├── .github
└── workflows
│ └── build.yml
├── .gitignore
├── 1_descriptive.Rmd
├── 2_inferential.Rmd
├── README.md
├── data
└── data.csv
├── docs
└── index.html
├── figures
├── 1_plot_density-1.pdf
├── 1_plot_density-1.png
├── 1_plot_scatter_basic-1.pdf
├── 1_plot_scatter_basic-1.png
├── 2_plot_model-1.pdf
├── 2_plot_model-1.png
└── demo.gif
├── index.Rmd
├── utils
├── Template_Word.docx
├── apa.csl
├── bibliography.bib
├── config.R
└── render.R
└── word_and_pdf
├── SupplementaryMaterials.docx
└── SupplementaryMaterials.pdf
/.github/workflows/build.yml:
--------------------------------------------------------------------------------
1 | on:
2 | push:
3 | branches:
4 | - main
5 | schedule: # run every week
6 | - cron: '0 0 * * 1'
7 |
8 | name: Build
9 |
10 | jobs:
11 | render:
12 | name: Generate documents
13 | runs-on: macOS-latest
14 | steps:
15 | - uses: actions/checkout@v2
16 | - uses: r-lib/actions/setup-r@v1
17 | - uses: r-lib/actions/setup-pandoc@v1
18 | - uses: r-lib/actions/setup-tinytex@v1
19 | - run: tlmgr --version
20 | - name: Install Core Dependencies
21 | run: |
22 | Rscript -e 'install.packages(c("rmarkdown", "remotes", "tidyverse", "insight", "bayestestR", "performance", "parameters", "effectsize", "modelbased", "correlation", "see", "ggrepel"))'
23 | Rscript -e 'remotes::install_github("easystats/report")'
24 | Rscript -e '# remotes::install_github("easystats/easystats")'
25 | - name: Install Other Dependencies
26 | run: |
27 | Rscript -e 'install.packages(c("qqplotr", "gridExtra"))'
28 | # The section below can be removed for added building speed on GitHub if you don't use Python
29 | - name: Install Python
30 | run: |
31 | Rscript -e "remotes::install_github('rstudio/reticulate')"
32 | Rscript -e "reticulate::install_miniconda()"
33 | - name: Render
34 | run: Rscript -e 'source("utils/render.R")'
35 | - name: Commit results
36 | run: |
37 | git commit README.md -m 'Build README.md' || echo "No changes to commit"
38 | git commit docs/index.html -m 'Build docs/index.html' || echo "No changes to commit"
39 | git commit word_and_pdf/SupplementaryMaterials.docx -m 'Build word_and_pdf/SupplementaryMaterials.docx' || echo "No changes to commit"
40 | git commit word_and_pdf/SupplementaryMaterials.pdf -m 'Build word_and_pdf/SupplementaryMaterials.pdf' || echo "No changes to commit"
41 | git push origin || echo "No changes to commit"
42 |
--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
1 | # History files
2 | .Rhistory
3 | .Rapp.history
4 |
5 | # Session Data files
6 | .RData
7 |
8 | # User-specific files
9 | .Ruserdata
10 |
11 | # Example code in package build process
12 | *-Ex.R
13 |
14 | # Output files from R CMD build
15 | /*.tar.gz
16 |
17 | # Output files from R CMD check
18 | /*.Rcheck/
19 |
20 | # RStudio files
21 | .Rproj.user/
22 |
23 | # produced vignettes
24 | vignettes/*.html
25 | vignettes/*.pdf
26 |
27 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
28 | .httr-oauth
29 |
30 | # knitr and R markdown default cache directories
31 | *_cache/
32 | /cache/
33 |
34 | # Temporary files created by R markdown
35 | *.utf8.md
36 | *.knit.md
37 |
38 | # R Environment Variables
39 | .Renviron
40 |
--------------------------------------------------------------------------------
/1_descriptive.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | output: html_document
3 | editor_options:
4 | chunk_output_type: console
5 | ---
6 |
7 | ## Part 1
8 |
9 | Here's a cool plot:
10 |
11 | ```{r 1_plot_scatter_basic, warning=FALSE, message=FALSE, fig.heiht=figheight, fig.width=figwidth, dpi=150}
12 | ggplot(df, aes(x=V1, y=V2, color=Participant)) +
13 | geom_point() +
14 | see::theme_modern()
15 | ```
16 |
17 |
18 |
19 | ## Part 2
20 |
21 | That's another great plot:
22 |
23 |
24 | ```{r 1_plot_density, warning=FALSE, message=FALSE, fig.heiht=figheight, fig.width=figwidth, dpi=150}
25 | plot(bayestestR::estimate_density(df[c("V1", "V2")])) +
26 | see::theme_blackboard()
27 | ```
28 |
29 | ## Part 3
30 |
31 | Did you ever hear the tragedy of Darth Plagueis The Wise? I thought not. It's not a story the Jedi would tell you. It's a Sith legend. Darth Plagueis was a Dark Lord of the Sith, so powerful and so wise he could use the Force to influence the midichlorians to create life... He had such a knowledge of the dark side that he could even keep the ones he cared about from dying. The dark side of the Force is a pathway to many abilities some consider to be unnatural. He became so powerful... the only thing he was afraid of was losing his power, which eventually, of course, he did. Unfortunately, he taught his apprentice everything he knew, then his apprentice killed him in his sleep. Ironic. He could save others from death, but not himself.
