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class: title-slide
count: false

.title[
  # 05 - Coding
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella &amp; Davide Massidda
]

.institute[

]

---
class: center, middle, inverse

# Step IV: Coding [with] Style

---

# Coding Style

--
## The ideal code

--
- It works
--

.font-18[
&gt;*“Any fool can write code that a computer can understand.&lt;br&gt;Good programmers write code that humans can understand.”* – Martin Fowler

]
--

- It is readable
- It is easy to maintain

---
# Coding Style

--
.move-up-30[
.bad-code[

```r
y&lt;-c(1,0,1,1,0,1,1);p&lt;-sum(y)/length(y);if(p&gt;=.6){"Passed"}else{"Failed"}
## [1] "Passed"
```
]
]
--

.good-code[

```r
# Load subj test answers
exam_answers &lt;- c(1,0,1,1,0,1,1) # 0 = wrong; 1 = correct

# Get exam score as proportion of correct answers
exam_score &lt;- sum(exam_answers) / length(exam_answers)

# Set exam pass threshold [0,1]
threshold &lt;- .6

# Check if subj passed the exam
if (exam_score &gt;= threshold) {
  "Passed"
} else {
  "Failed"
}
## [1] "Passed"
```
]

--

&gt;*“Good coding style is like using correct punctuation. You can manage without it,&lt;br&gt; but it sure makes things easier to read.”* – Hadley Wickham

---
# Coding Good Practices

.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
{{content}}
]
]
.pull-right-70[

]
--

- Naming variables
- Spacing and indentation
- Comments

---
# Coding Good Practices

.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

{{content}}
]

--
&gt; *“There are only two hard things in Computer Science: cache invalidation and naming things.”* – Phil Karlton

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
.bad-code[

```r
y # generic name without useful information
```
]
.good-code[

```r
exam_answers # clear descriptive name
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
- Right Length
.bad-code[

```r
average_outcome_score_of_the_control_gorup # too long

  avg_scr_ctr # difficult to guess the abbreviation meaning
```
]
.good-code[

```r
avg_score_control # clear descriptive name
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
- Right Length
- Consistent naming style
.good-code[

```r
myObjectName    # camelCase

  MyObjectName    # PascalCase

  my_object_name  # snake_case
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
- Right Length
- Consistent naming style
.good-code[

```r
myObjectName    # camelCase

  MyObjectName    # PascalCase

  my_object_name  # snake_case
```
]
.warn-code[

```r
my.object.name  # snake.case (deprecated)
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
- Right Length
- Consistent naming style
- Avoid special characters (e.g., è, ü, ñ, etc.)

&lt;img src="images/05-code/unicode.jpg" width="60%" style="display: block; margin: auto;" /&gt;

]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Auto-descriptive
- Right Length
- Consistent naming style
- Avoid special characters (e.g., è, ü, ñ, etc.)
- Avoid naming objects with function names&lt;br&gt;(e.g., `data`, `list`, or `sum`)
- Avoid similar names that could be easily confused
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Naming variables
- .alpha[Spacing and indentation]
- .alpha[Comments]
]
]
.pull-right-70[

#### Extra: Temporary Variables

.li-small[
- Position Index: `i`, `index`, `row_i`, or `col_i`
.good-code[
.code-size-12[

```r
# Cities names
  cities &lt;- c("Amsterdam", "Berlin", "Cardiff", "Dublin")
  
  # Loop by position index
  for (i in seq_len(length(cities))) {
    cat(cities[i], " ")
  }
  ## Amsterdam  Berlin  Cardiff  Dublin
```
]
]

- Element: `k`, parts (`slice` of `pizza`), or singular
.good-code[
.code-size-12[

```r
# Loop by element
  for (city in cities) {
    cat(city, " ")
  }
  ## Amsterdam  Berlin  Cardiff  Dublin
```
]
]
]
]
---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Line length (e.g, 80 characters)
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Line length (e.g, 80 characters)

