6 |
7 | These short sessions (45min to 1hr) will be focused on tools and practices for NMFS scientists to help you be **faster, more efficient and organized** in your coding and in merging reports with code. The focus of these workshops is practical skills and tools. Each session will be stand-alone. While the sessions will be introductory, I will give you links to my GitHub repositories that illustrate more complex examples (and that you can copy and build on).
8 |
9 | **Target audience**: You already code in R, maybe use RStudio too, but want to learn some tips about being more efficient from a seasoned NWFSC R programmer who does the kind of coding and work that you do.
10 |
11 | **About me**: I am a modeler/applied mathematician and I am immersed in R. I develop R packages for public use. I teach time-series analysis at the University of Washington (using R) and I teach workshops on R and reproducible research.
12 |
13 | ## Topics
14 |
15 | * [Week 1](week1-rstudio.html). Introduction to workflow using RStudio and Git/GitHub/GitLab [Video](https://www.youtube.com/watch?v=HxIpxVdQsDs)
16 |
17 | * [Week 2](week2-coding.html). More Git/GitHub/GitLab + Basic coding practices for reproducible and extendible code [Video](https://www.youtube.com/watch?v=k0P3e39qcA4)
18 |
19 | * [Week 3](week3-RMarkdown.html). Rmarkdown for reports: how to do big tables and export formats for Word docs [Video](https://www.youtube.com/watch?v=IGc2cgMFoPs)
20 |
21 | * [Week 4](week4-packages.html). Part 1. Organizing your R code into a package [Video](https://youtu.be/6d62KvS5v7Q)
22 |
23 | * [Week 5](week5-roxygen.html). Part 2. Documenting your code and data with Roxygen [Video](https://youtu.be/zHPSbhGtkz4)
24 |
25 | *Unfortunately at about 40min in, I managed to corrupt my R packages and could not demo any more so covered the material verbally. The problem demonstrates why I try to have few dependencies in my packages! One of the dependencies in my* **SardineForecast** *package had an install problem and corrupted the* **pkgload** *package.*
26 |
27 | * [Week 6](week6-more-packages.html). Part 3. Vignettes and plot/print methods for your package. [Video](https://youtu.be/O4rojT7aeb0)
28 |
29 | * [Week 7](week7-more-git.html). More Git. Merge conflicts, branches, and reverting changes. [Video](https://youtu.be/ZoB3dsZId9U )
30 |
31 | * [Week 8](week8-ggplot2.html). Introduction to plotting with ggplot. [Video](https://youtu.be/odCam8JxvKI)
32 |
33 | * [Week 9](week9-data-wrangling.html). Introduction to Tidyverse verbs.
34 |
35 |
45 |
46 | 47 | 48 |
49 | NWFSC Math Bio Program
50 |
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/jekyll.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Jekyll Websites"
3 | output:
4 | html_document:
5 | toc: true
6 | include:
7 | after_body: footer.html
8 | ---
9 |
10 | ```{r setup, include=FALSE}
11 | knitr::opts_chunk$set(echo = TRUE)
12 | ```
13 |
14 | Jekyll is another simple and popular way to make websites. There are many templates on GitHub that you can copy (fork) to make your own website.
15 |
16 |
17 | # jekyll-simple-blog
18 |
19 | This code is from [M Koehnke](http://mkoehnke.github.io). Per M Koehnke: This is an anonymized version of [Chris Eidhof's](http://github.com/chriseidhof) brilliant [blog theme](http://github.com/chriseidhof/chris.eidhof.nl) converted from Cactus to Jekyll.
20 |
21 | A live demo can be found [here](http://rverse-tutorials.github.io/jekyll-simple-blog/).
22 |
23 | Go to the [RVerse-Tutorials\jekyll-simple-blog](https://github.com/RVerse-Tutorials/jekyll-simple-blog) repository and click the Fork button in the upper right. You will need to be logged into your GitHub account. Then open RStudio and create a new project from that repository. This creates a copy of jekyll-simple-blog that is linked to the copy of the repository that you makde in your GitHub account.