32 |
--------------------------------------------------------------------------------
/2_inferential.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | output: html_document
3 | editor_options:
4 | chunk_output_type: console
5 | ---
6 |
7 | Here is another analysis that is contained in a separate file. Let's check-out this linear regression model (note that, in the code chunk parameters, I multiplied `figheight` by 2 to have a taller plot):
8 |
9 | ```{r 2_plot_model, warning=FALSE, message=FALSE, fig.heiht=figheight * 2, fig.width=figwidth, dpi=150}
10 | model <- lm(Petal.Length ~ Sepal.Length, data=iris)
11 | performance::check_model(model)
12 | ```
13 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 |
4 |
5 | Introduction
6 | ============
7 |
8 | 
9 | [](https://github.com/RealityBending/TemplateResults)
10 | [](https://realitybending.github.io/TemplateResults/)
11 | [](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
12 | [](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)
13 |
14 | This is a template for a data analysis folder that can be easily
15 | exported as a
16 | [**webpage**](https://realitybending.github.io/TemplateResults/) or as
17 | **Supplementary Materials** (e.g., as a [**Word
18 | document**](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
19 | or a
20 | [**PDF**](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)).
21 |
22 | How does it look like? Just like this! The README page of this
23 | repository, alongside the
24 | [webpage](https://realitybending.github.io/TemplateResults/) and the
25 | word and PDF documents, were all created from the
26 | [index.Rmd](https://github.com/RealityBending/TemplateResults/blob/main/index.Rmd)
27 | file.
28 |
29 | This means you can easily **share your data analysis**, either by
30 | attaching the *PDF* or *Word* file to the publication (as
31 | **Supplementary Materials**), or by directly providing the URL of your
32 | GitHub repository: the readers can then enjoy your awesome open-access
33 | work in a convenient and transparent way.
34 |
35 | Features
36 | --------
37 |
38 | - [x] Automatically generates different types of document:
39 | - [**README
40 | page**](https://github.com/RealityBending/TemplateResults/blob/main/README.md)
41 | - [**Published
42 | website**](https://realitybending.github.io/TemplateResults/)
43 | - [**Word
44 | document**](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
45 | - [**PDF
46 | document**](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)
47 | - [x] APA citations
48 | - [x] Automatic citations and [reference
49 | list](https://github.com/RealityBending/TemplateResults#package-references)
50 | for all packages
51 | - [x] Tidy organisation (separate files for independent analyses)
52 | - [x] Great default configuration
53 | - [x] And more!
54 |
55 | 
56 |
57 | Installation
58 | ------------
59 |
60 | - **What is this?**
61 |
62 | This repository is a template to set up a reproducible, convenient and
63 | shareable workflow for your data analysis. It consists of several
64 | [*Rmarkdown*](https://rmarkdown.rstudio.com/lesson-1.html) files
65 | (`.Rmd`), that allow you to have R code and text (markdown) in the same
66 | document. Importantly, these files can be transformed into other
67 | documents formats.
68 |
69 | - **How to use this template?**
70 |
71 | Download it ([**click here to
72 | download**](https://github.com/RealityBending/TemplateResults/archive/main.zip)),
73 | unzip it and edit. Alternatively, you click on the [**Use this
74 | template**](https://github.com/RealityBending/TemplateResults/generate)
75 | button at the top of this screen to create a GitHub repository with all
76 | the content copied (then you just need to clone the repo to your local
77 | machine).
78 |
79 | The main files you need to edit are the `.Rmd` files, that you can open
80 | with some editor (e.g., [Rstudio](https://rstudio.com/)), and edit the
81 | text and the R chunks of code.
82 |
83 | - **How to upload it to a website?**
84 |
85 | If your repo is not already connected to GitHub, then create a new
86 | repository and upload all the content (so that it looks like this repo).
87 | Then, go to settings of the repo and enable **GitHub pages** (i.e., that
88 | gives you a webpage from an html stored on GitHub), and select the
89 | `docs/` folder as the location of the webpage. Indeed, rendering
90 | (knitting) the files will generate an “index.html” file in the `/docs/`
91 | folder, which is used as the website. You can see an example at
92 | .
93 |
94 | - **To knit or not to knit**
95 |
96 | In this repo, with have set up a [GitHub
97 | action](https://github.com/RealityBending/TemplateResults/blob/main/.github/workflows/website.yml)
98 | that generates all the output files everytime someone commit to the
99 | repository. This means that the final documents here are always
100 | “up-to-date” with the *Rmds* (as shown by the green badge). That said,
101 | you can remove this GitHub action (just remove the
102 | `.github/workflows/website.yml` file) if you prefer to generate the
103 | documents manually only.
104 |
105 | - **But I don’t want do upload all my data**
106 |
107 | In that case, you’ll need to 1) deactivate (i.e., remove the action
108 | file) the automatic rendering by GitHub (as no data will be stored on
109 | GitHub) and 2) mark the **data** folder as “to be ignored” (so that it
110 | won’t be uploaded). This can be done by adding `/data/` to the
111 | [**.gitignore**](https://github.com/RealityBending/TemplateResults/blob/main/.gitignore)
112 | file (that you can open with a notepad). This means that you can still
113 | store the data here locally, and generate the documents accordingly, but
114 | the data folder will be ignored by git and never uploaded to GitHub.
115 | This way, you can still have a cool website, an open-access script, but
116 | the data is safe with you. The only down side is that you have to build
117 | it manually (cannot use GitHub actions).
