/
02_computational_reproducibility.Rmd
96 lines (60 loc) · 2.81 KB
/
02_computational_reproducibility.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
---
title: "Organizing files"
author: "Jae Yeon Kim"
date: "8/26/2020"
output: html_document
---
# Setup
```{r}
pacman::p_load(
tidyverse, # tidyverse
here # computational reproducibility
)
```
- Note that `setwd()` is not reproducible outside the author's local machine. Instead, learn to use `here()`'.
- `rm(list = ls())` does not completely remove everything in your environment (e.g., packages).
# Making a project computationally reproducible and self-contained
- Read Jenny Bryan's wonderful piece on [project-oriented workflow](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/).
- Key idea: separate workflow (e.g., workspace information) from products (code and data)
## `here`: alternative to `setwd()`
- Example
```{r}
# Old: You won't be able to run this code
ggplot(mtcars, aes(x = mpg, y = wt)) +
geom_point()
ggsave("/home/jae/efficient-reproducible-project-management-in-R/project/outputs/example.png")
```
```{r}
# New: Reproducible
ggplot(mtcars, aes(x = mpg, y = wt)) +
geom_point()
ggsave(here("project", "outputs", "example.png"))
```
- How it works
`here()` function shows what's the top-level project directory.
```{r}
here::here()
```
- Build a path including subdirectories
```{r}
here("project", "outputs")
```
- How `here` defines the top-level project directory. The following list came from [the here package repository](https://github.com/jennybc/here_here)).
- Note that we already defined an RStudio Project!
- Is a file named .here present?
- Is this **an RStudio Project**? Literally, can I find a file named something like foo.Rproj?
- Is this an R package? Does it have a DESCRIPTION file?
- Is this a remake project? Does it have a file named remake.yml?
- Is this a projectile project? Does it have a file named .projectile?
- Is this a checkout from a version control system? Does it have a directory named .git or .svn? Currently, only Git and Subversion are supported.
- If there's no match then use `set_here()` to create an empty `.here` file.
**Challenge 1**
1. Can you define computational reproducibility?
2. Can you explain why sharing code and data is not enough for computational reproducibility?
# Making a project usef-friendly
- README.md
- In this simple markdown file, note some basic information about the project including the structure of the directory.
- This is how I used the README.md file for this workshop. Check out [my GitHub account](https://github.com/jaeyk) to see how I manage my projects.
- Use [binder](https://mybinder.org/) if you want to capture environment. This is especially great if you want to use the code for teaching.