An Introduction to Remote Sensing with Earth Engine and R

class: center, middle, inverse, title-slide

# An Introduction to Remote Sensing with Earth Engine and R
### Alec Robitaille, Isabella C. Richmond
### Wildlife Evolutionary Ecology Lab - Memorial University
### 2020-12-10

---

# What is Earth Engine?

- A processing platform that allows you to run algorithms on georeferenced imagery and vectors on Google's servers

- Contains a **massive** catalog of geospatial data

- Accessible through the online Code Editor, and a Javascript and Python libraries

.pull-right[
![:scale 55%](images/ee_logo.png)
]

.footnote[
[1]: [Google Developers: Get Started with Earth Engine ](https://developers.google.com/earth-engine/guides/getstarted)
]

???

The code editor allows you to find relevant imagery, process it, share your code, and save your code and processed imagery to your Google Drive

---

# Data types

## Image
- `ee.Image`
- An image composed of one or many bands
- Properties: name, data type, scale, mask and projection
- E.g.: a single Landsat scene, a single land cover raster

```js
var l7scene = ee.Image('LANDSAT/LE07/C01/T1_RT/LE07_001004_20000610');
```

## Image Collection
- `ee.Image.Collection`
- A stack or sequence of images
- E.g. *All* the Landsat 7 imagery 
]

```js
var l7 = ee.ImageCollection('LANDSAT/LE07/C01/T1_RT');
```

???
Differences between R and EE:

Image in EE = `ee.Image`
Image in R = mainly `raster`

---
# Data types

## Feature
- `ee.Feature`
- A feature composed of a Geometry object and properties
- `Features` can be created in Earth Engine or uploaded
- E.g. points, lines and polygons, a study area polygon

```js
// Create an ee.Geometry.
var polygon = ee.Geometry.Polygon([
  [[-35, -10], [35, -10], [35, 10], [-35, 10], [-35, -10]]
]);

// Create a Feature from the Geometry.
var polyFeature = ee.Feature(polygon, {foo: 42, bar: 'apple'});
```

// Create a Feature from the Geometry.
var polyFeature = ee.Feature(polygon, {foo: 42, bar: 'apple'});
</script>

---

# Data types

## Feature Collection
- `ee.FeatureCollection`
- Groups of related `Features`
- Do not need to have the same geometries or properties to be in a Feature Collection
- E.g. Relocation points for all animals in a study

```js
var fc = ee.FeatureCollection('TIGER/2016/Roads');
```

???
Properties = dictionary

Differences between R and EE:

`ee.Feature` ~~ `sf::st_geometry()`
`ee.FeatureCollection` ~~ `sf`, `sfc`

---
# Data types

.pull-left[

### String

```js
// Use single (or double) quotes 
//  to make a string.
var potato = 'yukon gold';
// Use parentheses to pass 
//  arguments to functions.
print(potato);
```

### Numbers

```js
// Store a number in a variable.
var number = 17;
print(number);
```

]

.pull-right[

### Dictionary

```js
// Use curly brackets {} to make a 
//  dictionary of key:value pairs.
var object = {
  foo: 'bar',
  baz: 13,
  stuff: ['kilo', 'lima', 'mike']
};

print('Print stuff:', object['stuff']);
```

print('Print stuff:', object['stuff']);
</script>

### List

```js
// Use square brackets [] to 
//  make a list.
var listOfNumbers = [0, 1, 1, 2, 3, 5];
```

]

.footnote[
[1]: [Basic JavaScript data types](https://developers.google.com/earth-engine/tutorials/tutorial_js_01
)
]

???
Dictionary: key value
Lists []
Array

---
# Data types -  comparing R and EE

.pull-left[
## Earth Engine

### Images
* `ee.Image`
* `ee.ImageCollection`

### Features
* `ee.Feature`
* `ee.FeatureCollection`

]

.pull-left[
## R

### Rasters
* `raster`
* `raster` stack, `stars`, ...

### Vectors
* `sf::st_geometry`
* `sf`, `sfc`
]

---
background-image: url(https://developers.google.com/earth-engine/images/Code_editor.png)
background-position: center
background-size: contain

# Earth Engine code editor

???
[EE Playground](https://developers.google.com/earth-engine/guides/playground)

Code editor also called the EE Playground

---
# Sources of data

1. Imagery
  - Landsat
  - Sentinel 
  - MODIS 
  - Derived imagery (e.g. NDVI)
  
2. Geophysical
  - Elevation, terrain
  - Land cover
  - Cropland
 
3. Climate
  - Surface temperature
  - Atmosphere
  - Weather

---
class: review

# Example - sources of data

## Image
- Script: [Examples/Image/From Name](https://code.earthengine.google.com/856e0c5d65858be858aabada28a5d5da)

## Image Collection
- Script: [Exploring image collections](https://code.earthengine.google.com/1a5ee71d43b85ac287afe0285126f804)
- Use the Search bar to see all the Image Collections that are available
- Use the asset id to load the image collection and add them to the map

---
# Filtering data

- Unlike R, Earth Engine optimizes the *final* call using deferred execution. In short, this means that operations like "clip" are usually unnecessary.