&lt;img src="images/05-code/rstudio-line.png" width="50%" style="display: block; margin: auto;" /&gt;
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Line length (e.g, 80 characters)
- Alignment
.bad-code[

```r
# too long
my_very_long_list&lt;-list(first_argument="something-very-long",second_argument=c("many","objects"),third_argument=c(1,2,3,4,5))
#
```
]
.good-code[

```r
my_very_long_list &lt;- list(
      first_argument = "something-very-long",
      second_argument = c("many", "objects"),
      third_argument = c(1, 2, 3, 4, 5)
      )
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Line length (e.g, 80 characters)
- Alignment
- Spacing and named arguments
.bad-code[

```r
# es. 1
x&lt;-sum(c(1:10,99),rnorm(5,mean=3,1))
# es. 2
if(test&gt;=5&amp;test&lt;=10)print("...")
```
]
.good-code[

```r
# es. 1
x &lt;- sum(c(1:10, 99), rnorm(n = 5, mean = 3, sd = 1))
# es. 2
if (test &gt;= 5 &amp; test &lt;= 10) print("...")
```
]
]
]
---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

&lt;br&gt;

.li-small[
- Line length (e.g, 80 characters)
- Alignment
- Spacing and named arguments
- Indentation
]
.move-up-30[
.pull-left-50[
.bad-code[

```r
for (...) {   # Outer loop
...
for (...) {   # Inner loop
...
if (...) {    # Conditional 
...
}}}
```
]
]
.pull-right-50[
.good-code[

```r
for (...) {   # Outer loop
  ...

  for (...) {   # Inner loop
    ...

    if (...) {    # Conditional

      ...
    }
  }
}
```
]
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

#### Extra: Do not mix-up tabs and spaces!!

{{content}}

]

--

&lt;img src="images/05-code/rstudio-indent.png" width="60%" style="display: block; margin: auto;" /&gt;

---

# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- Spacing and indentation
- .alpha[Comments]
]
]
.pull-right-70[

#### Extra: Do not mix-up tabs and spaces!!

&lt;br&gt;

.move-up-30[
&lt;iframe width="672" height="378" src="https://www.youtube-nocookie.com/embed/SsoOG6ZeyUI" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen&gt;&lt;/iframe&gt;
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- .alpha[Spacing and indentation]
- Comments
]
]
.pull-right-70[

&lt;br&gt;

&lt;br&gt;

.li-small[
{{content}}
]
]

--

- Describe the aim and the logic
- Not duplicate the code

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- .alpha[Spacing and indentation]
- Comments
]
]
.pull-right-70[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Describe the aim and the logic
- Not duplicate the code

.bad-code[

```r
# Set x to 10
x &lt;- 10 
```
]
.good-code[

```r
# Define maximum answer number
x &lt;- 10
```
]
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- .alpha[Spacing and indentation]
- Comments
]
]
.pull-right-70[

&lt;br&gt;

&lt;br&gt;

.li-small[
- Describe the aim and the logic
- Not duplicate the code
- Explain unidiomatic code
- Provide links and references
]
]

---
# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- .alpha[Spacing and indentation]
- .alpha[Comments]
- Extra
]
]
.pull-right-70[
.center[
.move-up-30[
{{content}}
]
]
]

--
## KISS

{{content}}

--
*Keep It Simple Stupid!*

---

# Coding Good Practices


.pull-left-30[

&lt;br&gt;

&lt;br&gt;

.li-small[
- .alpha[Naming variables]
- .alpha[Spacing and indentation]
- .alpha[Comments]
- Extra
]
]
.pull-right-70[
.center[
.move-up-30[

## KISS

*Keep It Simple Stupid!*

]
]
.pull-left-50[
.bad-code[
.code-small[

```r
check_value &lt;- function(x){

  if (x &gt; 0) {
    if (x &gt; 100) {
      return("x is a positive large value")
    } else {
      return("x is a positive value")
    }
  } else {
    if (x &lt; - 100) {
      return("x is a negative small value")
    } else {
      return("x is a negative value")
    }
  }

}
```
]
]
]
.pull-right-50[
.good-code[
.code-small[

```r
check_value &lt;- function(x){

  if(x &lt; - 100) return("x is a negative small value")
  if(x &lt; 0) return("x is a negative value")
  if(x &lt; 100) return("x is a positive value")

  return("x is a positive large value")
}
}
```
]
]
]
]

---

# R Good Practices
--

.move-up-50[
.pull-left-50[
### Assign

`&lt;-` vs `=`

.code-size-12[

