GeoScripting_Concept_Intro.Rmd

---
title: "Geo-scripting"
author: "Jan Verbesselt"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: 
  ioslides_presentation:
    footer: "Geo-scripting 2020"
---

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add explanation on evaluation criteria - rubrics - evaluation and feedback system
add explanation on "reproducible example"
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## Did you know?!

Scripting can be used to process satellite data easily to monitor deforestation globally

- Google Earth Engine for global deforestation monitoring
      - https://earthengine.google.org/#intro

![](figs/forest-cover-global.png)

Image Credit: NASA Goddard, based on data from Hansen et al., 2013.

## Why geo-scripting?

![](figs/solve-cool-problems.png)

## Why geo-scripting?

- Reproducible: you keep track of what you have done 

- Efficient: you can write a script to do something and repeat your analysis x1000... 

-	Good for finding errors

Can you think of other advantages?

## Why geo-scripting?

-  Enable collaboration
    - a huge social R and Python community
    
![](figs/facebook.png)

## Why geo-scripting?

- Build your own tools and functions (e.g. automated web-processing, etc.)

![](figs/16199604.jpg)

[See Lesson 2 demo's!](https://geoscripting-wur.github.io/Scripting4Geo/#why-scripting)

## Geo-scripting learning objectives

- Read, write, and visualize spatial data using a script
- Find and use  functions for geo-data handling
- Know how to find help
    - Write a clear and reproducible script
    - Learn how to help each other
- Apply learned concepts for your own geo-challenge

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## The geo-scripting course

Goal:

- Scripting to solve spatial challenges!
- **Learn by doing**
- **Learn how to keep on learning**


A team of `R` & `Python` experts who use geo-scripting languages 
every day helped to develop this course

## Course concept

Flipped Classroom concept:

![](figs/flipping-the-classroom.jpg)

* Experts from companies, research institutes and 
university will present (guest lectures)

## Course concept

Day planning See our course guide.
See also Brightspace

- Dayly automatically evaluated Exercises!

## Team work & helping each other

- Teams of two:

- select the team (2 persons, e.g. 1st with 2nd year MGI ) and fill in the form (see blackboard)

- Other teams can be selected for the project work

<div class="centered">
![](figs/teamwork.jpeg)
</div>

## Team work & helping each other

- Microsoft teams question and answer Forum

- Microsoft team - Staff announcements


## Scoring

- 3 weekly assignments - 30%
- Questions & Answers support and activity - 10%
- Project - 60%

Details -see the course guide!

## Individual assessment

- Question and answer forum
- DataCamp website: challenges
    - Free access to all courses for 6 months
   
- Script reviewing can be done on an individual basis both team member need to
equally use Git

## Learning outcomes of today:

- Refreshing and assessing R scripting skills to see if you can continue with the course
- Able to write a function
- Know how to visualize a spatial map in R

*Socrative Quiz at the end of this presentation!*
    
## What  is a scripting language?

- A scripting language can interpret and automate the execution of tasks, instead of clicking!!!
- A scripting language is the glue, between different commands, functions, and objectives without the need to compile it for each OS (e.g. windows)
- This is different from like C/C++/Fortran 
    - these are languages that need to be compiled first.

## Compiling

Passing the source code through a compiler, which translates the `high-level language` instructions into an `exe`.

```{r, echo=FALSE, fig.align='center', fig.width=6, strip.white=TRUE}
library(png)
library(grid)
img <- readPNG("figs/traditionalCompiler.png")
grid.raster(img)
```

## The main scripting languages for GIS and Remote sensing currently are: 

- R
- Python
- GRASS (grass function are included in QGIS)
- JavaScript for geoweb scripting
- Matlab
- IDL (ENVI)
- ...

## Python versus R

- Python is a general purpose programming language
- R is particularly strong in statistical computing and graphics
- Syntactic differences between R and Python can be confusing  
- There are many R and Python packages for spatial analyses

![](figs/RPythonS.png)

## R packages
![](figs/worldcloudRpackage.png)

## Many programs have support for

 Python & R e.g.:
 
 - QGIS
 - GRASS
 - PostGIS

## Challenge

Login to socrative: http://www.socrative.com

Room: GEOSCRIPTING

Quiz: Geo-scripting intro

## Time for R action!

- Linux
- Git
- What is a "reproducible script"?

## Reproducibility

![](figs/rep_sci_cover.png)

## Rubric

[Rubric](https://docs.google.com/document/d/1wdqcrqh4Bt-tNwhEFRa4esq7ozwo36tfOjGmbBTK5B4/edit?usp=sharing)

## Tomorrow morning

- Provide feedback
- Lesson 2
    - an overview of what is possible with scripting
    - no need to understand the code: lesson 2 is a demonstration lesson!

[See Lesson 2 demo's!](https://geoscripting-wur.github.io/Scripting4Geo/#why-scripting)

<!--
```{r, fig.align='center', echo=FALSE, message=FALSE, eval=FALSE}
if (!file.exists(fn <- "figs/worldcloudRpackage.png")) {
    fn <- "figs/worldcloudRpackage.png"
    require(XML)
    require(tm)
    require(wordcloud)
    require(RColorBrewer)
    u = "http://cran.r-project.org/web/packages/available_packages_by_date.html"
    t = readHTMLTable(u)[[1]]
    ap.corpus <- Corpus(DataframeSource(data.frame(as.character(t[,3]))))
    ap.corpus <- tm_map(ap.corpus, removePunctuation)
    # ap.corpus <- tm_map(ap.corpus, tolower)
    #  txt.corpus <- tm_map(txt.corpus, tolower)
    # must be changed to
    ap.corpus <- tm_map(ap.corpus, content_transformer(tolower))
    ap.corpus <- tm_map(ap.corpus, function(x) removeWords(x, stopwords("english")))
    ap.tdm <- TermDocumentMatrix(ap.corpus)
    ap.m <- as.matrix(ap.tdm)
    ap.v <- sort(rowSums(ap.m),decreasing=TRUE)
    ap.d <- data.frame(word = names(ap.v),freq=ap.v)
    table(ap.d$freq)
    pal2 <- brewer.pal(8,"Dark2")
    png(fn, width=1280, height=800)
    wordcloud(ap.d$word,ap.d$freq, scale=c(8,.2),min.freq=3,
    max.words=Inf, random.order=FALSE, rot.per=.15, colors=pal2)
    dev.off()    
}
```
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