118 |
119 | - **How to add references?**
120 |
121 | References have to be added in `bib` format in the
122 | [*utils/bibliography.bib*](https://github.com/RealityBending/TemplateResults/blob/main/utils/bibliography.bib)
123 | file, and further referenced in the text like this
124 | `[@ludecke2019insight]` (Lüdecke, Waggoner, & Makowski, 2019).
125 |
126 | - **I don’t like the Word (.docx) theme**
127 |
128 | The theme for the word document is defined in the
129 | [\*\*Template\_Word.docx](https://github.com/RealityBending/TemplateResults/tree/main/utils)
130 | file, in the `/utils/` folder. You need to edit the “styles” (not just
131 | the content, but the style itself) to your preference.
132 |
133 | - **I have Python code**
134 |
135 | Thanks to R’s possibilities when it comes to integration with Python,
136 | it’s super easy to enable it in your pipeline. Just uncomment the
137 | [Python installation
138 | line](https://github.com/RealityBending/TemplateResults/blob/main/utils/config.R#L24)
139 | in the `utils/config.R` file and you’re ready to go!
140 |
141 | - **It doesn’t work / I have questions / I have ideas**
142 |
143 | Just [**open an
144 | issue**](https://github.com/RealityBending/TemplateResults/issues) and
145 | we’ll be happy to assist ☺
146 |
147 | Structure
148 | ---------
149 |
150 | Most files that you’ll need to create / edit will be written in
151 | [**rmarkdown**](https://rmarkdown.rstudio.com/lesson-1.html), which
152 | consists of a mix of markdown text and R chunks of code.
153 |
154 | The main file is named
155 | [**index.Rmd**](https://github.com/RealityBending/TemplateResults/blob/main/index.Rmd).
156 | However, to avoid having overly long files, the different (and
157 | independent) analyses parts are actually split in other documents. For
158 | instance, in this template example, the descriptive statistics section
159 | is in the
160 | [**1\_descriptive.Rmd**](https://github.com/RealityBending/TemplateResults/blob/main/1_descriptive.Rmd)
161 | file. As you can [see in the index
162 | file](https://github.com/RealityBending/TemplateResults/blob/690f7947da0fc8ac85eaf6fb87fafeaa46fb3c50/index.Rmd#L89-L90),
163 | this file is then integrated as a child document (i.e., it is merged).
164 | This makes it very convenient to have a clear structure with
165 | well-organized files, that are put together only when merged.
166 |
167 | Render and Publish
168 | ------------------
169 |
170 | Importantly, in order to render all the files, do not Knit this document
171 | by pressing the ‘Knit’ button. If you do, it will create an output file
172 | (for instance `index.html`) in the root folder, alongside `index.Rmd`.
173 | This is **not what we want**, as we want to keep the output files tidy
174 | in separate folders (for instance, the html version should be in the
175 | `/docs/` folder, as this is where the website will look for).
176 |
177 | There an R script,
178 | [utils/render.R](https://github.com/RealityBending/TemplateResults/blob/main/utils/render.R),
179 | that contains the lines to render everything in its correct location.
180 | So, when you have the “index.Rmd” file opened (and your working
181 | directory is at its root), simply run **`source("utils/render.R")`** in
182 | the console (or the relevant lines in that file). This will run the
183 | rendering file and create all the files.
184 |
185 | Contribution
186 | ------------
187 |
188 | Do not hesitate to improve this template by updating, documenting, or
189 | expanding it!
190 |
191 | Packages & Data
192 | ===============
193 |
194 | Packages
195 | --------
196 |
197 | This document was prepared on 2021-08-02.
198 |
199 | ``` r
200 | library(bayestestR)
201 | library(parameters)
202 | library(performance)
203 | library(report)
204 | library(see)
205 | library(ggplot2)
206 |
207 | summary(report::report(sessionInfo()))
208 | ```
209 |
210 | The analysis was done using the R Statistical language (v4.1.0; R Core
211 | Team, 2021) on macOS Catalina 10.15.7, using the packages ggplot2
212 | (v3.3.5), stringr (v1.4.0), forcats (v0.5.1), tidyr (v1.1.3), readr
213 | (v2.0.0), dplyr (v1.0.7), rmarkdown (v2.9), tibble (v3.1.3), purrr
214 | (v0.3.4), parameters (v0.14.0.1), performance (v0.7.3.1), see (v0.6.4),
215 | bayestestR (v0.10.5), report (v0.3.5) and tidyverse (v1.3.1).
216 |
217 | Data
218 | ----
219 |
220 | ``` r
221 | df <- read.csv("data/data.csv")
222 |
223 | cat(paste("The data consists of",
224 | report::report_participants(df,
225 | participants = "Participant",
226 | age = "Age")))
227 | ```
228 |
229 | The data consists of 10 participants (Mean age = 29.9, SD = 0.5, range:
230 | \[29.0, 30.91\])
231 |
232 | Note that the chunks generating figures in the code below have some
233 | arguments specified in their header, such as `fig.width` and
234 | `fig.height`, which controls the figure size. These were filled with an
235 | eponym argument defined in
236 | [`utils/config.R`](https://github.com/RealityBending/TemplateResults/blob/main/utils/config.R#L26-L27).
237 | We also set the resolution, i.e., `dpi`, to a low value so that the
238 | resulting file is lighter. But **don’t forget to crank this value up**
239 | (to 300-600) to get nice-looking results.