24 |
25 | [Watch a video of this step](https://youtu.be/xeeKrGuaFRg)
26 |
27 | *INCOIS participants: You will find a copy of the repository in the RWorkflow directory that you copied from the thumb drive. However, without internet you won't be able to build your jekyll website.*
28 |
29 | ## Making the blog live
30 |
31 | * Go to settings of your jekyll-simple-blog GitHub repository and set Github Pages source as master.
32 | * Your new site should be ready at https://yourusername.github.io/jekyll-simple-blog/ . Note it can take awhile (5-10 min) for the website to appear and for changes to appear.
33 | * If you change the name of your repository (meaning change it from jekyll-simple-blog to something else), **change the baseurl in `_config.yml`**
34 |
35 | ## Making changes
36 |
37 | * Edit posts in `_posts`
38 | * Add posts in `_posts`
39 | * Upload the changes to GitHub via GitHub Desktop or Git in RStudio.
40 |
41 | # simple-cv
42 |
43 | This is a super simple online resume forked from [http://webjeda.com/online-cv/](http://webjeda.com/online-cv/). [Eli Holmes](https://eeholmes.github.io/) simplified Webjeda's design to make it more suitable for a simple flat resume and make it printable.
44 |
45 | ## Installation
46 | * Fork the repository https://github.com/RVerse-Tutorials/simple-cv
47 | * Go to settings of your repository and set Github Pages source as master.
48 | * Your new site should be ready at https://username.github.io/simple-cv/
49 | * If you change the name of your repository, change the baseurl in `_config.yml`
50 |
51 | ## Enter your data
52 | * Edit `_config.yml` with your name, education and summary. The summary will appear in About Me.
53 | * Edit `_data\experiences.yml` with your work experience.
54 | * Edit `_data\coursework.yml` with your coursework.
55 | * Edit `_data\skills.yml` with your skills.
56 | * Add your picture to `assets\images\` and put the file name in `_config.yml` in `pic:`
57 |
58 |
--------------------------------------------------------------------------------
/more-git.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "More Git"
3 | output:
4 | html_document:
5 | toc: true
6 | include:
7 | after_body: footer.html
8 | ---
9 |
10 | ```{r setup, include=FALSE}
11 | knitr::opts_chunk$set(echo = TRUE)
12 | ```
13 |
14 | ```{r echo=FALSE, message=FALSE, warning=FALSE}
15 | library(kableExtra)
16 | dt <- data.frame("Compartmentalized", "Documented", "Extendible", "Reproducible", "Robust")
17 | kable(dt, col.names=NULL) %>%
18 | kable_styling(full_width = TRUE) %>%
19 | row_spec(1, bold = FALSE, color = "white", background = "blue") %>%
20 | column_spec(column = 1:5, width = "20%")
21 | ```
22 |
23 |
24 | # Overview
25 |
26 | Here I will cover a few more come Git tasks and show some straight-forward ways to do these tasks
27 |
28 | * How to clone someone else's GitHub or GitLab repository
29 | * How to clone your own repository--when you want to make a copy and use that as a template for something new.
30 |
31 |
36 |
37 | ## Downloading other people's repositories
38 |
39 | There are two easy ways to do this. Use the one that seems more logical to you.
40 |
41 | Method 1.
42 |
43 | 1. In a browser, go to the GitHub (or GitLab) repository you want to copy.
44 | 2. Copy its url.
45 | 3. Open GitHub or GitLab.
46 | 4. If using GitHub, click the `+` in top right and click `import repository`. Paste in the url and give your repo a name.
47 | 4. If using GitLab, click `New Project` on right, then `Import Repository` tab, then click `Repo by URL`. Paste in url and give repo a name.
