = ymd(DATE)) %>%
#   pad(interval = "day") %>%
#   mutate(year = year(DATE), month = month(DATE), day = day(DATE),
#          prcp = PRCP, temp = (TMAX + TMIN)/2, season = month) %>%
#   mutate(daymonth = strftime(DATE, format="%m-%d")) %>%
#   transform(t.clim = ave(temp, daymonth, FUN=function(x) mean(x, na.rm=TRUE))) %>%
#   transform(temp = ifelse(is.na(temp),t.clim,temp)) %>%
#   dplyr::select(year, month, day, prcp, temp, season)
#   
#   if(fi.p$month[1] != 1 | fi.p$day[1] != 1){
#     fi.p = subset(fi.p, year > fi.p$year[1])
#   }
#   
#   if(tail(fi.p$month, 1) != 12 | tail(fi.p$day, 1) != 31){
#     fi.p = subset(fi.p, year < tail(fi.p$year, 1))
#   }
#   
#   out = list(staNum, staNam, fi.p)
#   names(out) = c("Station ID", "Station Name", "Data")
#   
#   fileList[[i]] = out
# 
# }
```

### Read in pre-processed GHCN station data
```{r}
data(stationData)

glimpse(stationData)
```

### Rename data
```{r}
fileList = stationData
n = length(stationData)
```

### run loop of wxgenR on each station
```{r, results = 'hide'}

datList = vector("list", n)

nsim = 23   #number of simulation years
nrealz = 2 #number of traces in ensemble
  
run = T

if(run == T){

  i = 1
  for(i in 1:n){
    
    cat(paste0("Starting: ", fileList[[i]][[2]], "\n"))
    
    dat.i = fileList[[i]][[3]]
    
    trnDat = subset(dat.i, year >= 2000)
       
    verDat = subset(dat.i, year >= 2000)
    
    z = wx(trainingData = trnDat,
           nsim = nsim, nrealz = nrealz, aseed = 20190409,
           wwidth = 3, unitSystem = "U.S. Customary", ekflag = T,
           awinFlag = T, tempPerturb = T, numbCores = 2)
  
    # out = list(fileList[[i]][[1]], fileList[[i]][[2]], trnYrs, trnDat, verDat, z)
  
    out = list(fileList[[i]][[1]], fileList[[i]][[2]], verDat, z)
    
    datList[[i]] = out
    
  }

}

```

The wx() function will return a list containing both your input/training data, and a variety of processed outputs, named here as the variable `z`. Within `z`, `dat.d` is the original input data as well as some intermediary variables. `simyr1` contains the years within your training data that were sampled to generate simulated values for each trace. `X` is the occurrence of daily precipitation for each trace, where 1 and 0 indicate the presence and absence of precipitation, respectively. `Xseas` is the season index for each day and trace. `Xpdate` shows which days from the training data were sampled for each simulated day and trace, if precipitation was simulated to occur on a given day. `Xpamt` is the simulated precipitation amount for each day and trace. `Xtemp` is the simulated temperature for each day and trace. 

Generally, `Xpamt` and `Xtemp` will be of most interest to users as these are the desired outputs of simulated daily precipitation and temperature.


### Option to create output directories for plots and data (not run)
```{r, eval = FALSE}
outTag = "inSample"

outDir = paste0(".../path to output directory/", outTag)
dir.create(outDir)

outDirPlots = paste0(".../path to output directory/", outTag, "/plots/")
dir.create(outDirPlots)

outDirPlotsSta = paste0(".../path to output directory/", outTag, "/plots/stations/")
dir.create(outDirPlotsSta)

```

### Option to save simulation data or read in previously created data (not run)
```{r, eval = FALSE}
if(run == T){
  saveRDS(datList, paste0(outDir,"/trainingData_and_simResults.Rds"))
}else if(run == F){
  datList = readRDS(paste0(outDir,"/trainingData_and_simResults.Rds"))
}
```

### Step 3: Analyze simulated weather
### First, use modified approach from writeSim function to post-process/format output
```{r}

# z = datList[[1]][[4]]
# verDat = datList[[1]][[3]]

postProcess = function(z, verDat = NULL){

  #parse variables from wx() output
  dat.d = z$dat.d
  simyr1 = z$simyr1
  X = z$X
  Xseas = z$Xseas
  Xpdate = z$Xpdate
  Xpamt = z$Xpamt
  Xtemp = z$Xtemp
  
  #write simulation output
  #
  it1 <- seq(1, length(X[,1]), 366)
  it2 = it1+366-1
  
  #initialize storage
  sim.pcp = matrix(NA, nrow = nsim*366, ncol = nrealz+3)
  sim.tmp = matrix(NA, nrow = nsim*366, ncol = nrealz+3)
  sim.szn = matrix(NA, nrow = nsim*366, ncol = nrealz+3)
  
  #loop through realization
  irealz = 1
  for (irealz in 1:nrealz){
    
    outmat <- vector()
  
    #loop through simulation years
    isim = 1
    for (isim in 1:nsim){
      leapflag = FALSE
      ayr = simyr1[isim, irealz]
      if (leap_year(ayr)) leapflag = TRUE
      col1 = rep(isim, 366)        #column 1, simulation year
      d1 = ayr*10^4+01*10^2+01; d2 = ayr*10^4+12*10^2+31
      i1 = which(dat.d$date1 == d1)
      i2 = which(dat.d$date1 == d2)
      col2 = dat.d$date1[i1:i2]   #column 2, simulation date
      if (leapflag == FALSE) col2 = c(col2,NA)
      i1 = it1[isim]
      i2 = it2[isim]
      col3 = Xseas[i1:i2, irealz]  #column 3, simulation season
      col4 = X[i1:i2, irealz]      #column 4, precipitation occurrence
      col5 = Xpdate[i1:i2, irealz] #column 5, precipation resampling date
      col6 = Xpamt[i1:i2, irealz]  #column 6, resampled precipitation amount
      col7 = Xtemp[i1:i2, irealz]  #column7, simulated temperature
  
