02-workflow_basics.Rmd

# Workflow: basics

**Learning objectives:**

-   Review some basic R coding.
-   Follow good **style conventions** when writing code.
-   Explain the importance of commenting your code.
-   Recognize good practices when naming objects.
-   Confidently call **functions** in R.

## Basic math calculations {-}

```{r 03-basic-math}
1 / 200 * 30
(59 + 73 + 2) / 3
sin(pi / 2)
```

## Create new objects {-}

Use the 'assignment operator' `<-`

-   Windows: 'ALT -'. 
-   Mac: 'Option -'.
-   Pronunciation: `x <- 3*4`
    -   "to ... assign" or "is assigned to": "To object x ***assign*** three by four" OR "three by four ***is assigned to*** object x" 
    -   "gets": "x ***gets*** 3 times 4".

## Create new objects: Reverse assign {-}

Can go the other way `->`, eg graphs:

```{r 03-reverse-assign}
library(ggplot2)
ggplot(mtcars, aes(wt, hp)) +
  geom_point() -> plot01

plot01
```

## Create new objects: Double assign {-}

-   *Double assign or scoping assign `<<-`?!*

## Combining elements {-}

-   Combine elements into a vector with `c()`
-   Basic arithmetic operations applied to every element of a vector. 

```{r 03-vector-arithmetic}
primes <- c(2, 3, 5, 7, 11, 13)
primes * 2
```


## Comments {-}

Use `#` to insert comments in R. 
  
```{r 03-comments, eval = FALSE}
# Create vector of primes 
primes <- c(2, 3)

# Multiply primes by 2
primes * 2
```

## Comments: Why? {-}

-   Commenting your own code can save (future) you & and collaborators time.
- *Why* of your code, not the *how* or *what.* 
    -   Bad: `# Changed default value to 0.9`
    -   Good: `# Increased smoothing parameter to better capture the trend in the data.`


## Assigning names {-}

-   Names must start with a letter, contain letters, numbers, `_`, `.`. 
-   Good style convention ➡️ more readable code.
-   Use descriptive names. Long names are ok!
-   Book recommends `snake_case` (see next slide). 
-   R is case-sensitive! And it can't read your mind.
-   Typos matter! 

## Assigning names: Cases {-}

![](images/cases.png)

## Calling Functions {-}

Functions overall look like this: 

```{r 03-function-signature, eval=FALSE}
function_name(argument1 = value 1, 
              argument2 = value 2, 
              ...)
```

-   Functions and objects are always displayed in the Environment tab in RStudio. 

## Calling Functions: Arguments {-}

-   TAB to show possible completions of function & arguments.
    -   Use ESC to abort the suggestions. 
-   Can usually skip arg names, but can make code more readable. 
-   Order of named args isn't important
-   If you skip names remember the order of the defined function. 

```{r 03-arg-order, eval = FALSE}
# All of these are equivalent
seq(from = 1,  to = 10)
seq(to = 10,  from = 1)
seq(1, 10)
#> [1]  1  2  3  4  5  6  7  8  9 10
```
  
## Other RStudio Features {-}

Explore on your own:

-   Console: ⬆️ to see console history
-   Console: type, then (ctrl/cmd)- ⬆️ to search history
-   (alt/opt)-shift-k to see lots of shortcuts
-   *One of my recent favorites: alt-command-⬇️.*

## Exercises

1. Why does this code not work? 

```{r 03-ex-01, eval=FALSE}
my_variable <- 10
my_varıable 
#> Error in eval(expr, envir, enclos): object 'my_varıable' not found
```

> Because the name on the second line doesn't include and `i`. Remember, typos matter. 

2. Tweak each of the following R commands so that they run correctly:

```{r 03-ex-02, eval = FALSE}
libary(todyverse)

ggplot(dTA = mpg) + 
  geom_point(maping = aes(x = displ y = hwy)) +
  geom_smooth(method = "lm)
```

> Here is the correct code with no typos: 

```{r 03-ex-02b, eval=FALSE}
library(tidyverse)

ggplot(data = mpg)+
  geom_point(mapping = aes(x = display, y = hwy)) +
  geom_smooth(method = "lm")
```

3. Press Option + Shift + K / Alt + Shift + K. What happens? How can you get to the same place using the menus?

> This takes you to the list of shortcuts. Another way of getting here is: Tools > Keyboard shortcuts help. 

4. Let’s revisit an exercise from the Section 2.6. Run the following lines of code. Which of the two plots is saved as mpg-plot.png? Why?

```{r 03-ex-04, eval=FALSE}
my_bar_plot <- ggplot(mpg, aes(x = class)) +
  geom_bar()
my_scatter_plot <- ggplot(mpg, aes(x = cty, y = hwy)) +
  geom_point()
ggsave(filename = "mpg-plot.png", plot = my_bar_plot)
```

> The arguments for ggsave are (`?ggsave` in the console): filename, plot, device, path, ...). Plot refers to the plot to be saved, so in this case the first plot named `my_bar_plot` will be saved as mpg-plot.png. 

## Meeting Videos {-}

### Cohort 5

`r knitr::include_url("https://www.youtube.com/embed/nQnMm6kyJbE")`

<details>

<summary>Meeting chat log</summary>

```         
00:14:44    Jon Harmon (jonthegeek):    Ignore the URL on these, I should have made my coworker crop those out since it isn't relevant outside of our work environment 🙃
00:47:00    Jon Harmon (jonthegeek):    ?variable.names
00:58:53    Becki R. (she/her): jon_doe is an object?
00:59:05    Wai-Yin:    Yes.
01:10:33    Becki R. (she/her): Is there a list of verbal substitutions like "<- = get"?
01:16:05    Jon Harmon (jonthegeek):    Not yet! Some more will come up as we go through the book... and I plan on putting something together with them before too long!
01:16:56    Becki R. (she/her): Nice!
01:20:44    docksbox@pm.me: Thanks
01:22:41    Becki R. (she/her): Thanks everyone! I will not be here next week.
```

</details>

### Cohort 7

`r knitr::include_url("https://www.youtube.com/embed/JDOQDfpYBmY")`

<details>

<summary>Meeting chat log</summary>

```         
00:29:38    Dolleen Osundwa:    is a tibble similar to the table () function?
```

</details>

### Cohort 8

`r knitr::include_url("https://www.youtube.com/embed/FeSYfRx2esU")`

<details>

<summary>Meeting chat log</summary>

```         
00:06:13    Shamsuddeen Muhammad:   book_club-py4da
00:06:16    Shamsuddeen Muhammad:   #book_club-py4da
00:08:47    Shamsuddeen Muhammad:   https://www.youtube.com/watch?v=8tq1C8spV_g
00:09:03    Abdou Daffeh:   Hey everyone
00:34:25    Abdou Daffeh:   sorry do you mean vscode?
00:34:45    Hamza:  Yes he is using VSCode
00:35:13    Abdou Daffeh:   thanks, I have to check it out
00:41:22    Shamsuddeen Muhammad:   https://www.rscreencasts.com/content_pages/hbcu-enrollment.html
```

</details>