03_magrittr.Rmd

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title: "03_magrittr"
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# 3 `palmerpenguins`:<br><br>Palmer Archipelago (Antarctica) Penguin Data

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## 3 `palmerpenguins`: Palmer Archipelago<br>(Antarctica) Penguin Data
.pull-left[
From here on, to illustrate the features of the `tidyverse` core packages we use data from the `palmerpenguins` package by [Allison Horst](https://allisonhorst.github.io/palmerpenguins/).

The package comes with data about penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
]
.pull-right[
```{r, echo=F, fig.align='center', out.width='60%'}
knitr::include_graphics("https://tenor.com/view/penguin-fat-the-struggle-is-real-lazy-gif-4242854.gif")
```
]

---

## 3 `palmerpenguins`: Palmer Archipelago<br>(Antarctica) Penguin Data

.pull-left[
```{r, eval=F}
library(palmerpenguins)

penguins
```
```{r, echo=F}
print(penguins, width = 50)
```
]
.pull-right[
```{r, echo=F, fig.align='center', out.width='65%', out.height='65%'}
knitr::include_graphics("https://raw.githubusercontent.com/allisonhorst/palmerpenguins/master/man/figures/lter_penguins.png")
knitr::include_graphics("https://raw.githubusercontent.com/allisonhorst/palmerpenguins/master/man/figures/culmen_depth.png")
```
]

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# 4.1 `magrittr`:<br><br>A Forward-Pipe Operator for `R`

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## 4.1 `magrittr`: The Forward-Pipe Operator

`magrittr` comes with a set of operators:
- **Pipe Operator:** `%>%`<br><br>
- **Assignment Operator:** `%<>%`<br><br>
- **"Tee" Operator:** `%T>%`<br><br>
- **Exposition Operator:** `%$%`

--

<br>
Essentially, these operators aim to improve the readability of your code in multiple ways:
- arrange operations into an easily readable pipeline of chained commands (left-to-right),
- avoid nested function calls (inside-out), 
- minimize the use of local variable assignments (`<-`) and function definitions, and
- easily add and/or delete steps in your pipeline without breaking the code.

???
The exposition operator: %$% (explodes out variables in a data frame, no need to use pull())

---

## 4.1 `magrittr`: The Forward-Pipe Operator

**Basic Piping:** forward a value or object (LHS) into the next function call (RHS) as **first** argument
```{r, eval=F}
x %>% f                            # equivalent to: f(x)
x %>% f(y)                         # equivalent to: f(x, y)
x %>% f %>% g %>% h                # equivalent to: h(g(f(x)))
```

--

**Piping with placeholders:** forward a value or object (LHS) into the next function call (RHS) as **any** argument
```{r, eval=F}
x %>% f(.)                         # equivalent to: x %>% f
x %>% f(y, .)                      # equivalent to: f(y, x)
x %>% f(y, z = .)                  # equivalent to: f(y, z = x)
x %>% f(y = nrow(.), z = ncol(.))  # equivalent to: f(x, y = nrow(x), z = ncol(x))
```

--

**Building functions and pipelines:** a sequence of code starting with the placeholder (`.`) returns a function which can be used to later apply the pipeline to concrete values
```{r, eval=F}
f <- . %>% cos %>% sin             # equivalent to: f <- function(.) sin(cos(.))
f(20)                              # equivalent to: the pipeline 20 %>% cos %>% sin
```

.footnote[
*Note: Find out more about `%>%` by running `vignette("magrittr")`. Type `%>%` using the shortcut: Ctrl + Shift + M.*
]

---

## 4.1 `magrittr`: The Forward-Pipe Operator

**Question:** What is the average body mass in grams for all penguins observed in the year 2007 (after excluding missing values)?

**In a pipeless world:**
```{r, eval=F}
mean(subset(penguins, year == 2007)$body_mass_g, na.rm = T)

# alternatively:
peng_bm_2007 <- subset(penguins, year == 2007)$body_mass_g
mean(peng_bm_2007, na.rm = T)
```

--

.pull-left[
**In a world full of pipes:**
```{r, eval=F}
penguins %>% 
  subset(year == 2007) %>% 
  .$body_mass_g %>% 
  mean(na.rm = T)
```
]
.pull-right[
<br>
- Sequential style improves readability!
- Less deciphering of nested function calls!
- No need to store intermediate results!
- Modular modification of pipeline steps!
]

.footnote[
*Note: As of version `4.1.0`, base `R` comes with a native pipe operator as well (`|>`).*
]

???
- Add or remove individual steps easily in your pipeline
- The `magrittr` forward pipe is imported by the `tidyverse`, no need to load it separately

---

## 4.1 `magrittr`: The Forward-Pipe Operator

**Advanced piping:** Use the more advanced pipe operators to further streamline your workflow.

.panelset[
.panel[.panel-name[Tee Pipe]
`%T>%` can be used to trigger the side-effect of a function, e.g., for plotting or printing results, and let the original data bypass the respective step.
```{r}
penguins[1:5, c("island", "bill_length_mm")] %T>% print %>% .$bill_length_mm %>% mean(na.rm=T)
```
]
.panel[.panel-name[Exposition Pipe]
`%$%` exposes the names in LHS object to the RHS expression. This is useful if the RHS expression does not allow for a separate `data` argument.
```{r, fig.width=6, fig.asp=0.618, fig.retina=3}
penguins %$% plot(species, bill_length_mm)  # equivalent to: plot(penguins$species, penguins$bill_length_mm)
```
]
.panel[.panel-name[Assignment Pipe]
`%<>%` can be used equivalently to the base `R` assignment operator (`<-`). It reassign the result of the of the pipeline to the starting variable.
```{r}
var <- penguins$bill_length_mm

var %<>% mean(na.rm=T)

var
```
]
]