      #create time series of 'simulation day'
      sim.yr = rep(isim, length(col2))
      sim.month = month(ymd(col2))
      sim.day = day(ymd(col2))
  
      outmat = rbind(outmat, cbind(sim.yr, sim.month, sim.day, col6, col7, col3))
    } #isim
  
    colnames(outmat) = c("simulation year", "month", "day", "prcp", "temp", "season")
    
    if(irealz == 1){
      sim.pcp[,1:3] = outmat[,1:3]
      sim.tmp[,1:3] = outmat[,1:3]
      sim.szn[,1:3] = outmat[,1:3]
    }
    
      sim.pcp[,irealz+3] = outmat[,4]
      sim.tmp[,irealz+3] = outmat[,5]
      sim.szn[,irealz+3] = outmat[,6]
  
  } #irealz
  
  #format
  sim.pcp = formatting(df = sim.pcp, dat.d)
  sim.tmp = formatting(df = sim.tmp, dat.d)
  sim.szn = formatting(df = sim.szn, dat.d)
    
  #format training data
  if(is.null(verDat) == FALSE){
    
    verDat$date = ymd(paste(verDat$year, verDat$month, verDat$day, sep = "-"))

    verDat.p = verDat %>%
      mutate(yday = as.numeric(yday(date)),
           week = as.numeric(week(date))
           )
    
    #format training data
    # colnames(dat.d)[11] = "yday"
    obs.pcp = dplyr::select(verDat.p, year, month, day, week, date, yday, prcp)
    obs.pcp$prcp = replace_na(obs.pcp$prcp, 0)
    obs.tmp = dplyr::select(verDat.p, year, month, day, week, date, yday, temp)
    
  } else{
    
    #format training data
    colnames(dat.d)[11] = "yday"
    obs.pcp = dat.d[,c(1:3,8:9,11,4)]
    obs.tmp = dat.d[,c(1:3,8:9,11,5)]  
    
  }
    
  out = list(sim.pcp, sim.tmp, sim.szn, obs.pcp, obs.tmp)

  names(out) = c("sim.pcp", "sim.tmp", "sim.szn", "obs.pcp", "obs.tmp")
  
  return(out)
  
}

```

#Format dataframes for simulated precip, temperature, and season
```{r}

# df = sim.pcp

formatting = function(df, dat.d){
  
  df = as.data.frame(df)
  
  colnames(df) = c("simulation year", "month", "day", paste0("Trace_", 1:nrealz))

  #remove 366 days for non-leap years
  df = drop_na(df, c(month, day))
  
  #assign simulation year to start at the same time as training data
  df$`simulation year` = df$`simulation year` + dat.d$year[1] - 1    
  
  #format date
  df$Date = ymd(paste(df$`simulation year`, df$month, df$day, sep = "-"))
  
  #remove years that aren't leap years
  # df = drop_na(df, Date)
  
  df = df %>%
    mutate(yday = as.numeric(yday(Date)),
           week = as.numeric(week(Date))) %>%
    relocate(c(Date,yday,week), .after = day) %>%
    reshape2::melt(id = 1:6)
    
  return(df)
}

```

```{r}

if(run == T){

  datListProc = vector("list", n)
  
  i = 1
  for(i in 1:n){
    
    z = datList[[i]][[4]]
    
    verDat = datList[[i]][[3]]
    
    z.p = postProcess(z, verDat)
    
    z.p.c = list(z.p, datList[[i]][[1]], datList[[i]][[2]])
    
    datListProc[[i]] = z.p.c
    
  }

}

```

### Option to save post-processed simulation results or read in previously saved data (not run)
```{r, eval = FALSE}
if(run == T){
  saveRDS(datListProc, paste0(outDir,"/simResultsPostProcessed.Rds"))
}else if(run == F){
  datListProc = readRDS(paste0(outDir,"/simResultsPostProcessed.Rds"))
}
```

### Rename two stations for better readability
```{r}
datListProc[[4]][[3]] = "BLACKSBURG NWS, VA US"
datListProc[[5]][[3]] = "BANGOR INTL AIRPORT, ME US"
```

```{r}
# i = 1
# simDat = datListProc[[i]][[1]]$sim.tmp
# obsDat = datListProc[[i]][[1]]$obs.tmp
# Tag = "Temp"
# ID = datListProc[[i]][[2]]

i = 1
simDat = datListProc[[i]][[1]]$sim.pcp
obsDat = datListProc[[i]][[1]]$obs.pcp
Tag = "Precip"
ID = datListProc[[i]][[2]]

monthlyPlot = function(simDat, obsDat, Tag, ID){
  
  if(Tag == "Temp"){
    
    simM = simDat %>%
      drop_na() %>%
      group_by(variable, month, `simulation year`) %>%
      summarise(
        mean = mean(value, na.rm = T),
        max = max(value, na.rm = T),
        min = min(value, na.rm = T),
        sd = sd(value, na.rm = T),
        skew = skewness(value, na.rm = T)
        ) %>%
      ungroup()
    