240 |
241 | Descriptive Stats
242 | =================
243 |
244 | Notice the `{.tabset}` tag after the section name. This will show the
245 | subsections as different tabs (in the [html
246 | version](https://realitybending.github.io/TemplateResults/#Descriptive_Stats)
247 | only, because the other formats are static).
248 |
249 | Part 1
250 | ------
251 |
252 | Here’s a cool plot:
253 |
254 | ``` r
255 | ggplot(df, aes(x=V1, y=V2, color=Participant)) +
256 | geom_point() +
257 | see::theme_modern()
258 | ```
259 |
260 | 
261 |
262 | Part 2
263 | ------
264 |
265 | That’s another great plot:
266 |
267 | ``` r
268 | plot(bayestestR::estimate_density(df[c("V1", "V2")])) +
269 | see::theme_blackboard()
270 | ```
271 |
272 | 
273 |
274 | Part 3
275 | ------
276 |
277 | Did you ever hear the tragedy of Darth Plagueis The Wise? I thought not.
278 | It’s not a story the Jedi would tell you. It’s a Sith legend. Darth
279 | Plagueis was a Dark Lord of the Sith, so powerful and so wise he could
280 | use the Force to influence the midichlorians to create life… He had such
281 | a knowledge of the dark side that he could even keep the ones he cared
282 | about from dying. The dark side of the Force is a pathway to many
283 | abilities some consider to be unnatural. He became so powerful… the only
284 | thing he was afraid of was losing his power, which eventually, of
285 | course, he did. Unfortunately, he taught his apprentice everything he
286 | knew, then his apprentice killed him in his sleep. Ironic. He could save
287 | others from death, but not himself.
288 |
289 | Inferential Stats
290 | =================
291 |
292 | Here is another analysis that is contained in a separate file. Let’s
293 | check-out this linear regression model (note that, in the code chunk
294 | parameters, I multiplied `figheight` by 2 to have a taller plot):
295 |
296 | ``` r
297 | model <- lm(Petal.Length ~ Sepal.Length, data=iris)
298 | performance::check_model(model)
299 | ```
300 |
301 | 
302 |
303 | Full Code
304 | =========
305 |
306 | The full script of executive code contained in this document is
307 | reproduced here.
308 |
309 | ``` r
310 | # Set up the environment (or use local alternative `source("utils/config.R")`)
311 | source("https://raw.githubusercontent.com/RealityBending/TemplateResults/main/utils/config.R")
312 |
313 | fast <- FALSE # Make this false to skip the chunks
314 | # This chunk is a bit complex so don't worry about it: it's made to add badges to the HTML versions
315 | # NOTE: You have to replace the links accordingly to have working "buttons" on the HTML versions
316 | if (!knitr::is_latex_output() && knitr::is_html_output()) {
317 | cat("
318 | [](https://github.com/RealityBending/TemplateResults)
319 | [](https://realitybending.github.io/TemplateResults/)
320 | [](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
321 | [](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)")
322 | }
323 | # Let's include a demo GIF (this doesn't work in PDF documents)
324 | if (!knitr::is_latex_output()) {
325 | knitr::include_graphics("figures/demo.gif")
326 | }
327 | library(bayestestR)
328 | library(parameters)
329 | library(performance)
330 | library(report)
331 | library(see)
332 | library(ggplot2)
333 |
334 | summary(report::report(sessionInfo()))
335 | df <- read.csv("data/data.csv")
336 |
337 | cat(paste("The data consists of",
338 | report::report_participants(df,
339 | participants = "Participant",
340 | age = "Age")))
341 | report::cite_packages(sessionInfo())
342 | ggplot(df, aes(x=V1, y=V2, color=Participant)) +
343 | geom_point() +
344 | see::theme_modern()
345 | plot(bayestestR::estimate_density(df[c("V1", "V2")])) +
346 | see::theme_blackboard()
347 | model <- lm(Petal.Length ~ Sepal.Length, data=iris)
348 | performance::check_model(model)
349 | ```
350 |
351 | Package References
352 | ==================
353 |
354 | ``` r
355 | report::cite_packages(sessionInfo())
356 | ```
357 |
358 | - H. Wickham. ggplot2: Elegant Graphics for Data Analysis.
359 | Springer-Verlag New York, 2016.
360 | - Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for
361 | Common String Operations. R package version 1.4.0.
362 | https://CRAN.R-project.org/package=stringr
363 | - Hadley Wickham (2021). forcats: Tools for Working with Categorical
364 | Variables (Factors). R package version 0.5.1.
365 | https://CRAN.R-project.org/package=forcats
366 | - Hadley Wickham (2021). tidyr: Tidy Messy Data. R package version
367 | 1.1.3.
368 | https://CRAN.R-project.org/package=tidyr
369 | - Hadley Wickham and Jim Hester (2021). readr: Read Rectangular Text
370 | Data. R package version 2.0.0.
371 | https://CRAN.R-project.org/package=readr
372 | - Hadley Wickham, Romain François, Lionel Henry and Kirill Müller
373 | (2021). dplyr: A Grammar of Data Manipulation. R package version
374 | 1.0.7.
375 | https://CRAN.R-project.org/package=dplyr
376 | - JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi
377 | and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and
378 | Winston Chang and Richard Iannone (2021). rmarkdown: Dynamic
379 | Documents for R. R package version 2.9. URL
380 | https://rmarkdown.rstudio.com.
