r-intro.Rmd

---
title: "Introduction to R"
subtitle: "`http://bit.ly/cr18-r-intro`"
author: \@mauro_lepore
output: ioslides_presentation
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE
)
```

## Data Science http://r4ds.had.co.nz/

<img src="ds_pkg.png" align="right" width = 750 />

## https://www.tidyverse.org/

<img src="tidyverse.png" align="right" width = 750 />

# Transform data

## Tools for data science

```{r}
library(tidyverse)
```

## Example dataset

```{r}
library(fgeo.data)
dim(luquillo_tree6_random)
```

## Overview

```{r}
luquillo_tree6_random

tree <- luquillo_tree6_random
```

## dplyr: Main verbs

<img src="verbs.png" align="right" width = 750 />

## Filter rows with `filter()`

```{r}
filter(tree, sp == "PREMON", quadrat == "1017")
```
## Equivalent

```{r}
tree[tree$sp == "PREMON" & tree$quadrat == "1017", ]
```

## Arrange rows with `arrange()`

```{r}
arrange(tree, sp, quadrat)
```

## Arrange in descending order `desc()`

```{r}
arrange(tree, desc(sp), quadrat)
```

## Select columns with `select()`

```{r}
select(tree, sp, quadrat, treeID, status, dbh)
```

## Select range

```{r}
select(tree, treeID:quadrat)
```

## Exclude range

```{r}
select(tree, -(treeID:quadrat))
```

## Rename columns with `rename()`

```{r}
rename(tree, tree_id = treeID)
```

## Add new columns with mutate()

```{r}
mutate(tree, 
  dbh_mm = dbh,
  dbh_m = dbh_mm / 1000
)
```

## Only new variables with `transmute()`

```{r}
transmute(tree, 
  dbh_mm = dbh,
  dbh_m = dbh_mm / 1000
)
```

## Summarise values with `summarise()`

```{r}
by_quad_sp <- group_by(tree, quadrat, sp)
summarise(by_quad_sp,
  mean_dbh = mean(dbh, na.rm = TRUE),
  mean_gx = mean(gx, na.rm = TRUE),
  mean_gy = mean(gy, na.rm = TRUE)
)
```

## Anything by groups with `group_by()`

```{r}
by_sp <- group_by(tree, quadrat)

summarise(by_sp,
  mean_dbh = mean(dbh, na.rm = TRUE)
)
```

# Learn more

## https://www.rstudio.com/

<img src="rstudio.png" align="right" width = 750 />

## https://rstudio.cloud/learn/primers

<img src="primers.png" align="right" width = 750 />

## https://www.rstudio.com/resources/cheatsheets/

<img src="cheet.png" align="right" width = 750 />