    simMM <- simM %>%
      group_by(variable, month) %>%
      summarise(
        mean=mean(mean),
        max=mean(max),
        min=mean(min),
        sd=sqrt(mean(sd^2)),
        skew=mean(skew, na.rm=T)
        ) %>%
      ungroup()
    
    obs <- obsDat %>%
      drop_na() %>%
      group_by(month, year) %>%
      summarise(
        mean = mean(temp, na.rm = T),
        max = max(temp, na.rm = T),
        min = min(temp, na.rm = T),
        sd = sd(temp, na.rm = T),
        skew = skewness(temp, na.rm = T),
        ) %>%
      ungroup()
    
    obsMM <- obs %>%
      group_by(month) %>%
      summarise(
        mean = mean(mean, na.rm = T),
        max = mean(max, na.rm = T),
        min = mean(min, na.rm = T),
        sd = sqrt(mean(sd^2)),
        skew = mean(skew, na.rm=T)
        ) %>%
      mutate(variable = "Observed") %>%
      relocate(variable) %>%
      ungroup()
    
  # colnames(obsMM)[-1] = paste0("obs_", colnames(obsMM)[-1])
  
  }else if(Tag == "Precip"){
    
    simM = simDat %>%
      drop_na() %>%
      group_by(variable, month, `simulation year`) %>%
      summarise(
        sum = sum(value, na.rm = T),
        max = max(value, na.rm = T),
        min = min(value, na.rm = T),
        sd = sd(value, na.rm = T),
        skew = skewness(value, na.rm = T)
        ) %>%
      ungroup()  
    
      simMM <- simM %>%
        group_by(variable, month) %>%
        summarise(
          sum=mean(sum),
          max=mean(max),
          min=mean(min),
          sd=sqrt(mean(sd^2)),
          skew=mean(skew, na.rm = T)
          ) %>%
        ungroup()
      
      obs <- obsDat %>%
        drop_na() %>%
        group_by(month, year) %>%
        summarise(
          sum = sum(prcp, na.rm = T),
          max = max(prcp, na.rm = T),
          min = min(prcp, na.rm = T),
          sd = sd(prcp, na.rm = T),
          skew = skewness(prcp, na.rm = T)
          ) %>%
        ungroup()
    
      obsMM <- obs %>%
        group_by(month) %>%
        summarise(
          sum = mean(sum, na.rm = T),
          max = mean(max, na.rm = T),
          min = mean(min, na.rm = T),
          sd = sqrt(mean(sd^2)),
          skew = mean(skew, na.rm = T)
          ) %>%
        mutate(variable = "Observed") %>%
        relocate(variable) %>%
        ungroup()
    
  # colnames(obsMM)[-1] = paste0("obs_", colnames(obsMM)[-1])
  
  }
  
  densityData = data.frame(simM[,c(2,4)], Tag = "Simulated")
  densityData = bind_rows(densityData, data.frame(obs[,c(1,3)], Tag = "Observed"))
  
  df.comb = rbind(obsMM, simMM)
  
  #plotting --------------------------------
  
  if(Tag == "Temp"){
    
    p1 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = mean, group = month)) +
      geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = mean), color = "blue", size = 0.5) +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = mean), color = "blue", size = 1.5, show.legend = T) +
      scale_colour_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab("Temperature (°F)") +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Mean Monthly Temperature \n", ID))
    
    #monthly pdf
    p6 = ggplot(densityData) + 
        geom_density_ridges(aes(y = as.factor(month), x = mean, fill = Tag, color = Tag), alpha = 0.5) +
        scale_fill_manual(values = c("blue", "black"), labels = c("Observed", "Simulated")) +
        scale_color_manual(values = c("blue", "black"), guide = "none") +
        ylab("Month") + xlab("Temperature (°F)") +
        theme_bw() +
        theme(axis.title = element_text(face = "bold"),
              text=element_text(size=12),
              panel.grid.major = element_line(),
              legend.title=element_blank(),
              plot.title = element_text(size=8)
              ) +
        # scale_x_continuous(breaks = 1:12) +
        ggtitle(paste0("Average Monthly Temperature \n", ID))
    
  }else if(Tag == "Precip"){
    
     p1 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = sum, group = month)) +
      geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = sum), size = 0.5, color = "blue") +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = sum), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab("Precipitation (inches)") +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Total Monthly Precipitation \n", ID))
     
    #monthly pdf
    p6 = ggplot(densityData) + 
        geom_density_ridges(aes(y = as.factor(month), x = sum, fill = Tag, color = Tag), alpha = 0.5) +
        scale_fill_manual(values = c("blue", "black"), labels = c("Observed", "Simulated")) +
        scale_color_manual(values = c("blue", "black"), guide = "none") +
        ylab("Month") + xlab("Precipitation (inches)") +
        theme_bw() +
        theme(axis.title = element_text(face = "bold"),
              text=element_text(size=12),
              panel.grid.major = element_line(),
              legend.title=element_blank(),
              plot.title = element_text(size=8)
              ) +
        # scale_x_continuous(breaks = 1:12) +
        ggtitle(paste0("Total Monthly Precipitation\n", ID))
    
  }

  if(Tag == "Temp"){
    yLabel = "Temperature "
    units = "(°F)"
  } else if(Tag == "Precip"){
    yLabel = "Precipitation "
    units = "(inches)"
  }
  