48 | 5. Open RStudio and click the project tab in the top right and select, `New Project`. Then select `Version Control` and paste in the url of **your** repository's url. For example, `https://github.com/
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/intro-git.Rmd:
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1 | ---
2 | title: "Introduction to Git within RStudio"
3 | output:
4 | html_document:
5 | toc: true
6 | include:
7 | after_body: footer.html
8 | ---
9 |
10 | ```{r setup, include=FALSE}
11 | knitr::opts_chunk$set(echo = TRUE)
12 | ```
13 |
14 | ```{r echo=FALSE, message=FALSE, warning=FALSE}
15 | library(kableExtra)
16 | dt <- data.frame("Compartmentalized", "Documented", "Extendible", "Reproducible", "Robust")
17 | kable(dt, col.names=NULL) %>%
18 | kable_styling(full_width = TRUE) %>%
19 | row_spec(1, bold = FALSE, color = "white", background = "blue") %>%
20 | column_spec(column = 1:5, width = "20%")
21 | ```
22 |
23 | # Overview
24 |
25 | I will introduce you to RStudio and GitHub/GitLab and show you how to use GitHub/GitLab without having to learn Git. If you have tried RStudio or Git and gotten frustrated or thought 'I don't have time to learn this', this is for you. If you want to learn how to easily keep track of changes in your code, this is for you. If you have never used RStudio, this is for you.
26 |
27 | I'm going to show you how to work with Git/GitHub/GitLab with no command-line interface. The goal is to futz with Git as little as possible. See the Links tab above for a nice online workshop on Git/GitHub if you want to learn more.
28 |
29 | # RStudio
30 |
31 | When you open RStudio you will see 4 panels:
32 |
33 | 
34 |
35 | ## Create an RStudio Project
36 |
37 | 1. In RStudio, choose "File->New Project..."
38 | 1. Then choose "New Directory" and then choose "Empty Project"
39 | 1. In the next dialog, choose a name (_it is best to use only letters, numbers, dashes, and underscores, and include no spaces in the name_).
40 | 1. Then click "Create Project".
41 |
42 | That should give you a new project.
43 |
44 | ### Add a new script file
45 |
46 | 1. Add a new file using 'File > New File > R Script'
47 | 2. Or you can click the new icon in top left corner.
48 | 2. Add some code to that file. Copy and paste in:
49 |
50 | ```
51 | require(graphics)
52 | ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
53 | ## Page 9: Plant Weight Data.
54 | ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
55 | trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
56 | group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
57 | weight <- c(ctl, trt)
58 | lm.D9 <- lm(weight ~ group)
59 | opar <- par(mfrow = c(2,2), oma = c(0, 0, 1.1, 0))
60 | plot(lm.D9, las = 1) # Residuals, Fitted, ...
61 | par(opar)
62 | ```
63 |
64 | ### Run the code
65 |
66 | 1. Select all the lines of code and select 'Run'
67 | 2. Run all the code by selecting 'Source'
68 |
69 | ## Project organization
70 |
71 | Keep your projects in separate folders with a uniform set of folder names. For example,
72 |
73 | * R - your functions
74 | * scripts - scripts (so not functions)
75 | * data - your RData files
76 | * output -
77 | * inst - random stuff
78 | * notes -
79 |
80 | The top right corner allows you to create projects and switch between projects.
81 |
82 | 
83 |
84 | ### Project settings
85 |
86 | Key one is to **not** save your `.Rdata` (your environment) when your are done for the day. Under Tools > Project Options... > General
87 |
88 | ## Super helpful features
89 |
90 | * Edit > Find in Files...
91 | * Code > Comment
92 | * Code > Reindent Lines
93 | * File > New (templates)
94 | * History tab
95 | * Help tab (index at bottom)
96 | * Help > Markdown quick reference
97 |
98 | ## More exercises
99 |
100 | R for Data Science is a great book to introduce you to working with data in R. Read through the following sections of the R for Data Science book and work through the examples.
101 |
102 | * [Workflow basics](http://r4ds.had.co.nz/workflow-basics.html): super basic review on how R works.
103 | * [Workflow: projects](http://r4ds.had.co.nz/workflow-projects.html): info about organizing RStudio projects.
104 | * [Workflow: scripts](http://r4ds.had.co.nz/workflow-scripts.html): how to evaluate code in scripts.
105 |
106 | # Git (GitHub/GitLab)
107 |
108 | Tracking your code (and project) changes. I am focusing on Git for individuals **not teams**. If you aren't using a change tracker (version control), then start just with a personal project and track only your changes. I will not cover *branches*.
