nb_spatqry_01_scgis21.Rmd

---
title: "Spatial Queries: Find Yosemite POIs in the Upeer Merced Subbasin"
output: 
  html_notebook:
    toc: yes
    toc_float: yes
---

```{css echo = FALSE}
h1,h2 {font-weight:bold;}
```


In this Notebook we'll use geoprocessing functions from `sf` to identify Yosemite Points-of-Interest that fall within the **Upper Merced Subbasin**. 

## Setup

Load the packages we'll need and set tmap mode to 'plot':

```{r chunk01, message = FALSE}
library(sf)
library(tmap)
tmap_mode("plot")
```

Load `dplyr` and set name conflict preferences:

```{r chunk02, message = FALSE}
library(dplyr)

## Load the conflicted package
library(conflicted)

# Set conflict preferences
conflict_prefer("filter", "dplyr", quiet = TRUE)
conflict_prefer("count", "dplyr", quiet = TRUE)
conflict_prefer("select", "dplyr", quiet = TRUE)
conflict_prefer("arrange", "dplyr", quiet = TRUE)
```

\

# Practice Querying with Sample Data

## Import Practice Data

First we import some practice data:

```{r chunk03}
circles_sf <- st_read("./data/test_circles.geojson")
circles_sf

pts_sf <- st_read("./data/test_pts.geojson")
pts_sf
```

\

Plot the points on top of the circles:

```{r chunk04, warning = FALSE}
tm_shape(circles_sf) +
  tm_borders(col = palette()[2:4] ) +
  tm_text("circle_id") +
tm_shape(pts_sf) +
  tm_dots(col = "dimgray") +
tm_grid(labels.show = TRUE, lines = FALSE)
```

## Identify the points in Circle A

Next we identify the points in circle A using a spatial predicate function (st_intersects). We could also copy the points in Cirlce A with st_intersection(), but there are times when you don't need or want to make copies of the data.

```{r chunk05}
circle_a_sf <- circles_sf %>% filter(circle_id == "A")

pt_in_circle_a_yn_mat <- pts_sf %>% 
  st_intersects(circle_a_sf,
                sparse = FALSE)
  
head(pt_in_circle_a_yn_mat)
```

Since we have a column of TRUE/FALSE values, we can subset those features using the dplyr `filter` function:

```{r chunk06, warning = FALSE}
## Copy the points in circle A to a new object. Note in the filter expression
## we use square bracket notation to pull out the first column of the matrix 

a_pts_sf <- pts_sf %>% 
  filter(pt_in_circle_a_yn_mat[,1])

## Plot to verify
tm_shape(circles_sf) +
  tm_borders(col = palette()[2:4] ) +
  tm_text("circle_id") +
tm_shape(a_pts_sf) +
  tm_dots(col = "red", size = 0.1) +
tm_grid(labels.show = TRUE, lines = FALSE)
```

\

## CHALLENGE: How many points in cirlce B?

[Answer](https://bit.ly/3xwk0xV)

```{r chunk07}
## Your answer here
```

\

## CHALLENGE: Plot the points that fall within Circle B *and* Circle C

[Answer](https://bit.ly/3yvJk8H)

```{r chunk08}
## Your answer here
```

\

## CHALLENGE: How many points don't fall in any circle?

[Answer](https://bit.ly/2VCUfz3)

```{r chunk09}
## Your answer here
```

\

## CHALLENGE: Plot the points that lie within 0.25 map units of a circle, but are not contained within the circle

[Answer](https://bit.ly/3xsXgyR)

```{r chunk11}
## Your answer here
```

\

# Plot the Points of Interest that Fall within the Upper Merced Subbasin

Next, we'll apply what we learned to find the Yosemite Points-of-Interest that fall within the Upper Merced HUB-8 Subbasin.

## Import the Watersheds

Start by importing the planning watershed units from [calw221](https://frap.fire.ca.gov/mapping/gis-data/){target="_blank" rel="noopener"}:

```{r chunk13}
## Import the planning watersheds
gpkg_watershd_fn <- "./data/yose_watersheds.gpkg"
yose_watersheds_sf <- st_read(gpkg_watershd_fn, layer="calw221") 

## View attribute table
yose_watersheds_sf %>% st_drop_geometry() %>% slice(1:6)

## Plot results
tmap_mode("plot")
tm_shape(yose_watersheds_sf) + 
  tm_polygons("MAP_COLORS", palette = "Pastel1") 
```

Note the keyword `MAP_COLORS` tells tmap to select colors at random such that adjacent polygons have different colors.

