CCRP_Generate_Climate_Futures_Koppen.Rmd

---
title: "NPS park climate futures"
author: "Climate Change Response Program"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: html_document
---

```{r setup, warning=FALSE, include = FALSE}

knitr::opts_chunk$set(
  echo = FALSE, 
  collapse = TRUE,
  warning = TRUE, # set to FALSE when done
  message = TRUE # set to FALSE when done
)

library(here); library(plyr); # Use here::here when package lubridate is used
library(plotrix); library(zoo); library(ggplot2); library(grid); library(cowplot); library(reshape2); library(raster); library(ncdf4); library(reshape2); library(WriteXLS); library(data.table); library(RColorBrewer); library(ggrepel); library(lubridate); library(dplyr); library(forcats); library(openxlsx); library("WaterBalance"); library(sf); library(raster); library(rgdal); library(R.utils); library(tmap); library(tmaptools); library(ggmap); library(ggspatial);
library(gridExtra); library(SPEI); library(tidyr); library(tibble); library(sp); library(skimr); library(cft); library(stringr); library(ggpubr); library(lemon); library(ggfortify); library(extRemes);library(sp);library(terra)


```


# For loop that reads names from csv file for park

```{r user-inputs-1, warning=FALSE, include = FALSE}

rm(list = ls())

# -------------- Input site information -------------------------------------- #
Park = "MORA"  
Koppen = "MORA_27" #PARK_##
SiteName = "MORA" #"MORA-Paradise VC" #optional - set at SiteID if don't want to use
set.seed(50)

# --------------- Input local folder information ----------------------------- #

project_root_dir <- here::here() 

local_rss_dir <- 'C:/Users/arunyon/3D Objects/Local-files/RCF_Testing/' # local directory where you want this repo copied. Should be something like 'C:/Users/adillon/Documents/RSS/'. Next lines create folder for park
local_rss_dir <- paste0(local_rss_dir,Koppen)

if(dir.exists(local_rss_dir) == FALSE){
  dir.create(local_rss_dir)
}


if(dir.exists(here::here( "PARK")) == FALSE){
  dir.create(here::here( "PARK"))
}

OutDir = paste0('./PARK/',Koppen,"/") # for .csv's
if(dir.exists(OutDir) == FALSE){
  dir.create(OutDir)
}

DataDir = paste0(OutDir,'input-data/') # for .csv's
if(dir.exists(DataDir) == FALSE){
  dir.create(DataDir)
}

```

## `r SiteID`

```{r site-info, message=FALSE, warning=FALSE, include = FALSE,error=TRUE}

source(here::here("scripts", "get_site_info_Koppen.R")) # Extract local inputs; seconds to run

source(here::here("scripts", "create_site_maps_Koppen.R")) # Create site maps

source(here::here("scripts", "get_params_Koppen.R"))