109 |
110 | For NOAA staff, GitHub can be used for publishing public projects:
111 | [NOAA GitHub](https://github.com/NOAAGov/NOAA-Affiliated-Projects) and a NWFSC example
112 | [NWFSC Timeseries](https://nwfsc-timeseries.github.io/). NWFSC has a GitLab server if you want a repository server for your non-public projects and for internal collaboration.
113 |
114 | ## Basics
115 |
116 | * Repo: Repository. It is your code and the record of your changes. In a hidden folder called `.git` (so if you wanted to get rid of the history and other Git info, you could delete that folder). You have a local repo and a remote repo (on GitHub/GitLab).
117 | * Actions: Commit, Push, Pull
118 | * Git: The program that keeps track of the changes on local and remote repo.
119 | * Git GUIs: A graphical interface for Git (which is command line). There are [many](https://git-scm.com/downloads/guis). I am teaching an easy-entry one, GitHub Desktop.
120 |
121 | Workflow (to get started):
122 |
123 | * Make local changes to code.
124 | * Record what those changes were about and commit to the code change record (history).
125 | * Push those changes to your remote copy (aka your backup)
126 |
127 | 
128 |
129 | Goals today:
130 |
131 | 1. Get you started.
132 | 2. Show you a simple workflow.
133 | 3. Show some simple GitHub/GitLab features.
134 |
135 | ## Let's get started!
136 |
137 | I am going to show a workflow that is usually robust. Connecting Git on your computer and GitHub (or GitLab) is a source of much misery, and in my experience **creating the repo on GitHub (or GitLab) first** eliminates the problems. This really important for the first time you connect your computer to the remote repository server (GitHub or GitLab). Start with a new repo created on GitHub or GitLab.
138 |
139 | ### Make a GitHub or GitLab Repo
140 |
141 | 1. Go to GitHub or GitLab and create a new repository (the + in the top right or New Project)
142 | 2. Click add Readme.md and add .gitignore (type R to get the R .gitignore)
143 | 3. Copy the url of your new repo
144 |
145 | ### Add to RStudio
146 |
147 | 1. Open RStudio and click `New Project` (upper right, blue cube with R)
148 | 2. Click New Project... > Version Control > Git and paste in the url. Give your project a name and make sure the directory is where you want the project.
149 | 3. Done!
150 |
151 | ### Make some changes and commit
152 |
153 | 1. Add a file. File > New File > R Script
154 | 2. Type something and then save the file.
155 | 3. Click the `Git` tab in the upper right.
156 | 4. Click the changes that you want to commit (do all). And click `Commit`. Add a comment: first line is subject, newline, description (options).
157 | 5. Click the Green up arrow to Push to GitHub or GitLab.
158 |
159 | ### Make some changes and look at the history
160 |
161 | 1. Repeat 1-4 a few times.
162 | 2. Now look at the history. The little clock-like icon (or History in the Git window).
163 |
164 | * Click on `filter by file` to see just the changes to one file.
165 | * Do a search in the upper right.
166 | * Click on an early commit and click `View file @...`
167 |
168 | 3. Push changes up the GitHub or GitLab
169 |
170 | ## Copy someone's else rep
171 |
172 | 1. In a browser, https://github.com/RVerse-Tutorials/Test.
173 | 2. Copy its url.
174 | 3. Open GitHub or GitLab.
175 | 4. If using GitHub, click the `+` in top right and click `import repository`. Paste in the url and give your repo a name.
176 | 4. If using GitLab, click `New Project` on right, then `Import Repository` tab, then click `Repo by URL`. Paste in url and give repo a name.
177 | 5. Open RStudio and click the project tab in the top right and select, `New Project`. Then select `Version Control` and paste in the url of **your** repository's url. For example, `https://github.com/
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302 |
303 | Website for the RWorkflow INCOIS Short Course
294 |-
295 |
- Simple website built with R Markdown ‘Build Website’ function. 296 |
- Click the ‘Build Website’ button in RStudio to make. 297 |