```r
# both are valid
a &lt;- 3
b = 4

# which one is more clear?
a &lt;- b
a = b
```
]

]
.pull-right-50[]
]

---
# R Good Practices

.move-up-50[
.pull-left-50[
### Assign

`&lt;-` vs `=`

.code-size-12[

```r
# both are valid
a &lt;- 3
b = 4

# which one is more clear?
a &lt;- b
a = b
```
]

]
.pull-right-50[

### Logical Values

`TRUE`/`FALSE` vs `T`/`F`

.code-size-12[

```r
# Check value
TRUE == T
## [1] TRUE

# Change values
TRUE &lt;- "Hello"
## Error in TRUE &lt;- "Hello": 
## invalid (do_set) left-hand side to assignment

T &lt;- "World"
T
## [1] "World"

TRUE == T
## [1] FALSE

# If you want to be evil
T &lt;- FALSE
FALSE == T
## [1] TRUE
```
]
]
]
---
class: inverse, middle, center

# Functional Style

---
# Functional Style

---
# Functional Style

.pull-left-50[
.bad-code[

```r
# Standardize variables
x1_std &lt;- (x1 - mean(x1)) / sd(x1)
x2_std &lt;- (x2 - mean(x2)) / sd(x2)
x3_std &lt;- (x3 - mean(x3)) / sd(x3)
```
]

.center[
{{content}}
]
]
.pull-right-50[
.good-code[

]
]

--
## DRY

*Don’t Repeat Yourself!*
---
# Functional Style

.pull-left-50[
.bad-code[

```r
# Standardize variables
x1_std &lt;- (x1 - mean(x1)) / sd(x1)
x2_std &lt;- (x2 - mean(x2)) / sd(x2)
x3_std &lt;- (x3 - mean(x3)) / sd(x3)
```
]
.center[
## DRY

*Don’t Repeat Yourself!*
]
]
.pull-right-50[
.good-code[

```r
#----    my-functions.R    ----#

# Define custom function
std_var &lt;- function(x){
  
  res &lt;- (x - mean(x)) / sd(x)
  
  return(res)
}

#----    my-analysis-script.R    ----#

# Apply custom function
x1_std &lt;- std_var(x1)
x2_std &lt;- std_var(x2)
x3_std &lt;- std_var(x3)
```
]
]

---
# Functional Style

.pull-left-50[
.bad-code[

```r
# Standardize variables
x1_std &lt;- (x1 - mean(x1)) / sd(x1)
x2_std &lt;- (x2 - mean(x2)) / sd(x2)
x3_std &lt;- (x3 - mean(x3)) / sd(x3)
```
]
.center[
## DRY

*Don’t Repeat Yourself!*
]

.li-small[
&lt;br&gt;

- Maintainability
- Readability
- Reuse
]
]
.pull-right-50[
.good-code[

```r
#----    my-functions.R    ----#

# Define custom function
std_var &lt;- function(x){
  
  res &lt;- (x - mean(x)) / sd(x)
  
  return(res)
}

#----    my-analysis-script.R    ----#

# Apply custom function
x1_std &lt;- std_var(x1)
x2_std &lt;- std_var(x2)
x3_std &lt;- std_var(x3)
```
]
]
---

# Functional Style - Wrap function

--

.pull-left-50[

#### &amp;nbsp;


```r
#----    my-analysis-script.R    ----#

# Data cleaning
my_data &lt;- read_csv("my-data.csv") %&gt;% 
  select(...) %&gt;% 
  mutate(...) %&gt;% 
  gorup_by(...) %&gt;% 
  summarize(...)

```

]
.pull-right-50[

]

---
# Functional Style - Wrap function

.pull-left-50[

#### &amp;nbsp;


```r
#----    my-analysis-script.R    ----#

# Data cleaning
my_data &lt;- read_csv("my-data.csv") %&gt;% 
  select(...) %&gt;% 
  mutate(...) %&gt;% 
  gorup_by(...) %&gt;% 
  summarize(...)

```

]
.pull-right-50[

#### &amp;nbsp;