  #monthly SD
  p2 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = sd, group = month)) +
      geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = sd), size = 0.5, color = "blue", show.legend = T) +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = sd), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab(paste0("Standard Deviation ", units)) +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Standard Deviation in Monthly ", yLabel, "\n", ID))
  
  
  #monthly Skew
  p3 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = skew, group = month)) +
      geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = skew), size = 0.5, color = "blue", show.legend = T) +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = skew), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab("Skew (-)") +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Skew in Monthly ", yLabel, "\n", ID))
  
  #monthly max
  p4 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = max, group = month)) +
       geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = max), size = 0.5, color = "blue", show.legend = T) +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = max), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab(paste0("Maximum ", units)) +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Monthly Maximum ", yLabel, "\n", ID))
  
  #monthly min
  p5 = ggplot(df.comb) + 
      geom_boxplot(data = subset(df.comb, variable != "Observed"), aes(x = month, y = min, group = month)) +
       geom_line(data = subset(df.comb, variable == "Observed"), aes(x = month, y = min), size = 0.5, color = "blue", show.legend = T) +
      geom_point(data = subset(df.comb, variable == "Observed"), aes(x = month, y = min), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
      xlab("Month") + ylab(paste0("Minimum ", units)) +
      theme_bw() +
      theme(axis.title = element_text(face = "bold"),
            text=element_text(size=12),
            panel.grid.major = element_line(),
            legend.title=element_blank(),
            plot.title = element_text(size=8)
            ) +
      scale_x_continuous(breaks = 1:12) +
      ggtitle(paste0("Average Monthly Minimum ", yLabel, "\n", ID))
  
  if(Tag == "Temp"){
    p.comb = ggarrange(p1, p2, p5, p4, nrow = 2, ncol = 2, common.legend = TRUE, legend = "right")
  }else if(Tag == "Precip"){
    p.comb = ggarrange(p1, p2, p3, p4, nrow = 2, ncol = 2, common.legend = TRUE, legend = "right")
  }  
  
  print(p.comb)
  
  #don't save plot to file
  # p.out = paste0(outDirPlotsSta, "/monthlyStats_", Tag, "_", ID, ".png")
  # ggsave(filename = p.out, plot = p.comb, device = "png", height = 8, width = 8, units = "in")

  
  #skew and pdf case study
  if(Tag == "Temp"){
    p.comb = ggarrange(p3, p6, nrow = 1, ncol = 2, common.legend = TRUE, legend = "right")
    print(p.comb)
  
    # p.out = paste0(outDirPlotsSta, "/monthly_skewAndPDF_", Tag, "_", ID, ".png")
    # ggsave(filename = p.out, plot = p.comb, device = "png", height = 4, width = 8, units = "in")
  }  
  
 

  
  df.comb.o = df.comb %>%
    mutate(ID = ID, Tag = Tag)
  
  return(df.comb.o)
  
}

```

### plot monthly precipitation
```{r, fig.width=8, fig.height=8}

df.monthly.pcp = NULL

for(i in 1:n){
  
  simDat = datListProc[[i]][[1]]$sim.pcp
  obsDat = datListProc[[i]][[1]]$obs.pcp
  Tag = "Precip"
  ID = datListProc[[i]][[3]]
  df.i = monthlyPlot(simDat, obsDat, Tag, ID)
  
  df.monthly.pcp = rbind(df.monthly.pcp, df.i)
  
}

```

### plot monthly temperature
```{r, fig.width=8, fig.height=8}

df.monthly.tmp = NULL

for(i in 1:n){
  
  simDat = datListProc[[i]][[1]]$sim.tmp
  obsDat = datListProc[[i]][[1]]$obs.tmp
  Tag = "Temp"
  ID = datListProc[[i]][[3]]
  df.i = monthlyPlot(simDat, obsDat, Tag, ID)
  
  df.monthly.tmp = rbind(df.monthly.tmp, df.i)

}

```

```{r, fig.width=10, fig.height=10}
#plotting - facet plot

  p1 = ggplot(df.monthly.tmp) + 
    geom_boxplot(data = subset(df.monthly.tmp, variable != "Observed"), aes(x = month, y = mean, group = month)) +
    geom_line(data = subset(df.monthly.tmp, variable == "Observed"), aes(x = month, y = mean), size = 0.5, color = "blue", show.legend = T) +
    geom_point(data = subset(df.monthly.tmp, variable == "Observed"), aes(x = month, y = mean), size = 1.5, color = "blue", show.legend = T) +
      scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +
    xlab("Month") + ylab("Temperature (°F)") +
    theme_bw() +
    theme(axis.title = element_text(face = "bold"),
          text=element_text(size=12),
          panel.grid.major = element_line(),
          legend.title=element_blank(),
          plot.title = element_text(size=10),
          strip.text.x = element_text(size = 8)
          ) +
    scale_x_continuous(breaks = 1:12) +
    ggtitle(paste0("Average Mean Monthly Temperature ")) +
    facet_wrap(~ID, scales = "free")

print(p1)

