commit 21f6fa045a2f6254199596ccaf6835c079e6c1ac
parent 7a1c1fe3dd18c20bd3c595b712a2a3870cbd4b8a
Author: Derek Sollberger <dsollberger@ucmerced.edu>
Date: Wed, 14 Aug 2024 11:27:16 -0400
cohort 9, chapter 12 (#68)
* cohort 9, chapter 12
- added picture and quote of John Chambers
- split long slides into two slides each
- added example of polymorphism
- added two concept maps
- noted Bioconductor with S4
- went down the rabbit hole wondering why that package was called "sloop"
* R7 to S7
---------
Co-authored-by: Jon Harmon <jonthegeek@gmail.com>
Diffstat:
5 files changed, 134 insertions(+), 15 deletions(-)
diff --git a/12_Base_types.Rmd b/12_Base_types.Rmd
@@ -5,15 +5,31 @@
- Understand what OOP means--at the very least for R
- Know how to discern an object's nature--base or OO--and type
+
+
+<details>
+<summary>Session Info</summary>
+```{r}
+library("DiagrammeR")
+```
+
+```{r}
+utils::sessionInfo()
+```
+
+</details>
+
+
## Why OOP is hard in R
-- Multiple OOP systems exist: S3, R6, S4, and (now/soon) R7.
+- Multiple OOP systems exist: S3, R6, S4, and (now/soon) S7.
- Multiple preferences: some users prefer one system; others, another.
- R's OOP systems are different enough that prior OOP experience may not transfer well.
-## What is OOP in general?
+[](https://xkcd.com/927/)
+
-### Two big ideas
+## OOP: Big Ideas
1. **Polymorphism.** Function has a single interface (outside), but contains (inside) several class-specific implementations.
```{r, eval=FALSE}
@@ -28,18 +44,33 @@ some_function <- function(x) {
} ...
}
```
+
+<details>
+<summary>Example of polymorphism</summary>
+
+```{r polymorphism_example}
+# data frame
+summary(mtcars[,1:4])
+
+# statistical model
+lin_fit <- lm(mpg ~ hp, data = mtcars)
+summary(lin_fit)
+```
+
+</details>
+
2. **Encapsulation.** Function "encapsulates"--that is, encloses in an inviolate capsule--both data and how it acts on data. Think of a REST API: a client interacts with with an API only through a set of discrete endpoints (i.e., things to get or set), but the server does not otherwise give access to its internal workings or state. Like with an API, this creates a separation of concerns: OOP functions take inputs and yield results; users only consume those results.
-### A few practical ideas
+## OOP: Properties
-#### Objects have class
+### Objects have class
- Class defines:
- Method (i.e., what can be done with object)
- Fields (i.e., data that defines an instance of the class)
- Objects are an instance of a class
-#### Class is inherited
+### Class is inherited
- Class is defined:
- By an object's class (e.g., ordered factor)
@@ -49,9 +80,7 @@ some_function <- function(x) {
- If an object doesn't have a method, use the method of the parent class
- The process of finding a method, is called dispatch
-## What about OOP in R?
-
-### Two main paradigms
+## OOP in R: Two Paradigms
**1. Encapsulated OOP**
@@ -68,9 +97,42 @@ some_function <- function(x) {
- From the outside, look like regular functions: `generic(object, arg2, arg3)`
- From the inside, components are also functions
-### Overview of the systems
+### Concept Map
+
+```{r, echo = FALSE, eval = TRUE}
+DiagrammeR::mermaid("
+graph LR
+
+OOP --> encapsulated_OOP
+OOP --> functional_OOP
-In base R:
+functional_OOP --> S3
+functional_OOP --> S4
+
+encapsulated_OOP --> R6
+encapsulated_OOP --> RC
+")
+```
+
+<details>
+<summary>Mermaid code</summary>
+```{r, echo = TRUE, eval = FALSE}
+DiagrammeR::mermaid("
+graph LR
+
+OOP --> encapsulated_OOP
+OOP --> functional_OOP
+
+functional_OOP --> S3
+functional_OOP --> S4
+
+encapsulated_OOP --> R6
+encapsulated_OOP --> RC
+")
+```
+</details>
+
+## OOP in base R
- **S3**
- Paradigm: functional OOP
@@ -79,7 +141,7 @@ In base R:
- Downsides: no guarantees
- **S4**
- Paradigm: functional OOP
- - Noteworthy: rewrite of S3
+ - Noteworthy: rewrite of S3, used by `Bioconductor`
- Use case: "more guarantees and greater encapsulation" than S3
- Downsides: higher setup cost than S3
- **RC**
@@ -88,7 +150,7 @@ In base R:
- Use cases: problems that are hard to tackle with functional OOP (in S3 and S4)
- Downsides: harder to reason about (because of modify-in-place logic)
-In packages:
+## OOP in packages
- **R6**
- Paradigm: encapsulated OOP
@@ -104,7 +166,7 @@ In packages:
- Paradigm: hybrid functional and encapsulated (?)
- **proto**
- Paradigm: prototype OOP
- - Noteworthy: OOP style used in ggplot2
+ - Noteworthy: OOP style used in `ggplot2`
## How can you tell if an object is base or OOP?
@@ -127,6 +189,12 @@ is.object(mtcars)
sloop::otype(mtcars)
```
+### sloop
+
+* **S** **L**anguage **O**bject-**O**riented **P**rogramming
+
+[](https://en.wikipedia.org/wiki/Sloop_John_B)
+
### Class
OO objects have a "class" attribute:
@@ -135,7 +203,7 @@ OO objects have a "class" attribute:
# base object has no class
attr(1:10, "class")
-# OO object has one or more class
+# OO object has one or more classes
attr(mtcars, "class")
```
@@ -188,6 +256,57 @@ typeof(quote(a + 1))
typeof(formals(my_fun))
```
+### Concept Map
+
+
+
+<details>
+<summary>Sankey graph code</summary>
+
+The graph above was made with [SankeyMATIC](https://sankeymatic.com/)
+
+```
+// toggle "Show Values"
+// set Default Flow Colors from "each flow's Source"
+
+base\ntypes [8] vectors
+base\ntypes [3] functions
+base\ntypes [1] environments
+base\ntypes [1] S4 OOP
+base\ntypes [3] language\ncomponents
+base\ntypes [6] C components
+
+vectors [1] NULL
+vectors [1] logical
+vectors [1] integer
+vectors [1] double
+vectors [1] complex
+vectors [1] character
+vectors [1] list
+vectors [1] raw
+
+functions [1] closure
+functions [1] special
+functions [1] builtin
+
+environments [1] environment
+
+S4 OOP [1] S4
+
+language\ncomponents [1] symbol
+language\ncomponents [1] language
+language\ncomponents [1] pairlist
+
+C components [1] externalptr
+C components [1] weakref
+C components [1] bytecode
+C components [1] promise
+C components [1] ...
+C components [1] any
+```
+
+</details>
+
## Be careful about the numeric type
1. Often "numeric" is treated as synonymous for double:
diff --git a/images/base_types/base_types_Sankey_graph.png b/images/base_types/base_types_Sankey_graph.png
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diff --git a/images/base_types/john_chambers_about_objects.png b/images/base_types/john_chambers_about_objects.png
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diff --git a/images/base_types/sloop_john_b.png b/images/base_types/sloop_john_b.png
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diff --git a/images/base_types/standards.png b/images/base_types/standards.png
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