381 | - Kirill Müller and Hadley Wickham (2021). tibble: Simple Data Frames.
382 | R package version 3.1.3.
383 | https://CRAN.R-project.org/package=tibble
384 | - Lionel Henry and Hadley Wickham (2020). purrr: Functional
385 | Programming Tools. R package version 0.3.4.
386 | https://CRAN.R-project.org/package=purrr
387 | - Lüdecke D, Ben-Shachar M, Patil I, Makowski D (2020).
388 | “Extracting,Computing and Exploring the Parameters of Statistical
389 | Models using R.”*Journal of Open Source Software*, *5*(53), 2445.
390 | doi:10.21105/joss.02445
391 | (URL:
392 | https://doi.org/10.21105/joss.02445).
393 | - Lüdecke et al., (2021). performance: An R Package for Assessment,
394 | Comparison and Testing of Statistical Models. Journal of Open Source
395 | Software, 6(60), 3139.
396 | https://doi.org/10.21105/joss.03139
397 | - Lüdecke, Patil, Ben-Shachar, Wiernik, Waggoner & Makowski (2020).
398 | Visualisation Toolbox for ‘easystats’ and Extra Geoms, Themes and
399 | Color Palettes for ‘ggplot2’. CRAN. Available from
400 | https://easystats.github.io/see/
401 | - Makowski, D., Ben-Shachar, M., & Lüdecke, D. (2019). bayestestR:
402 | Describing Effects and their Uncertainty, Existence and Significance
403 | within the Bayesian Framework. Journal of Open Source Software,
404 | 4(40), 1541.
405 | doi:10.21105/joss.01541
406 | - Makowski, D., Ben-Shachar, M.S., Patil, I. & Lüdecke, D. (2020).
407 | Automated Results Reporting as a Practical Tool to Improve
408 | Reproducibility and Methodological Best Practices Adoption. CRAN.
409 | Available from
410 | https://github.com/easystats/report.
411 | doi: .
412 | - R Core Team (2021). R: A language and environment for statistical
413 | computing. R Foundation for Statistical Computing, Vienna, Austria.
414 | URL
415 | https://www.R-project.org/.
416 | - Wickham et al., (2019). Welcome to the tidyverse. Journal of Open
417 | Source Software, 4(43), 1686,
418 | https://doi.org/10.21105/joss.01686
419 |
420 | References
421 | ==========
422 |
423 | Lüdecke, D., Waggoner, P. D., & Makowski, D. (2019). Insight: A unified
424 | interface to access information from model objects in r. *Journal of
425 | Open Source Software*, *4*(38), 1412.
426 |
--------------------------------------------------------------------------------
/data/data.csv:
--------------------------------------------------------------------------------
1 | "V1","V2","Participant","Age"
2 | 0.998072128174793,-2.01179284515834,"A",31.8984875007729
3 | 1.25543512312882,-1.61196207947937,"A",37.5396504378135
4 | 1.35153531256135,0.263277759617659,"A",29.2359719771985
5 | 0.377303667377935,-1.07767385369871,"A",29.4373561217579
6 | 0.292486703657284,0.125164653028218,"A",32.6376300539629
7 | 0.570267701787081,-0.758259716536296,"A",31.1471448260466
8 | 0.99964257889472,-0.998919353878836,"A",35.8092956053321
9 | 1.07470902123249,-0.248293472690667,"A",36.8384931951477
10 | 1.52959180863949,-1.91862991063954,"A",27.7923303645699
11 | 3.14436074208602,-1.40328893284913,"A",30.9868900904746
12 | 0.284852417591154,-0.119459969531577,"A",23.9213782321947
13 | 1.14907617754221,0.583683533530168,"A",27.8288691346543
14 | -1.03046360143711,-2.33702666837055,"A",27.2499869526444
15 | 0.478216119150675,0.0317794555240569,"A",36.113354353749
16 | -0.222155021777618,-3.30365148267868,"A",34.9867241564758
17 | 0.290253864750059,-1.46678904786266,"A",33.1266114390689
18 | 0.684957229570084,-1.03985153064513,"A",31.2169220886957
19 | 4.46066755530003,1.1757460211296,"A",29.081521301894
20 | 0.816501641774448,0.1237606333332,"A",27.2632436932158
21 | 0.506590110269223,-0.552048966933304,"A",35.3489618538304
22 | -0.14769064034226,-2.95976077047935,"A",29.3025206119081
23 | -0.998152335825685,-1.67386718683517,"A",31.7518895602061
24 | 1.19413470034106,-0.586494431639517,"A",31.049056685358
25 | 1.85910081602701,-0.227199246913761,"A",34.9192759065936
26 | 0.632168965365619,-1.00203109056252,"A",33.9846600454559
27 | 0.727883530178096,-0.769776271063097,"A",26.1891327609018
28 | 2.62994540822847,0.347249461809682,"A",28.6629387138951
29 | 0.839580197061424,-1.60594174043237,"A",21.6194134756789
30 | 0.504264758237988,-2.158609964966,"A",30.9661392583708
31 | -0.000585667422283276,-1.27494147162927,"A",33.9902711171596