# p.out = paste0(outDirPlots, "/monthlyStats_faceted_temperature.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```


```{r, fig.width=10, fig.height=10}

p1 = ggplot(df.monthly.pcp) + 
    geom_boxplot(data = subset(df.monthly.pcp, variable != "Observed"), aes(x = month, y = sum, group = month)) +
    geom_line(data = subset(df.monthly.pcp, variable == "Observed"), aes(x = month, y = sum), size = 0.5, color = "blue", show.legend = T) +
    geom_point(data = subset(df.monthly.pcp, variable == "Observed"), aes(x = month, y = sum), size = 1.5, color = "blue", show.legend = T) +
    scale_color_manual(values = c('blue'='blue'), labels = c('Observed')) +  
    xlab("Month") + ylab("Precipitation (inches)") +
    theme_bw() +
    theme(axis.title = element_text(face = "bold"),
          text=element_text(size=12),
          panel.grid.major = element_line(),
          legend.title=element_blank(),
          plot.title = element_text(size=10),
          strip.text.x = element_text(size = 8)
          ) +
    scale_x_continuous(breaks = 1:12) +
    ggtitle(paste0("Average Total Monthly Precipitation ")) +
    facet_wrap(~ID, scales = "free")

print(p1)

# p.out = paste0(outDirPlots, "/monthlyStats_faceted_precipitation.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")
  
```

#process and plot daily data

```{r, fig.width=10, fig.height=10}
i = 1
simDat = datListProc[[i]][[1]]$sim.pcp
obsDat = datListProc[[i]][[1]]$obs.pcp
Tag = "Precip"
ID = datListProc[[i]][[2]]
Name = datListProc[[i]][[3]]

dailyPlot = function(simDat, obsDat, Tag, ID, Name){
  
  simD = simDat %>%
    drop_na() %>%
    group_by(variable, yday) %>%
    summarise(
      mean = mean(value, na.rm = T),
      max = max(value, na.rm = T),
      min = min(value, na.rm = T),
      sd = sd(value, na.rm = T),
      skew = skewness(value, na.rm = T)
      ) %>%
    ungroup()
    
  simDq <- simD %>%
    group_by(yday) %>%
    summarise(
      mean_q5 = quantile(mean, 0.05, na.rm = T),
      mean_med = median(mean, na.rm = T),
      mean_q95 = quantile(mean, 0.95, na.rm =T),
      max_q5 = quantile(max, 0.05, na.rm = T),
      max_med = median(max, na.rm = T),
      max_q95 = quantile(max, 0.95, na.rm = T),
      min_q5 = quantile(min, 0.05, na.rm = T),
      min_med = median(min, na.rm = T),
      min_q95 = quantile(min, 0.95, na.rm = T),
      sd_q5 = quantile(sd, 0.05, na.rm = T),
      sd_med = median(sd),
      sd_q95 = quantile(sd, 0.95, na.rm = T),
      skew_q5 = quantile(skew, 0.05, na.rm = T),
      skew_med = median(skew, na.rm = T),
      skew_q95 = quantile(skew, 0.95, na.rm = T)
      ) %>%
      # drop_na() %>%
    ungroup()
  
  if(Tag == "Temp"){
    obs <- obsDat %>%
      drop_na() %>%
      group_by(yday) %>%
      summarise(
        mean = mean(temp, na.rm = T),
        max = max(temp, na.rm = T),
        min = min(temp, na.rm = T),
        sd = sd(temp, na.rm = T),
        skew = skewness(temp, na.rm = T)
        ) %>%
      ungroup()
  } else if(Tag == "Precip"){
    obs <- obsDat %>%
      drop_na() %>%
      group_by(yday) %>%
      summarise(
        mean = mean(prcp, na.rm = T),
        max = max(prcp, na.rm = T),
        min = min(prcp, na.rm = T),
        sd = sd(prcp, na.rm = T),
        skew = skewness(prcp, na.rm = T)
        ) %>%
      ungroup()
    }

  colnames(obs)[-1] = paste0("obs_", colnames(obs)[-1])
  
  df.comb = left_join(simDq, obs, by = "yday")
  
  #calc performance metrics
  
  ensMed.rmse = rmse(sim = simDq$mean_med, obs = obs$obs_mean)
  # ensMed.nse = NSE(sim = simDq$mean_med, obs = obs$obs_mean)
  
  ensMed.cor = cor(x = simDq$mean_med, y = obs$obs_mean, method = "spearman")

  ensDat = as.matrix(pivot_wider(simD, names_from = variable, values_from = mean, id_cols = yday))
  
  if(Tag == "Precip") ensRef =  as.matrix(pivot_wider(obsDat, names_from = year, values_from = prcp, id_cols = yday))
  if(Tag == "Temp") ensRef =  as.matrix(pivot_wider(obsDat, names_from = year, values_from = temp, id_cols = yday))

  crps.Dat = mean(EnsCrps(ens = ensDat[,-1], obs = obs$obs_mean))
  crps.Ref = mean(EnsCrps(ens = ensRef[,-1], obs = obs$obs_mean))

  crpss = 1 - crps.Dat/crps.Ref

  perfMetrics = data.frame(ID = ID, Name = Name, EnsMedRMSE = ensMed.rmse, CRPSS = crpss, EnsMedCor = ensMed.cor, Tag = Tag)
  
  #plotting --------------------------------
  lgdLoc = c(0.8, 0.9)
  
  if(Tag == "Temp"){
    yLabel = "Daily Temperature "
    units = "(°F)"
  } else if(Tag == "Precip"){
    yLabel = "Daily Precipitation "
    units = "(inches)"
  }
  
  trnAlpha = 0.65
  
  #daily mean
  p1 = ggplot(df.comb) +
  geom_ribbon(aes(x = yday, ymin = mean_q5, ymax = mean_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = mean_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_mean), size = 0.3, alpha = trnAlpha, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_mean), size = 0.6, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = lgdLoc,
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Mean ", yLabel, units))   
  
  #daily SD
  p2 = ggplot(df.comb) +
  geom_ribbon(aes(x = yday, ymin = sd_q5, ymax = sd_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = sd_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_sd), size = 0.3, alpha = trnAlpha, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_sd), size = 0.6, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = lgdLoc,
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Std. Deviation of ", yLabel, units))   
  
  #daily skew
  p3 = ggplot(df.comb) +
  geom_ribbon(aes(x = yday, ymin = skew_q5, ymax = skew_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = skew_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_skew), size = 0.3, alpha = trnAlpha, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_skew), size = 0.6, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = lgdLoc,
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Skew of ", yLabel, " (-)"))  
    
  
  #daily Max
  p4 = ggplot(df.comb) +
  geom_ribbon(aes(x = yday, ymin = max_q5, ymax = max_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = max_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_max), size = 0.3, alpha = trnAlpha, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_max), size = 0.6, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = lgdLoc,
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Maximum ", yLabel, units))  
  
  #daily Min
  p5 = ggplot(df.comb) +
  geom_ribbon(aes(x = yday, ymin = min_q5, ymax = min_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = min_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_max), size = 0.3, alpha = trnAlpha, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_min), size = 0.6, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = lgdLoc,
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Minimum ", yLabel, units))  
  
  if(Tag == "Temp"){
    p.comb = ggarrange(p1, p2, p5, p4, nrow = 2, ncol = 2, common.legend = TRUE, legend = "top")
  }else if(Tag == "Precip"){
    p.comb = ggarrange(p1, p2, p3, p4, nrow = 2, ncol = 2, common.legend = TRUE, legend = "top")
  }
  
  p.comb = annotate_figure(p.comb, top = text_grob(paste(ID, Name, sep = " - ")))
  
  print(p.comb)
  
  # p.out = paste0(outDirPlotsSta, "/dailyStats_", Tag, "_", Name, ".png")
  # ggsave(filename = p.out, plot = p.comb, device = "png")
  
  df.comb.o = df.comb %>%
    mutate(ID = ID, Name = Name, Tag = Tag)
  
  return(list(df.comb.o, perfMetrics))

}