```

```{r user-inputs-2, warning=FALSE, include = FALSE}

CFs_all <- c("Warm Wet", "Hot Wet", "Central", "Warm Dry", "Hot Dry")

##Color schemes

#Colors for CF values plotted side by side (match order of CFs vector)
colors5 <- c("#2B83BA", "#ABDDA4","#FDAE61", "#D7191C", "grey") #RColorBrewer Spectral
# colors5.2 <- c("#6EB2D4", "#05689F", "grey", "#F6B294", "#CA0020")#Old colors
colors5.2 <- c("#2B83BA", "#ABDDA4", "grey","#FDAE61", "#D7191C") #RColorBrewer Spectral

centroids_csv <- "Y" #Switch for using Tercek csvs or downloading own data

Indiv_method <- "pca" # Switch for method Indiv_method = c("corner", "pca")

Percent_skill_cutoff = .1 #percentage of models to drop from ranking
MethodCaption="Y" # Indicates whether Q/I present at bottom of plot to ID CF method used

# --------- Information for Climate Futures Analyses (MACA) ------------------ #

# Specify parameters:

Yr = 2050 #Central year
Range = 30  #Number of years to summarize (should be at least 30)
BasePeriod = "1979-2012"
rollLen = 10 #rolling mean length for timeseries plots

# Threshold percentages for defining Climate futures. Default low/high:  0.25, 0.75
CFLow = 0.25     
CFHigh = 0.75

QuantileLow = 0.05   #Quantiles for temperature threshold calculations
QuantileHigh = 0.95

HotTemp = 95
ColdTemp = 32
PrecipThreshold = 0.05

# ------------ Information for WB analyses ------------------------ #

#Method for PET calculation 
PET_Method = "Oudin"  #Hamon is default method for daily PRISM and MACA data (containing only Tmax, Tmin, and Date). 


# ------------ Information for drought analyses ------------------------ #

## SPEI variables

SPEI_per<-6 # This is the value for the period SPEI is aggregated. 6-months is standard but could change if want. 
truncation<- -.5 # SPEI value, under which drought events are considered
SPEI_start <- 1980
SPEI_end <- 2012

```



```{r Climate-Futures, message=FALSE, warning=FALSE, include = FALSE}
SiteID = Koppen
if(centroids_csv == "Y") {
  source(here::here("scripts", "download_Park_csvs.R"), local = knitr::knit_global())
} else {
  print("Other data needed")
  #source(here::here("scripts", "Climate-Futures", "CFT_CF_parsing_v1.R")) # Parse MACA data. Output = "_init_parsed.RData". # 9-8-21: CFT parsing script is not working due to an issue with the package or MACA servers. ACR to talk to CU Boulder about the issue. For now, add _init_parsed.RData file manually to parsed-data folder. 
}

source(here::here("scripts", "Plotting_Functions.R"), local = knitr::knit_global())
SiteID=Park
source(here::here("scripts", "Plot_Table_Creation.R"), local = knitr::knit_global()) # Requires "PARK_init_parsed.RData"; Output = "PARK_lat_long_Final_Environment.RData". 
SiteID=SiteName
source(here::here("scripts", "Scatter_and_diagnostic.R"), local = knitr::knit_global()) # Creates scatter and diagnostic plots. Outputs to Figs MACA folder. 
```

```{r WarmWet/HotDry, message=FALSE, warning=FALSE, include = FALSE}
# Specify Climate Futures

## Run this section if already downloaded data objects
OutDir <- "C:/Users/arunyon/3D Objects/Local-files/Git-repos/CCRP_automated_climate_futures/PARK/MORA_27/"
# OutDir <- 'C:/Users/achildress/Documents/RCF_Testing/WHSA/'
# OutDir <- "C:/Users/achildress/Documents/RCF_Testing/JOTR_07/"
DataDir = paste0(OutDir,'input-data/') # for .csv's
######################################################
DataFile <- list.files(path = DataDir, pattern = 'Final_Environment.RData', full.names = TRUE) # Environment needs to be added if not parsing MACA data
load(DataFile)

SiteID <- SiteName
FutureSubset <- CFs_all[c(1,5)]; CFs = FutureSubset  # Pick pair of climate futures.
CF_abbreviation <- "WW-HD"
# WB_GCMs <- subset(WB_GCMs, CF %in% CFs)

colors2<- colors5[c(1,4)] # Select pair of climate futures - WarmWet/HotDry
#colors2<- c("#F3D3CB","#12045C")  # Select pair of climate futures - HotWet/WarmDry

colors3<-c("white",colors2)
col<- c("darkgray",colors2)  # WarmWet/HotDry
#col<- c("darkgray","#F3D3CB","#12045C")  # HotWet/WarmDry

CFDir = paste0(OutDir,"WarmWet_HotDry/") # for .csv's
if(dir.exists(CFDir) == FALSE){
  dir.create(CFDir)
}

TableDir = paste0(CFDir,"tables/") # for .csv's
if(dir.exists(TableDir) == FALSE){
  dir.create(TableDir)
}

FigDir = paste0(CFDir,"figures/") # for .csv's
if(dir.exists(FigDir) == FALSE){
  dir.create(FigDir)
}

if (exists("FutureSubset") == FALSE) stop("Please specify Climate Futures") # At the top of the script, please enter a combination of futures, e.g. Warm Wet/Hot Dry

source(here::here("scripts", "Threshold_Bar_Charts.R")) # Requires "PARK_lat_long_Final_Environment.RData". Outputs plots and Excel Workbook 

source(here::here("scripts","Daily_WB_Model.R"))

source(here::here("scripts", "Drought_characteristics.R"))

# source(here::here("scripts", "WBgrid_plotting.R")) # Run the Water Balance Model

source(here::here("scripts", "Return_Events.R"))

source(here::here("scripts", "Summary plots.R"))

source(here::here("scripts", "Report_plots.R"))