```r
#----    my-functions.R    ----#

# Define data cleaning function
clean_my_data &lt;- function(file){
  res &lt;- read_csv(file) %&gt;% 
    select(...) %&gt;% 
    mutate(...) %&gt;% 
    gorup_by(...) %&gt;% 
    summarize(...)
  
  return(res)
}
```
]

---

# Functional Style - Wrap function

.pull-left-50[

#### Before


```r
#----    my-analysis-script.R    ----#

# Data cleaning
my_data &lt;- read_csv("my-data.csv") %&gt;% 
  select(...) %&gt;% 
  mutate(...) %&gt;% 
  gorup_by(...) %&gt;% 
  summarize(...)

```


#### After


```r
#----    my-analysis-script.R    ----#

# Data cleaning
my_data &lt;- clean_my_data("my-data.csv")

# other steps ...
```

]
.pull-right-50[

#### &amp;nbsp;


```r
#----    my-functions.R    ----#

# Define data cleaning function
clean_my_data &lt;- function(file){
  res &lt;- read_csv(file) %&gt;% 
    select(...) %&gt;% 
    mutate(...) %&gt;% 
    gorup_by(...) %&gt;% 
    summarize(...)
  
  return(res)
}
```
]

---
# Function Good Practices

--
.pull-left-30[

&lt;br&gt;

.li-small[
- Knowing your Beast
- Function Names
- Handling Conditions
- No Hard-Coded Values
- Checking Inputs
- Be Explicit
- KISS
- WET
]
]
.pull-right-70[
]
---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- Knowing your Beast
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

.bad-code[

```r
x &lt;- sqrt(2)
x^2 == 2  # WTF (Why is This False?)
## [1] FALSE
```
]

.good-code[

```r
all.equal(x^2, 2)
## [1] TRUE
```
]

.warn-code[
{{content}}
]
]
--


```r
# Not intuitive behaviour
round(1.5)
## [1] 2

round(2.5)
## [1] 2
```

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- Function Names
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

&lt;br&gt;

.bad-code[

```r
f()
my_data()
```
]

.good-code[

```r
get_my_data()
```
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- Handling Conditions
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[
.pull-left-50[
.bad-code[
.code-size-12[

```r
solve_condition &lt;- function(x){
  ...

  if (is_condition_A){
    ...
  } else {
    ...
  }

  ...

  if (is_condition_B){
    ...
  } else {
    ...
  }

  ...

  return(res)
}
```
]
]
]
.pull-right-50[
.good-code[
.code-size-12[

```r
solve_A &lt;- function(x){

  # All code related to 
  # condition A
  ...

  return(res)
}

solve_B &lt;- function(x){

  # All code related to 
  # condition B
  ...

  return(res)
}
```
]
]
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- No Hard-Coded Values
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

.bad-code[

```r
format_perc &lt;- function(x){

  perc_values &lt;- round(x * 100, digits = 2)
  res &lt;- paste0(perc_values, "%")

  return(res)
}
```
]

.good-code[

```r
format_perc &lt;- function(x, digits = 2){

  perc_values &lt;- round(x * 100, digits = digits)
  res &lt;- paste0(perc_values, "%")

  return(res)
}
```
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- No Hard-Coded Values
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

.bad-code[

```r
format_perc &lt;- function(x){

* perc_values &lt;- round(x * 100, digits = 2)
  res &lt;- paste0(perc_values, "%")

  return(res)
}
```
]

.good-code[

```r
format_perc &lt;- function(x, digits = 2){

* perc_values &lt;- round(x * 100, digits = digits)
  res &lt;- paste0(perc_values, "%")

  return(res)
}
```
]
]


---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- Checking Inputs
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[
.bad-code[

```r
safe_division &lt;- function(x, y){
  res &lt;- x / y
  return(res)
}

safe_division(x = 1, y = 0)
## [1] Inf
```
]

.good-code[

```r
safe_division &lt;- function(x, y){
  if(y == 0) stop("you can not divide by zero")
  
  res &lt;- x / y
  return(res)
}

safe_division(x = 1, y = 0)
## Error in safe_division(x = 1, y = 0): 
## you can not divide by zero
```
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- Checking Inputs
- .alpha[Be Explicit]
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[
.bad-code[