```


### plot monthly precipitation
```{r, fig.width=10, fig.height=10}
df.daily.pcp = NULL
df.daily.pcp.perf = NULL

for(i in 1:n){
  
  simDat = datListProc[[i]][[1]]$sim.pcp
  obsDat = datListProc[[i]][[1]]$obs.pcp
  Tag = "Precip"
  ID = datListProc[[i]][[2]]
  Name = datListProc[[i]][[3]]
  
  df.i = dailyPlot(simDat, obsDat, Tag, ID, Name)
  
  df.daily.pcp = rbind(df.daily.pcp, df.i[[1]])
  df.daily.pcp.perf = rbind(df.daily.pcp.perf, df.i[[2]])

}
```


```{r, fig.width=8, fig.height=8}
# lgdLoc = c(0.8, 0.9)
  
if(Tag == "Temp"){
  yLabel = "Daily Temperature "
  units = "(°F)"
} else if(Tag == "Precip"){
  yLabel = "Daily Precipitation "
  units = "(inches)"
}

trnAlpha = 0.5

#daily mean
p1 = ggplot(df.daily.pcp) +
  geom_ribbon(aes(x = yday, ymin = mean_q5, ymax = mean_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = mean_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_mean), size = 0.15, alpha = trnAlpha-0.15, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_mean), size = 0.3, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "top",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Mean ", yLabel, units)) +
  facet_wrap(~Name, scales = "free")

print(p1)

# p.out = paste0(outDirPlots, "/dailyStats_faceted_precipitation.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```

### plot temp
```{r, fig.width=8, fig.height=8}

df.daily.tmp = NULL
df.daily.tmp.perf = NULL

for(i in 1:n){
  
  simDat = datListProc[[i]][[1]]$sim.tmp
  obsDat = datListProc[[i]][[1]]$obs.tmp
  Tag = "Temp"
  ID = datListProc[[i]][[2]]
  Name = datListProc[[i]][[3]]

  df.i = dailyPlot(simDat, obsDat, Tag, ID, Name)
  
  df.daily.tmp = rbind(df.daily.tmp, df.i[[1]])
  df.daily.tmp.perf = rbind(df.daily.tmp.perf, df.i[[2]])

}

```

```{r, fig.width=8, fig.height=8}
# lgdLoc = c(0.8, 0.9)
  
if(Tag == "Temp"){
  yLabel = "Daily Temperature "
  units = "(°F)"
} else if(Tag == "Precip"){
  yLabel = "Daily Precipitation "
  units = "(inches)"
}

trnAlpha = 0.5

#daily mean
p1 = ggplot(df.daily.tmp) +
  geom_ribbon(aes(x = yday, ymin = mean_q5, ymax = mean_q95), alpha = 0.25) +
  geom_line(aes(x = yday, y = mean_med, color = "red"), size = 1, alpha = 0.8) +
  # geom_line(aes(x = yday, y = obs_mean), size = 0.15, alpha = trnAlpha-0.15, linetype = "solid", color = "blue") +
  geom_point(aes(x = yday, y = obs_mean), size = 0.3, alpha = trnAlpha, color = "blue") +
  scale_colour_manual(values =c('blue'='blue','red'='red', 'grey' = 'grey'), labels = c('Observed','Simulation Median', '95% Confidence')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "top",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.key = element_blank()) +
  xlab("Day of Year") + ylab(paste0("Mean ", yLabel, units)) +
  facet_wrap(~Name, scales = "free")

print(p1)