32 | -1.31478816811429,-2.93723616828132,"A",25.9895253999209
33 | 0.462859240018517,-1.59693027267591,"A",36.1002653993307
34 | 1.02669261242358,-0.649404502664474,"A",33.9028095840323
35 | 1.33721628108342,-0.637541512089692,"A",30.7500461537626
36 | 0.346622319561355,-0.318740350339025,"A",32.1800707150661
37 | 0.701479643207833,-2.49828339032464,"A",27.663235021886
38 | 1.36809189372264,-1.6990466551649,"A",28.6117433555625
39 | 1.49074191960855,0.300986224325711,"A",24.5798954361572
40 | 0.914797528439922,-0.656875068034227,"A",28.7271780644457
41 | 0.0378739530097245,-2.4463187917296,"A",25.4890114199939
42 | 0.176599683689979,-1.71821364084624,"A",32.2899918879692
43 | 0.850772573942022,-0.985180469823199,"A",26.6476997785874
44 | 0.234876163397424,-0.705036183794009,"A",25.1499219070009
45 | 0.784146662536668,-0.308189914512832,"A",27.6359806030037
46 | 1.20144626520952,-0.703220732674755,"A",31.1707746360192
47 | 0.372384669501338,-1.3202990049163,"A",37.2677780255309
48 | 1.01782458279435,-0.955593929463397,"A",33.9610483305484
49 | 1.30277870704585,0.677583090268699,"A",31.5233713567097
50 | 2.39733879062458,-0.796686435803855,"A",27.639291642853
51 | 1.46233904237523,-0.528098494727468,"A",34.5075286622583
52 | 0.457230997588934,-2.97192127146456,"A",30.6575283128449
53 | 0.806534852179753,-0.113660543179406,"A",24.7660516232776
54 | 1.56669715594423,-1.34503587896209,"A",31.1414903836229
55 | 3.08012544894125,0.604784250468399,"A",20.0322298690904
56 | 1.63265847891113,-0.0164241939159685,"A",27.0875893105549
57 | 2.25765292045233,-0.851284557732609,"A",31.6687864791729
58 | -0.290950730365525,-1.61942382530701,"A",25.8879393965666
59 | 1.41060133313987,-1.91050915541173,"A",27.7259594818591
60 | 1.53312599183099,-1.47540876846514,"A",20.519367919554
61 | 1.02733333688976,-1.199030814367,"A",29.6861260918858
62 | 1.57229199758971,-1.38043552765064,"A",38.9389517144623
63 | -0.0441946682444876,-0.197670797178889,"A",26.7327289663445
64 | 0.313682992688279,-2.40106802055049,"A",37.3878616173055
65 | -0.254526818987201,-0.752382640049805,"A",28.2931211853514
66 | 0.774023430517441,-0.144883920728776,"A",29.2801128445836
67 | 0.750928942506533,-1.69586508150247,"A",22.1592692016516
68 | 0.0274619913487589,-2.76798590632057,"A",24.4862119720995
69 | 0.131545807333878,-1.14385066397287,"A",28.1901671209583
70 | 0.297892792022777,-2.29798379145178,"A",27.4203209070163
71 | -0.370538312982598,-2.90707657812124,"A",34.8350647463212
72 | 1.23174873239095,-0.430629118722322,"A",20.6164285744061
73 | 0.17549962630183,0.248625688342449,"A",33.6812736314263
74 | 0.9195979357635,-1.10407143285564,"A",32.0981492902736
75 | 1.53253736409677,-1.13567088761565,"A",26.2226703007107
76 | 1.32586764564223,-1.07408676404527,"A",38.7916500573766
77 | -0.320079823946755,-1.47621270578498,"A",27.1784071033788
78 | 1.54576122910655,-0.478246860018611,"A",36.5678144650421
79 | 2.14577753835844,-0.273551209280552,"A",37.3279644041871
80 | 1.58726335395335,-1.95164613968888,"A",30.5162256746941
81 | 1.94234758196219,0.0714523182969033,"A",28.588313813291
82 | 0.997534304116837,-1.02212845341635,"A",31.1804059778408
83 | 3.05247547066796,-0.473703830446936,"A",36.3584273463194
84 | 1.67145021690902,-0.675339028182739,"A",30.3350915108364
85 | 0.460700141580273,-1.33480563075656,"A",28.0859076754686
86 | 1.17370733138414,-0.309918404823101,"A",24.8979552217326
87 | 0.824697940175889,-1.05156231958295,"A",29.2230149811619
88 | 1.19689160806693,-0.938691069896997,"A",32.8826283479302
89 | -0.957933644933091,-1.58357553541566,"A",22.4325552207495
90 | 0.456669492319702,-2.20331551564972,"A",26.5962567812046
91 | 1.55850549998974,-1.86517723187575,"A",31.0003177616926
92 | 1.34436526866651,-1.60760984484871,"A",29.9900399698075
93 | 1.5795714912876,-1.99501814402481,"A",23.5253998542079
94 | 0.852180918570941,-0.403427984450481,"A",33.3314928826051
95 | 1.30859544159674,0.207586040079275,"A",30.2224276841044
96 | 1.65859999968868,-1.79637974384686,"A",29.5618489546077
97 | 1.71734490477766,0.477304064647422,"A",29.1597421594413
98 | 0.333730590076666,-1.61142411066964,"A",32.578364611598
99 | 0.62991975423029,-0.214386604033834,"A",33.3354208173279
100 | 0.00397902057903943,-1.82323326077861,"A",30.5603614650603