```r
safe_division &lt;- function(x, y){
  res &lt;- x / y
  return(res)
}

safe_division(x = 1, y = 0)
## [1] Inf
```
]

.good-code[

```r
safe_division &lt;- function(x, y){
* if(y == 0) stop("you can not divide by zero")
  
  res &lt;- x / y
  return(res)
}

safe_division(x = 1, y = 0)
## Error in safe_division(x = 1, y = 0): 
## you can not divide by zero
```
]
]
---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- Be Explicit
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

.bad-code[

```r
get_mean &lt;- function(x){
  sum(x) / length(x)
}
```
]

.good-code[

```r
get_mean &lt;- function(x){

  res &lt;- sum(x) / length(x)

  return(res)
}
```
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- Be Explicit
- .alpha[KISS]
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;

.bad-code[

```r
get_mean &lt;- function(x){
  sum(x) / length(x)
}
```
]

.good-code[

```r
get_mean &lt;- function(x){

  res &lt;- sum(x) / length(x)

* return(res)
}
```
]
]

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- KISS
- .alpha[WET]
]
]
.pull-right-70[

&lt;br&gt;


&lt;br&gt;

.center[*Keep It Simple Stupid!*]


&lt;br&gt;

{{content}}
]

--

- Single Responsibility Principle
- From Small to Big

---
# Function Good Practices

.pull-left-30[

&lt;br&gt;

.li-small[
- .alpha[Knowing your Beast]
- .alpha[Function Names]
- .alpha[Handling Conditions]
- .alpha[No Hard-Coded Values]
- .alpha[Checking Inputs]
- .alpha[Be Explicit]
- .alpha[KISS]
- WET
]
]
.pull-right-70[

&lt;br&gt;

&lt;br&gt;

.center[*Write Everything Twice*]

]

---
# Documentation

.pull-left-30[
&lt;br&gt;

.li-small[
{{content}}
]
]
.pull-right-70[

]

--

- Title
- Description 
- Arguments
- Outputs
- Examples

---
# Documentation

.pull-left-30[
&lt;br&gt;

.li-small[
- Title
- Description 
- Arguments
- Outputs
- Examples
]
]
.pull-right-70[
.move-up-50[
.code-size-12[

```r
#----    format_perc    ----

# Format Values as Percentages
#
# Given a numeric vector, return a string vector with the values 
# formatted as percentage (e.g., "12.5%"). The argument `digits` 
# allows specifying the rounding number of decimal places.
#
# Arguments:
# - x : Numeric vector of values to format.
# - digits: Integer indicating the rounding number of decimal places 
#           (default 2)
#
# Output:
# A string vector with values formatted as percentages (e.g., "12.5%").
#
# Examples:
# format_perc(c(.749, .251))
# format_perc(c(.749, .251), digits = 0)

format_perc &lt;- function(x, digits = 2){
      
  perc_values &lt;- round(x * 100, digits = digits)
  res &lt;- paste0(perc_values, "%")
  
  return(res)
}
```
]
]
]

---
# Unit Tests

--

.pull-left-40[

```r
#----    get_mean    ----
get_mean &lt;- function(x){
  
  res &lt;- sum(x) / length(x)
  
  return(res)
}
```
]
.pull-right-60[

]

---
# Unit Tests

.pull-left-40[

```r
#----    get_mean    ----
get_mean &lt;- function(x){
  
  res &lt;- sum(x) / length(x)
  
  return(res)
}
```
]
.pull-right-60[

```r
#----    Unit Tests    ----

# Test 1
stopifnot(
  format_perc(.10) == '10%'
  )

# Test 2
stopifnot(
  format_perc(.101234, digits = 3) == '10.123%'
  )
```
]

---
# Unit Tests

.pull-left-40[

```r
#----    get_mean    ----
get_mean &lt;- function(x){
  
  res &lt;- sum(x) / length(x)
  
  return(res)
}
```

&lt;img src="images/05-code/no-errors.jpg" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-60[