# p.out = paste0(outDirPlots, "/dailyStats_faceted_temperature.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```


```{r}
perfComb = rbind(df.daily.pcp.perf, df.daily.tmp.perf)

# write.csv(perfComb, paste0(outDir, "/stations_dailyPerfMetrics.csv"), row.names = F)
```


### We can also calculate dry- and wet- spell length statistics for further verification.
Here, lower and upper boxplot whiskers are 5th and 95th percentiles, respectively.

```{r}
i = 1
x = subset(datListProc[[i]][[1]]$sim.pcp, variable == "Trace_1")$value
month = subset(datListProc[[i]][[1]]$sim.pcp, variable == "Trace_1")$month

spells = function(x, month){  
    
  df = data.frame(x, month)
  df$Flag = NA  
  n = nrow(df)  
    
  #flags (1 = day i pcp is below threshold (0.01 inch), 0 = above threshold)  
  i = 1  
  for(i in 1:n){  
  
    if(df$x[i] < 0.01){  
    df$Flag[i] = 1  
    } else{  
    df$Flag[i] = 0  
    }  
      
  }  
    
  #spell durations ------------
  
  #add dummy 0 at end of data  
  df[nrow(df)+1,] = NA  
  df$x[nrow(df)] = 0
  df$Flag[nrow(df)] = 0
  # tail(df$value, 1) = 0
    
  #dry spells -----
  duration.dry = c()  
  # s.m = c()
  e.m.dry = c()
  
  d.i = 0  

  i = 1  
  for(i in 1:n){  
      
    #if year i and year i + 1 flows are both below threshold, increment duration for spell  
    if(df$Flag[i] == 1 & df$Flag[i+1] == 1){    
      
    d.i = d.i + 1  

    #if year i is below threshold, but year i + 1 is not, that is the end of the dry spell, finish incrementing and save values, then reset for calculation of the next spell's stats  
    } else if(df$Flag[i] == 1 & df$Flag[i+1] == 0){  
      
    d.i = d.i + 1  

    e.m.dry = c(e.m.dry, df$month[i])
    duration.dry = c(duration.dry, d.i)  

    d.i = 0  

    }   
  
  }  
    
  out.dry = data.frame(duration = duration.dry, month = e.m.dry)
  
  #wet spells -----
  duration.wet = c()  
  # s.m = c()
  e.m.wet = c()
  
  w.i = 0  

  i = 1  
  for(i in 1:n){  
      
    #if year i and year i + 1 flows are both above threshold, increment duration for spell
    if(df$Flag[i] == 0 & df$Flag[i+1] == 0){    
      
    w.i = w.i + 1  

    #if year i is above threshold, but year i + 1 is not, that is the end of the wet spell, finish incrementing and save values, then reset for calculation of the next spell's stats  
    } else if(df$Flag[i] == 0 & df$Flag[i+1] == 1){  
      
    w.i = w.i + 1  

    e.m.wet = c(e.m.wet, df$month[i])
    duration.wet = c(duration.wet, w.i)  

    w.i = 0  

    }   
  
  }  
  
  out.wet = data.frame(duration = duration.wet, month = e.m.wet)
  
  return(list(dry = out.dry, wet = out.wet))  
}
```

```{r}

df.daily.spells = NULL

i = 1
for(i in 1:n){
  
  simDat = datListProc[[i]][[1]]$sim.pcp
  obsDat = datListProc[[i]][[1]]$obs.pcp
  ID = datListProc[[i]][[2]]
  Name = datListProc[[i]][[3]]

  j = 1
  for(j in 1:nrealz){
    
    trace.j = paste0("Trace_", j)
    
    df.j = subset(simDat, variable == trace.j)
    
    spells.j = spells(x = df.j$value, month = df.j$month)
    
    df.spells.dry = spells.j$dry %>% 
      group_by(month) %>%
      summarise(mean = mean(duration, na.rm = T),
                sd = sd(duration, na.rm = T),
                max = max(duration, na.rm = T)
                ) %>%
      mutate(Tag = "Dry Spells", ID = ID, Name = Name, Type = "Simulated", Trace = trace.j)
    
    df.spells.wet = spells.j$wet %>% 
      group_by(month) %>%
      summarise(mean = mean(duration, na.rm = T),
                sd = sd(duration, na.rm = T),
                max = max(duration, na.rm = T)
                ) %>%
      mutate(Tag = "Wet Spells", ID = ID, Name = Name, Type = "Simulated", Trace = trace.j)
    
    df.daily.spells = rbind(df.daily.spells, df.spells.dry, df.spells.wet)
    
  }
  
  spells.o = spells(x = obsDat$prcp, month = obsDat$month)

  df.spells.dry.o = spells.o$dry %>% 
    subset(duration <= 365) %>%
    group_by(month) %>%
    summarise(mean = mean(duration, na.rm = T),
              sd = sd(duration, na.rm = T),
              max = max(duration, na.rm = T)
              ) %>%
    mutate(Tag = "Dry Spells", ID = ID, Name = Name, Type = "Observed", Trace = "Observed")

  df.spells.wet.o = spells.o$wet %>% 
    subset(duration <= 365) %>%
    group_by(month) %>%
    summarise(mean = mean(duration, na.rm = T),
              sd = sd(duration, na.rm = T),
              max = max(duration, na.rm = T)
              ) %>%
    mutate(Tag = "Wet Spells", ID = ID, Name = Name, Type = "Observed", Trace = "Observed")

  df.daily.spells = rbind(df.daily.spells, df.spells.dry.o, df.spells.wet.o)

}