```

```{r WarmDry/HotWet, message=FALSE, warning=FALSE, include = FALSE}
# Specify Climate Futures
## Run this section if already downloaded data objects
OutDir <- "C:/Users/arunyon/3D Objects/Local-files/Git-repos/CCRP_automated_climate_futures/PARK/MORA_27/"
# OutDir <- 'C:/Users/achildress/Documents/RCF_Testing/WHSA/'
# OutDir <- "C:/Users/achildress/Documents/RCF_Testing/JOTR_07/"
DataDir = paste0(OutDir,'input-data/') # for .csv's
######################################################
DataFile <- list.files(path = DataDir, pattern = 'Final_Environment.RData', full.names = TRUE) # Environment needs to be added if not parsing MACA data
load(DataFile)

SiteID <- SiteName
FutureSubset <- CFs_all[c(4,2)]; CFs = FutureSubset  # Pick pair of climate futures.
CF_abbreviation <- "WD-HW"

# WB_GCMs <- subset(WB_GCMs, CF %in% CFs)

# colors2<- c("#9A9EE5","#E10720")  # Select pair of climate futures - WarmWet/HotDry
colors2<- colors5[c(3,2)] # Select pair of climate futures - HotWet/WarmDry

colors3<-c("white",colors2)
# col<- c("darkgray","#9A9EE5","#E10720")  # WarmWet/HotDry
col<- c("darkgray", colors2)  # HotWet/WarmDry

CFDir = paste0(OutDir,"WarmDry_HotWet/") # for .csv's
if(dir.exists(CFDir) == FALSE){
  dir.create(CFDir)
}

TableDir = paste0(CFDir,"tables/") # for .csv's
if(dir.exists(TableDir) == FALSE){
  dir.create(TableDir)
}

FigDir = paste0(CFDir,"figures/") # for .csv's
if(dir.exists(FigDir) == FALSE){
  dir.create(FigDir)
}

if (exists("FutureSubset") == FALSE) stop("Please specify Climate Futures") # At the top of the script, please enter a combination of futures, e.g. Warm Wet/Hot Dry

source(here::here("scripts", "Threshold_Bar_Charts.R")) # Requires "PARK_lat_long_Final_Environment.RData". Outputs plots and Excel Workbook 

source(here::here("scripts","Daily_WB_Model.R"))

source(here::here("scripts", "Drought_characteristics.R"))

# source(here::here("scripts", "WBgrid_plotting.R")) # Run the Water Balance Model

source(here::here("scripts", "Return_Events.R"))

source(here::here("scripts", "Summary plots.R"))

source(here::here("scripts", "Report_plots.R"))

```

```{r Copy-and-delete-files, message=FALSE, warning=FALSE, include = FALSE}
SiteID <- Koppen
source(here::here("scripts", "write_metadata.R"))

source(here::here("scripts", "copy_paste_delete_files.R")) # copies files and folders to specified local folder


```