Geospatial Analysis with R

class: center, middle, inverse, title-slide

.title[
# Geospatial Analysis with R
]
.subtitle[
## Class 3
]

---

```r
library(raster)
library(ggplot2)
library(rasterVis)
library(gstat)

# dummy grids, with spatial autocorrelation, normalized
xy <- expand.grid(1:50, 1:50)
names(xy) <- c('x', 'y')

set.seed(2)  # 2
gdummy <- gstat(formula = z ~ 1, locations = ~x + y, dummy = TRUE, beta = 1,
                model = vgm(psill = 0.35, range = 30, model = 'Sph'), 
                nmax = 20)

yy <- predict(gdummy, newdata = xy, nsim = 4)
gridded(yy) <- ~x + y
yy <- raster(yy)
yy <- focal(yy, w = matrix(1, 3, 3), mean, na.rm = TRUE, pad = TRUE)

png("inst/slides/figures/random-raster.png", height = 5, width = 5, res = 300,
    units = "in", bg = "transparent")
lattice.options(layout.heights = list(bottom.padding = list(x = 0), 
                                      top.padding = list(x = 0)),
                layout.widths = list(left.padding = list(x = 0), 
                                     right.padding = list(x = 0)))
levelplot(yy, scales = list(draw = FALSE), axes = FALSE,  
          colorkey = list(axis.line = list(col = "white"), 
                          axis.text = list(col = "white")))
dev.off()
```

---
# Today's Topics
- Trouble-shooting
- `R` packages
- `git` / GitHub
- Overview of assignment
- Keeping up to date with class materials
- Tips and tricks for productivity
  - Seeking help as a skillset
---

# R packages

- File structure
- Where packages live
- library versus package
- Exported functions, loading packages

---
## Types of packages

<div class="figure" style="text-align: center">
<img src="http://r-pkgs.had.co.nz/diagrams/package-files.png" alt="http://r-pkgs.had.co.nz/package.html" width="55%" />
<p class="caption">http://r-pkgs.had.co.nz/package.html</p>
</div>

---
## Installing packages

<div class="figure" style="text-align: center">
<img src="https://r-pkgs.org/diagrams/install-load.png" alt="http://r-pkgs.had.co.nz/package.html" width="90%" />
<p class="caption">http://r-pkgs.had.co.nz/package.html</p>
</div>
---

# `git` / GitHub

- Commits, pushes, pulls
- Branching
- Merging

---
<div class="figure" style="text-align: center">
<img src="https://kevintshoemaker.github.io/StatsChats/GIT1.png" alt="kevintshoemaker.github.io/StatsChats/GIT_tutorial" width="70%" />
<p class="caption">kevintshoemaker.github.io/StatsChats/GIT_tutorial</p>
</div>
---
<div class="figure" style="text-align: center">
<img src="https://kevintshoemaker.github.io/StatsChats/GIT2.png" alt="kevintshoemaker.github.io/StatsChats/GIT_tutorial" width="70%" />
<p class="caption">kevintshoemaker.github.io/StatsChats/GIT_tutorial</p>
</div>
---
<div class="figure" style="text-align: center">
<img src="https://i.stack.imgur.com/yof9f.png" alt="stackoverflow.com/questions/7212740/why-git-is-called-a-distributed-source-control-system" width="70%" />
<p class="caption">stackoverflow.com/questions/7212740/why-git-is-called-a-distributed-source-control-system</p>
</div>
---

## Our Branching Model

---

## Keeping current

- Using `git` and GitHub
- Following [4.3.4.](https://agroimpacts.github.io/geospaar/unit1-module1.html#cloning-the-remote-repo) of Unit 1 - Module 1

---

# [Assignment 1]("https://agroimpacts.github.io/geospaar/unit1-module1.html#unit-assignment")

- Due Monday (29th)

---

# Tips and Tricks

- Tab completion and shortcuts
- Reusing code
- Code syntax
- [Posting guide](https://www.r-project.org/posting-guide.html)

---

## Knowing how to get help as a skillset

- Slack posting guide
- Getting help via the search engine
- (Eventually) posting to listserves

---
## Search Engine Science

- Sometimes you just need the error message
<img src="figures/class3_4.jpeg" width="90%" style="display: block; margin: auto;" />

---
## Search Engine Science

- Sometimes you need to search
  ```
  fatal: unable to access 'https://github.com/agroimpacts/xyz346.git/': 
  error setting certificate verify locations:
   CAfile: C:/Users/xyz/Desktop/ADP/RStudio/xyz346/Git/mingw64/ssl/
   certs/ca-bundle.crt
   CApath: none
  ```
- How you search matters

---

---
## Listserves
<img src="figures/class3_3.png" width="90%" style="display: block; margin: auto;" />