```

```{r}

df.daily.spells = as.data.frame(df.daily.spells)
# colnames(df.daily.spells)[4] = "Type"
# 
# df.daily.spells[,6:8] = apply(df.daily.spells[,6:8], 2, as.numeric)

```



```{r, fig.width=8, fig.height=8}

#daily mean - wet
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Wet Spells"),
            aes(x = month, y = mean, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Average Wet Spell Length (days)") +
  labs(title = "Wet Spell - Mean") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Wet Spells"),
                     aes(x = month, y = mean, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/meanWetSpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```

```{r, fig.width=8, fig.height=8}

#daily mean - dry
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Dry Spells"),
            aes(x = month, y = mean, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Average Dry Spell Length (days)") +
  labs(title = "Dry Spell - Mean") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Dry Spells"),
                     aes(x = month, y = mean, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/meanDrySpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```


```{r, fig.width=8, fig.height=8}

#daily sd - wet
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Wet Spells"),
            aes(x = month, y = sd, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Std. Dev. of Wet Spell Length (days)") +
  labs(title = "Wet Spell - Standard Deviation") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Wet Spells"),
                     aes(x = month, y = sd, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/sdWetSpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```

```{r, fig.width=8, fig.height=8}

#daily sd
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Dry Spells"),
            aes(x = month, y = sd, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Std. Dev. of Dry Spell Length (days)") +
  labs(title = "Dry Spell - Standard Deviation") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Dry Spells"),
                     aes(x = month, y = sd, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/sdDrySpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```


```{r, fig.width=8, fig.height=8}

#daily max - wet
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Wet Spells"),
            aes(x = month, y = max, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Maximum Wet Spell Length (days)") +
  labs(title = "Wet Spell - Maximum") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Wet Spells"),
                     aes(x = month, y = max, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/maxWetSpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```

```{r, fig.width=8, fig.height=8}

#daily sd
p1 = ggplot(data = subset(df.daily.spells,
                          Type == "Simulated" & Tag == "Dry Spells"),
            aes(x = month, y = max, group = month)) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot() +
  facet_wrap(~Name, scales = "free") +
  scale_colour_manual(values=c('blue'='blue'), labels = c('Observed')) +
  theme_bw() +
  theme(axis.title = element_text(face = "bold"),
        # text=element_text(size=14),
        panel.grid.major = element_line(),
        legend.title=element_blank(),
        legend.position = "right",
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        ) +
  xlab("Month") +
  ylab("Maximum Dry Spell Length (days)") +
  labs(title = "Dry Spell - Maximum") +
  scale_x_continuous(labels = 1:12, breaks = 1:12)  

p1 = p1 + geom_point(data = subset(df.daily.spells,
                                   Type == "Observed" & Tag == "Dry Spells"),
                     aes(x = month, y = max, group = month),
                     color = "blue", alpha = 0.7,
                     shape = 4, size = 2, stroke = 1.5,
                     show.legend = T)


print(p1)

# p.out = paste0(outDirPlots, "/maxDrySpellLengths.png")
# ggsave(filename = p.out, plot = p1, device = "png", height = 8, width = 8, units = "in")

```

## Final notes

* The weather simulations use a 366-day per year framework in order to handle leap years. During leap years, all 366 days will have precipitation and temperature values (i.e., February 29th exists and contains data), but during non-leap years February 29th does not exist and a row of NULL values is added after December 31st in order to maintain the same length between leap years and non-leap years. Other datasets and algorithms use various approaches to handle leap years, such as avoiding leap years altogether, using a 360-day year, etc.

* Because leap years are acceptable in the `wxgenR` algorithm, it is possible (but unlikely) to have two or more leap years in a row in the weather simulations since years are sampled at random. 

* Please report any bugs or issues to either sgangopadhyay@usbr.gov or dwoodson@usbr.gov

## Citations

For more details and examples, including analysis of the dataset used in this vignette, see the following works:

    Bearup, L., Gangopadhyay, S., & Mikkelson, K. (2021). Hydroclimate Analysis Lower Santa Cruz River Basin Study (Technical Memorandum No ENV-2020-056). Bureau of Reclamation. <https://www.usbr.gov/lc/phoenix/programs/lscrbasin/LSCRBStudy.html>
    
    Gangopadhyay, S., Bearup, L. A., Verdin, A., Pruitt, T., Halper, E., & Shamir, E. (2019, December 1). A collaborative stochastic weather generator for climate impacts assessment in the Lower Santa Cruz River Basin, Arizona. Fall Meeting 2019, American Geophysical Union. <https://ui.adsabs.harvard.edu/abs/2019AGUFMGC41G1267G>

    Rajagopalan, B., Lall, U., and Tarboton, D. G.: Nonhomogeneous Markov Model for Daily Precipitation, Journal of Hydrologic Engineering, 1, 33–40, <https://doi.org/10.1061/(ASCE)1084-0699(1996)1:1(33)>, 1996.

    Verdin, A., Rajagopalan, B., Kleiber, W., and Katz, R. W.: Coupled stochastic weather generation using spatial and generalized linear models, Stoch Environ Res Risk Assess, 29, 347–356, <https://doi.org/10.1007/s00477-014-0911-6>, 2015.

    Verdin, A., Rajagopalan, B., Kleiber, W., Podestá, G., and Bert, F.: A conditional stochastic weather generator for seasonal to multi-decadal simulations, Journal of Hydrology, 556, 835–846, <https://doi.org/10.1016/j.jhydrol.2015.12.036>, 2018.