101 | 1.0005105358088,-0.811945443221226,"A",34.0573436087695
102 | -0.493986642842296,-2.65613335517877,"A",30.7040504690427
103 | 1.25044218737364,-1.63120906053211,"A",22.2764313707484
104 | 1.7262795801599,-0.595540196431008,"A",36.7092604022785
105 | 2.05422176008676,-0.490880770274844,"A",25.8401540774923
106 | -0.182687122559963,-1.61360027247043,"A",24.1965525181198
107 | 1.7181466841314,-0.77830078996545,"A",35.0085412948144
108 | 0.785523733401792,-0.608781170848491,"A",29.0538258289805
109 | 0.916966491876903,-0.00245995948299438,"A",32.0440846052088
110 | 1.24161346999327,-1.66045110436494,"A",31.0258133984271
111 | 1.03820471221313,1.16276239454446,"A",30.4756492649385
112 | 0.204801336233667,-1.36829645134566,"A",31.5972792920159
113 | 1.33350410623703,-0.776605035880291,"A",27.5988529833826
114 | 1.83718140301365,-0.818902980017897,"A",37.4542075061797
115 | 1.09100160449514,-2.25123899054806,"A",31.4982141190827
116 | 2.90501350200115,0.0907511519036581,"A",21.4392682859678
117 | -0.964425010033516,-2.42624589251063,"A",23.6763076886376
118 | -0.805701381889749,-1.05816732323938,"A",32.2540225389637
119 | 1.76709744978444,0.220447261311294,"A",34.448726268904
120 | 1.81829672295177,-0.433510616387367,"A",36.3386524614245
121 | 1.56082484972261,-1.09533186516113,"A",36.9381091499791
122 | 0.935186875837852,-1.71590477274772,"A",29.05279468544
123 | -1.69300375671294,-2.84659951940873,"A",28.0249260039991
124 | 1.44191051037557,-0.540135232024096,"A",25.8715577739801
125 | 0.675836978605961,-1.04372697777055,"A",29.7365668079556
126 | 1.85441760222212,-0.896388319378711,"A",27.8786945849331
127 | 3.86200118593907,0.184247525995972,"A",32.6790525662102
128 | -0.955168344431453,-4.1118129680259,"A",25.7103086676223
129 | 1.11698290565021,-1.54001314948371,"A",25.30409276448
130 | 0.194796405464676,-0.766129216697252,"A",21.1206887522491
131 | -0.782536440603489,-0.77417832323295,"A",31.9332799954138
132 | 1.33168141780063,-1.52103790586843,"A",31.3975029187303
133 | 0.968943530385102,-0.173209159898661,"A",31.7482514147195
134 | 2.28088735035544,0.870577998475334,"A",31.3777264938975
135 | 2.57785121156952,-0.276622090192512,"A",31.4140348707401
136 | -0.287446776880901,-0.0105259110627071,"A",28.0116693110074
137 | -0.0471566563941221,-2.54250137232091,"A",25.3939177629201
138 | 2.57369070471353,0.518375234143289,"A",28.9612517064894
139 | 2.79848833780135,-0.425135993783267,"A",40.5222420009391
140 | -0.105719359700285,-1.32325924552771,"A",22.8130701872353
141 | 0.523807253191629,-0.812012401045572,"A",28.9437135137223
142 | 1.13455495831975,-1.47988624746133,"A",29.5053102566895
143 | 2.19787815806715,-1.31951934748041,"A",27.7250865569692
144 | 1.34463803394562,-1.81019370535683,"A",30.5032348153819
145 | 0.509783778332976,-0.714393508335246,"A",25.0896331560429
146 | 2.99353563977135,-0.951759263080012,"A",24.9684998703411
147 | -0.307789765351342,-1.87508924554195,"A",26.9001801845963
148 | 1.55274159651559,-0.665950133594541,"A",24.6348854970533
149 | 1.44509653494587,0.314108717696321,"A",35.397474500402
150 | 0.882495084819596,-1.3015951225693,"A",29.4224102409108
151 | 1.30373776950026,-0.464736284440642,"A",34.0587629846278
152 | 0.225472099167707,-2.63779836331673,"A",17.9532561847096
153 | 3.15292700881326,-0.090385438406265,"A",23.8484142691899
154 | 1.36096340152072,-0.566945047015507,"A",27.827166797021
155 | 1.67099387439223,-2.43773852033058,"A",22.4926573136883
156 | 0.787172103791836,-1.5094403687086,"A",33.7085890534029
157 | 3.48117310442689,-0.695059091929354,"A",28.4060139333516
158 | 1.6651422324023,0.490749567801807,"A",25.312676559307
159 | 0.411606109216416,-1.37361922286086,"A",26.5577833741988
160 | 1.71445813141789,-0.159976200062455,"A",35.365832948212
161 | 0.534171382439582,-1.85226515406026,"A",33.0504875804601
162 | 0.901567065232628,-1.55851341771445,"A",32.6096886144242
163 | 1.6290234581762,-0.45693155433017,"A",25.6764099976771
164 | 0.422729648975425,-0.975468806475531,"A",31.2642321609575
165 | 0.857930547710551,-0.487115926389701,"A",34.1723876431457
166 | 1.29096274201899,-1.92907781035077,"A",33.1416398390124
167 | 2.03859177393319,-1.19295539053253,"A",28.743714033318
168 | 0.42528218979894,-3.31468461792567,"A",29.952232597918
