---
title: "Analyze Spatial Patterns"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Analyze Spatial Patterns}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  fig.width = 7.1,
  fig.height = 6
)
```

## Setup
Load packages and import HYPE model files.

```{r setup, message=FALSE}
# Load Packages
library(HYPEtools)
library(sf)
library(leaflet)
library(dplyr)

# Get Path to HYPEtools Model Example Files
model_path <- system.file("demo_model", package = "HYPEtools")

# Import HYPE Model Files
gd <- ReadGeoData(file.path(model_path, "GeoData.txt"))
gcl <- ReadGeoClass(file.path(model_path, "GeoClass.txt"))
stats.cout <- ReadSubass(file.path(model_path,"results","subass1.txt"))
mcrun <- ReadMapOutput(file.path(model_path,"results","mapCRUN.txt")) 
```

## Read GIS Files
```{r readGIS}
# Read GIS Files
map.subid <- st_read(file.path(model_path, "gis","Nytorp_map.gpkg"))

map.Qobs <- st_read(file.path(model_path,"gis", "Nytorp_station.gpkg")) %>%
  mutate(SUBID = 3587, .after = "long") # Add SUBID to gauge station attributes

# Show the column names of imported GIS file
names(map.Qobs)

# Plot Model Subbasins
plot(map.subid)
```

## Plot Model Performance on a Static Map
```{r plotperformance-static}
# Show the column names of imported subbasin performance file
names(stats.cout)

# Choose to plot NSE; Assign the selected statistics column number to stat.col.plot
stat.col.plot <- 2 # For NSE
stat.nm.plot <- "NSE"

# Generate Plot - There is only one observation station, so only one point appears on the map
PlotMapPoints(x = stats.cout[, c(1,stat.col.plot)], 
              sites = map.Qobs, sites.subid.column = 3, bg = map.subid)

```

## Plot Model Performance on an Interactive Leaflet Map
```{r plotperformance-leaflet, message=FALSE}
# Generate Plot - There is only one observation station, so only one point appears on the map
# PlotMapPoints(map.type = "leaflet",
#               x = stats.cout[, c(1,stat.col.plot)],
#               sites = map.Qobs, sites.subid.column = 3, bg = map.subid,
#               legend.pos = "bottomright",
#               plot.scale = FALSE, plot.arrow = FALSE, plot.label=TRUE, bg.label.column = 25, plot.bg.label="static")

```

## Plot Simulated Runoff on a Static Map
```{r plotrunoff-static}
# Show the column names of imported GIS file
names(map.subid)

# Generate Plot
PlotMapOutput(mcrun, map = map.subid, map.subid.column = 25, var.name = "CRUN", legend.title = "Runoff (mm/d)",
              col = ColQ, col.breaks = NULL, legend.pos = "right")

```

## Plot Simulated Runoff on an Interactive Leaflet Map
```{r plotrunoff-leaflet, message=FALSE}
# Generate Plot
# PlotMapOutput(mcrun, map.type = "leaflet", map = map.subid, map.subid.column = 25, var.name = "CRUN", legend.title = "Runoff (mm/d)",
#               col = ColQ, col.breaks = NULL, legend.pos = "bottomright", map.adj = 0, plot.scale = FALSE, plot.arrow = FALSE)

```

## Create Leaflet Map with Additional Bling
```{r bling, message=FALSE}
# Generate leaflet map with additional bling
# leafmap <- PlotMapOutput(mcrun, map.type = "leaflet", map = map.subid, map.subid.column = 25, var.name = "CRUN", legend.title = "Runoff (mm/d)",
#               col = ColQ, col.breaks = NULL, legend.pos = "bottomright", map.adj = 0, plot.scale = TRUE, plot.arrow = FALSE, plot.label = TRUE, plot.searchbar = TRUE)

# Add Additional Basemap and Marker for SMHI Location
# leafmap <- leafmap %>%
# 
#   # Update Layers Control to include the new Basemap and SMHI Marker
#   addLayersControl(
#     baseGroups=c("Map","Street","Topo","Satellite","Stamen Toner"),
#     overlayGroups=c("Subbasins","SMHI"),
#     options=layersControlOptions(collapsed = FALSE, autoIndex = TRUE)) %>%
# 
#   # Add Basemap
#   addProviderTiles(provider = providers$Stamen.Toner, group = "Stamen Toner") %>%
# 
#   # Add Marker on Map for SMHI Location
#   addMarkers(group = "SMHI",
#              lng = 16.151890,
#              lat = 58.578950,
#              popup = "SMHI")

# View Updated Map
# leafmap

```

## Plot Map Outputs in an Interactive Shiny App
```{r plotmappoints-shiny, message=FALSE}
# Start App - Symbolize with points
# VisualizeMapPoints(
#   results.dir = system.file("demo_model", "results", package = "HYPEtools"),
#   sites = system.file("demo_model", "gis", "Nytorp_centroids.gpkg", package = "HYPEtools"),
#   sites.subid.column = 25,
#   bg = system.file("demo_model", "gis", "Nytorp_map.gpkg", package = "HYPEtools")
# )
```

```{r plotmapoutput-shiny, message=FALSE}
# Start App - Symbolize with polygons
# VisualizeMapOutput(
#   results.dir = system.file("demo_model", "results", package = "HYPEtools"),
#   map = system.file("demo_model", "gis", "Nytorp_map.gpkg", package = "HYPEtools"),
#   map.subid.column = 25
# )
```