- Instead, we filter our data:
   - spatial filter e.g. within bounds
   - temporal filter e.g. within dates
   - attribute filter e.g. type equals "cheese"

```js
var point = ee.Geometry.Point(-122.262, 37.8719);

var start = ee.Date('2014-06-01');
var finish = ee.Date('2014-10-01');

var filteredCollection = ee.ImageCollection('LANDSAT/LC08/C01/T1')
  .filterBounds(point)
  .filterDate(start, finish);
```

var start = ee.Date('2014-06-01');
var finish = ee.Date('2014-10-01');

var filteredCollection = ee.ImageCollection('LANDSAT/LC08/C01/T1')
  .filterBounds(point)
  .filterDate(start, finish);
</script>

.footnote[
[Get Started: Filtering](https://developers.google.com/earth-engine/guides/getstarted#filtering-and-sorting)

[Deferred execution](https://developers.google.com/earth-engine/guides/deferred_execution)
]

---
class:review

# Example - filtering data

## Image Collection
- Script: [Examples/Image Collection/Filtered Composite Name](https://code.earthengine.google.com/6341485b408675e989a40ad039753f4d)

## Feature Collection
- Script: [Filtering attributes in feature collections](https://code.earthengine.google.com/6dbb2653b3d988049ff6ad115bc9b8e3)

---

# Importing features

Either a Shapefile (and related `.dbf`, `.shx` and `.prj` files) or a zip file of these, or a CSV

In R, take an example sf object and zip it

```r
library(sf)
dir.create('example-features')

df <- data.frame(id = LETTERS[1:3],
                 lon = c(-137.03, -136.94, -137.10),
                 lat = c(60.46, 60.50, 60.52))
points <- st_as_sf(df, coords = c('lon', 'lat'))

st_write(points, 'example-features/ex-abc.shp')

zip('example-abc.zip', 'example-features')
```

Upload the asset, then load the asset in your Earth Engine scripts

```js
var features = ee.FeatureCollection('users/robit.a/example-abc');
```

.footnote[
[Importing features](https://developers.google.com/earth-engine/guides/importing)
]

???
- You don't need to manually choose a point or polygon within Google Earth Engine when filtering data, you can import your relevant features and use them

- E.g. Importing relocation points, study grid, study area boundaries, etc.

---
class:review
# Example - band math

## Image

* Script: [Examples/Image/Normalized Difference](https://code.earthengine.google.com/afcb9f29454529683d855696f5a9d681)

## Image Collection

* Script: [Full example](https://code.earthengine.google.com/940ada34c9099e1df33259df21b3c649)

---
class:review

# Example - sampling

## Image
* Script: [Examples/Image/Reduce Region](https://code.earthengine.google.com/3eddec46a224a2491d070057ab73419f)

## Image Collection

* Script: [Full example](https://code.earthengine.google.com/940ada34c9099e1df33259df21b3c649)

---
# Exporting

Most common method: export to your Google Drive

```js
// Make a collection of points.
var features = ee.FeatureCollection([
  ee.Feature(ee.Geometry.Point(30.41, 59.933), {name: 'a'}),
  ee.Feature(ee.Geometry.Point(-73.96, 40.781), {name: 'b'}),
  ee.Feature(ee.Geometry.Point(6.4806, 50.8012), {name: 'c'})
]);

// Export the FeatureCollection to a CSV file.
Export.table.toDrive({
  collection: features,
  description:'vectorsToDriveExample',
  fileFormat: 'CSV'
});

```

// Export the FeatureCollection to a CSV file.
Export.table.toDrive({
  collection: features,
  description:'vectorsToDriveExample',
  fileFormat: 'CSV'
});

</script>

.footnote[
[Exporting Data](https://developers.google.com/earth-engine/guides/exporting)
]

???

Earth Engine exports your work to your Google Drive account (or to an asset or to a Cloud Storage account)

Note: MUN students have unlimited storage in their Google Drive and their email does not expire (as of right now)

---
# Resources

.left-column[
[Earth Engine Documentation](https://developers.google.com/earth-engine/guides)

Earth Engine user group

Github: [gee-community](https://github.com/gee-community/), specifically the [examples](https://github.com/gee-community/example-scripts)

]

.right-column[
[Javascript + Earth Engine](https://developers.google.com/earth-engine/tutorials/tutorial_js_01)

[Script modules](https://developers.google.com/earth-engine/guides/playground#script-modules)

[Charts](https://developers.google.com/earth-engine/guides/charts)

[Objects, gt/lt](https://developers.google.com/earth-engine/guides/image_objects)

[`rgee`](https://github.com/r-spatial/rgee)

[QGIS examples](https://github.com/giswqs/qgis-earthengine-examples)

]

.footnote[
Many examples throughout are taken directly, or adapted slightly for this workshop, from the [Earth Engine documentation](https://developers.google.com/earth-engine) and sidebar examples. Thanks to the EE team for the incredible tool, and accompanying documentation and support.

]