```r
#----    Unit Tests    ----

# Test 1
stopifnot(
  format_perc(.10) == '10%'
  )

# Test 2
stopifnot(
  format_perc(.101234, digits = 3) == '10.123%'
  )
```
]

---
# Unit Tests

.pull-left-40[

```r
#----    get_mean    ----
get_mean &lt;- function(x){
  
  res &lt;- sum(x) / length(x)
  
  return(res)
}
```

&lt;img src="images/05-code/no-errors.jpg" width="80%" style="display: block; margin: auto;" /&gt;
]
.pull-right-60[

```r
#----    Unit Tests    ----

# Test 1
stopifnot(
  format_perc(.10) == '10%'
  )

# Test 2
stopifnot(
  format_perc(.101234, digits = 3) == '10.123%'
  )
```

&lt;br&gt;

.li-small[
- Organizing tests `tests/`
- Testing applications and packages
- Testing analysis
]
]

---

# Extra

### Environments

.pull-left-50[

&lt;img src="images/05-code/fun-env.png" width="90%" style="display: block; margin: auto;" /&gt;

]
.pull-right-50[
.code-size-12[

&lt;br&gt;


```r
global_var &lt;- "I am Global!"

my_fun &lt;- function(){
  global_var &lt;- "I am local"

  return(global_var)
}

my_fun()
## [1] "I am local"
global_var
## [1] "I am Global!"
```
]
]
---

# Extra

### Aliasing

.pull-left-40[

&lt;br&gt;

&lt;img src="images/05-code/glob-env.png" width="95%" style="display: block; margin: auto;" /&gt;

]
.pull-right-60[
.pull-left-50[
.code-size-12[

```r
#----    R Code    ----

# Create objects
x = c(1, 2, 3)
y = c(1, 2, 3)
w = y

w[3] &lt;- 999 # change a value

# Check values
x
## [1] 1 2 3
y
## [1] 1 2 3
w
## [1]   1   2 999
```
]
]
.pull-right-50[
.code-size-12[

```r
#----    Python Code    ----

# Create objects
x = [1,2,3]
y = [1,2,3]
w = y

w[2] = 999 # change a value

# Check values
x
## [1, 2, 3]
y
## [1, 2, 999]
w
## [1, 2, 999]
```
]
]
]

---

# Extra

### Classes and Methods

.pull-left-50[

.li-small[
- **Object-Oriented Programming**&lt;br&gt;Object classes include the methods. Different objects have different methods.

&lt;br&gt;

- **Functional Programming**&lt;br&gt;Methods are not characteristics of the object itself but are functions defined separately for each object class.
]
]
.pull-right-50[


```r
# Object Oriented Programming
todo_list.whats_next()
  
## Write the paper
```

&lt;br&gt;


```r
# Functional Programming
whats_next(todo_list)
  
## Have a break
```
]

---
# Advantages

--

.pull-left-30[
&amp;nbsp;
]
.pull-right-70[

&lt;br&gt;

- Maintainability
- Readability
- Reuse

{{content}}
]

--

*From users to developers!*

---
class: inverse, center, middle

# R Package Project

---
# R Package Project

--

.pull-left-50[

Project Template

&lt;img src="images/05-code/create-pkg.png" width="85%" style="display: block; margin: auto;" /&gt;

]
.pull-right-50[

&lt;br&gt;

{{content}}

]

--
```
- &lt;pkg-name&gt;/
    |-- .Rbuildignore
    |-- DESCRIPTION
    |-- NAMESPACE
    |-- &lt;pkg-name&gt;.Rproj
    |-- man/
    |-- R/
    |-- tests/
```
---
# R Package Project

#### DESCRIPTION

.code-size-12[
```
#-----    DESCRIPTION    ----#