\

## Lump the Planning Watersheds into HUC-8 Subbasins

Next we'll group the little planning watersheds into bigger "HUC-8" subbasins. This is easy because there is a column for the HUC 8 id number (`HUC_8`) and name (`HUC_8_NAME`).

```{r chunk14}
yose_huc8_sf <- yose_watersheds_sf %>% 
  group_by(HUC_8) %>% 
  summarise(HUC_8_NAME = first(HUC_8_NAME), num_pws = n())

yose_huc8_sf
```

A convenient feature of `group_by()` is that when applied to a simple feature data frame it will also spatially aggregate (i.e., union) the features based on common values in the grouping column. Plot to verify:

```{r chunk15}
epsg_utm11n_nad83 <- 26911
yose_bnd_utm <- st_read(dsn="./data", layer="yose_boundary") %>% 
  st_transform(epsg_utm11n_nad83)

tm_shape(yose_huc8_sf) + 
  tm_polygons("MAP_COLORS", palette = "Pastel1") +
  tm_text("HUC_8_NAME", size = 0.7) +
tm_shape(yose_bnd_utm) +
  tm_borders(col = "red", lwd = 2)
```

## Extract Upper Merced HUC-8 Subbasin

Next, pull out just the Upper Merced subbasin and save it as a separate object:

```{r chunk16}
## Filter out just the Upper Merced Subbasin
merced_huc8_sf <- yose_huc8_sf %>% 
  filter(HUC_8_NAME == "UPPER_MERCED")
merced_huc8_sf
```

\

## Import the Points-of-Interest

Import the Yosemite POIs:

```{r chunk17}
## Import points of interest
yose_poi_utm <- st_read(dsn="./data", layer="yose_poi") %>% 
  select(OBJECTID, POINAME, POILABEL, POITYPE)
```

\

## Identify Intersecting Points-of-Interest

Find out which POIs intersect the Upper Merced subbasin with `st_intersects()`:

```{r chunk18}
try(merced_poi <- yose_poi_utm %>% st_intersects(merced_watershed))
```

Oh no - **ERROR message**! Spatial querying requires features to be in the same CRS!

\

To fix this, we can project the Merced HUC-8 layer (which is in CA Albers) to match the POIs (which are UTM):

```{r chunk19}
merced_huc8_utm_sf <- merced_huc8_sf %>% 
  st_transform(st_crs(yose_poi_utm))
```

\

Try the intersection test again:

```{r chunk20}
yose_poi_merced_mat <- yose_poi_utm %>% st_intersects(merced_huc8_utm_sf, sparse=FALSE)
head(yose_poi_merced_mat)
```

\

## CHALLENGE: How many points-of-interest fall within the Upper Merced subbasin?

*Hint 1*: This is equivalent to asking how many TRUE values there are in the first column of `yose_poi_merced_mat`.

*Hint 2*: To get the first column of a matrix `x`, use `x[ , 1]`.

[Answer](https://bit.ly/3rEOnzn)

```{r chunk21}
## Your answer here
```

\

## Subset the POIs that fall within the Upper Merced Subbasin

To extract the POIs in the Upper Merced subbasin, we can feed the first column of `yose_poi_merced_mat` into  `filter()` (which expects TRUE/FALSE values):

```{r chunk22}
## Extract the points that intersect the subbasin to a new sf object
merced_poi_utm <- yose_poi_utm %>% 
  filter(yose_poi_merced_mat[,1])
```

\

## Plot the Intersection

Plot to visually verify the results:

```{r chunk23}
## Plot
tm_shape(merced_huc8_utm_sf) +
  tm_polygons(col = "khaki") +
tm_shape(yose_poi_utm) +
  tm_dots(size = 0.1, col = "gray30") +
tm_shape(merced_poi_utm) +
  tm_dots(size = 0.1, col = "dodgerblue")
```

\

## CHALLENGE: How many YNP POIs fall witin the Upper Tuolumne HUC-8 subbasin?

[Answer](https://bit.ly/3AdasK6)

```{r chunk24}
## Your answer here
```


## End

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