Package: &lt;pkg-name&gt;
Title: One line description of the package
Version: the package version number
Authors@R:  # authors list
    c(person(given = "name",
             family = "surname",
             role = "aut",  # cre = creator and maintainer; aut = other authors;
             email = "name@email.com"),
      ...)
Description: A detailed description of the package
Depends: R (&gt;= 3.5) # Specify required R version
License: GPL-3      # Our  prefered license
Encoding: UTF-8
Imports: # list of required packages
Suggests: # list of suggested packages
Config/testthat/edition: 3
RoxygenNote: 7.1.2
VignetteBuilder: knitr
URL:     # add useful links to online resources or documentation 
```
]

---
# R Package Project

.pull-left-30[

#### Development

&lt;br&gt;

&lt;img src="images/05-code/devtools.png" width="55%" style="display: block; margin: auto;" /&gt;
]
.pull-right-70[
.pull-left-50[

&lt;br&gt;

{{content}}
]
.pull-right-50[

]
]
--
Commands

- `devtools::load_all()`&lt;br&gt;load all functions
- `devtools::document()`&lt;br&gt;generate documentation
- `devtools::test()`&lt;br&gt;run all unit tests

---
# R Package Project

.pull-left-30[

#### Development

&lt;br&gt;

&lt;img src="images/05-code/devtools.png" width="55%" style="display: block; margin: auto;" /&gt;
]
.pull-right-70[
.pull-left-50[

&lt;br&gt;

Commands

- `devtools::load_all()`&lt;br&gt;load all functions
- `devtools::document()`&lt;br&gt;generate documentation
- `devtools::test()`&lt;br&gt;run all unit tests

]
.pull-right-50[

&lt;br&gt;

Shortcuts

- `Ctrl+Shift+L`&lt;br&gt;(macOS `Cmd+Shift+L`)
- `Ctrl+Shift+D`&lt;br&gt;(macOS `Cmd+Shift+D`)
- `Ctrl+Shift+T`&lt;br&gt;(macOS `Cmd+Shift+T`)

]

]

---
# R Package Project

.pull-left-30[

#### Documentation

&lt;br&gt;

&lt;img src="images/05-code/roxygen2.png" width="55%" style="display: block; margin: auto;" /&gt;
]
.pull-right-70[
{{content}}
]

--

To activate Roxygen

&lt;img src="images/05-code/settings-doc.png" width="65%" style="display: block; margin: auto;" /&gt;

---
# R Package Project

.pull-left-30[

#### Documentation

&lt;br&gt;

&lt;img src="images/05-code/roxygen2.png" width="55%" style="display: block; margin: auto;" /&gt;

.li-small[
{{content}}
]
]
.pull-right-70[
.move-up-50[
.code-size-12[

```r
#----    format_perc    ----

#' Format Values as Percentages
#' 
#' Given a numeric vector, return a string vector with the values 
#' formatted as percentage (e.g.,"12.5%"). The argument `digits` allows 
#' to specify the rounding number of decimal places.
#'
#' @param x Numeric vector of values to format.
#' @param digits Integer indicating the rounding number o
#'               f decimal places (default 2)
#'
#' @return A string vector with values formatted as percentages 
#'  (e.g.,"12.5%").
#'
#' @examples
#' format_perc(c(.749, .251))
#' format_perc(c(.749, .251), digits = 0)
#' 

format_perc &lt;- function(x, digits = 2){
      
  perc_values &lt;- round(x * 100, digits = digits)
  res &lt;- paste0(perc_values, "%")
  
  return(res)
}
```
]
]
]

--
- Insert Roxygen skeleton&lt;br&gt;`Ctrl+Alt+Shift+R`&lt;br&gt;macOS `Cmd+Option+Shift+R`
---
# R Package Project

.pull-left-30[

#### Documentation

&lt;br&gt;

&lt;img src="images/05-code/roxygen2.png" width="55%" style="display: block; margin: auto;" /&gt;

&lt;br&gt;

`devtools::document()`
]
.pull-right-70[
.move-up-50[
&lt;img src="images/05-code/document-created.png" width="70%" style="display: block; margin: auto;" /&gt;
]
]

---
# R Package Project

.pull-left-30[

#### Unit Tests
]
.pull-right-70[

]
---
# R Package Project

.pull-left-30[

#### Unit Tests

&lt;br&gt;

&lt;img src="images/05-code/test-that.png" width="55%" style="display: block; margin: auto;" /&gt;

&lt;br&gt;

`devtools::test()`
]
.pull-right-70[

&lt;br&gt;


```r
#----    testing format_perc    ----

test_that("check format_perc returns the correct values", {
  
  # numbers
  expect_match(format_perc(.12), "12%")
  expect_match(format_perc(.1234, digits = 1), "12.3%")

  # string
  expect_error(format_perc("hello"))
  
})
```
]
---
class: inverse, center, middle

# From users to developers!

## Moving to the next step...
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