169 | 0.750926057900712,-0.402287363814023,"A",33.8981674348657
170 | 1.25248289787088,-2.12155298438937,"A",34.703030618367
171 | 0.632633765647073,-2.40618452658717,"A",32.0798250404149
172 | 0.210118366967949,0.0675015077427115,"A",27.6793960846273
173 | 1.6024875088475,-2.6550872418194,"A",29.3738290323015
174 | 1.76991870353989,-0.937970067784015,"A",27.1486984960736
175 | 2.01277365857822,-0.027932229116918,"A",19.9091266944702
176 | 0.803179154365515,-1.54799308074488,"A",28.4816111873559
177 | 1.76644371301234,0.0445225441741297,"A",22.5891920766479
178 | 0.171078120836705,1.05225280618645,"A",34.1566792854989
179 | -0.0926920424857958,-2.82015955451992,"A",33.4840623178676
180 | 0.770496631997377,0.541487705758766,"A",32.6045283319691
181 | -0.0917757796245962,-1.63567755695901,"A",22.9580644206516
182 | 1.12063518649122,-1.52538763752054,"A",25.3827472511094
183 | 1.55319835758924,-0.315260256681921,"A",28.3391476189689
184 | 3.72536304974726,0.342708514653954,"A",36.5534852176374
185 | 1.53638450546919,-0.232434047652492,"A",24.4110509800582
186 | 1.36031498751687,0.321675743152821,"A",26.6407080491577
187 | 1.96720866975196,-1.34287572499423,"A",22.1733841458321
188 | 2.51468255310415,-0.337157033999189,"A",24.6365405842811
189 | 0.755585247569024,0.276618565958759,"A",32.9306401266088
190 | -0.288429732946533,-1.03647839818499,"A",31.0003429922678
191 | 0.217460159914349,0.197337503170891,"A",27.7826550809911
192 | 0.679020298220657,-1.52373604453879,"A",29.0520163520469
193 | 1.58753478568103,1.27510604288186,"A",31.1109451954632
194 | 2.02437999120682,0.406018802317935,"A",33.4533629774722
195 | 0.775061914077059,-1.81599460267279,"A",31.9575124778647
196 | 1.57378968305481,0.673768221395638,"A",31.8360170647273
197 | 0.362573190747266,-1.31563097098134,"A",29.1142298894408
198 | -2.14410670282338,-3.50294245236728,"A",25.3983885580683
199 | -0.475961911398594,-1.99821887550049,"A",29.7905769294111
200 | 1.12363168998452,-1.42367832407992,"A",26.2275724005919
201 | 0.724953501051587,-0.554591113774666,"A",26.5911579308748
202 | 0.275840859683408,-2.37688127714311,"B",31.8051282593016
203 | 0.184600755272983,-3.15284444705466,"B",34.1748423263872
204 | 2.131050852625,-0.372624810281924,"B",34.6100584894804
205 | 1.06917202798334,-2.28964934502097,"B",28.6506166057105
206 | 2.93436851976067,-2.86018132319396,"B",36.8042377197009
207 | 1.37416735784108,-3.79071555253733,"B",36.0418173255458
208 | 2.38653397748979,-2.30287727137085,"B",31.2926171033614
209 | 1.10928294408006,-0.854821552983628,"B",26.0661773406027
210 | 1.25600194311429,-2.90196455362174,"B",23.2645189530344
211 | 2.61431723755208,-1.82656508042346,"B",30.9209925728221
212 | 1.63677174556325,-2.21986787298269,"B",33.5734558181608
213 | 1.0901606043298,-4.01028736909177,"B",35.643313721325
214 | 1.53860916626548,-2.18405257792987,"B",27.350962201379
215 | 1.66774269252584,-2.72172887136647,"B",37.5444950177892
216 | 2.03604059664903,-1.4100838309961,"B",25.1394897907559
217 | 2.80496811841275,-0.860702504601657,"B",32.6143115135285
218 | 2.63423134811514,-1.01922651061619,"B",38.2738960867586
219 | 1.39719578039533,-2.18783425477924,"B",24.847977406975
220 | 1.94723401763262,-1.94515643998584,"B",27.7072982463303
221 | 2.01520024817269,-1.92657296446751,"B",28.6390572894556
222 | 1.80010677961524,-1.82077791487123,"B",37.2875986056285
223 | 1.69670439799589,-1.95702411212389,"B",32.8501941782892
224 | 2.96766913509637,-2.53074798047912,"B",30.8356936472083
225 | 2.62795950676729,-1.99122568119708,"B",32.4025261778715
226 | 1.34774659930638,-2.73526137609111,"B",33.0355721226147
227 | 0.890406648981921,-0.512349300227295,"B",33.8775121660964
228 | 0.0282546167519786,-3.60593170340724,"B",29.9548606826441
229 | 1.85692796533367,-3.54112891870358,"B",29.9066836757576
230 | 0.965975751301129,-1.65524902082232,"B",31.8329159324227
231 | 1.3400963432163,-2.53249997678649,"B",34.2984689768144
232 | 2.48077460806686,-0.739297549128252,"B",32.9974898863316
233 | 1.78779191454753,-1.71446299705379,"B",31.6407582846667
234 | 1.16033504600287,-0.921688960039032,"B",31.5763747893201
235 | 0.985168762721327,-2.63287148075273,"B",35.0818898625254
236 | 0.48846925861266,-2.26659034309351,"B",35.5065181126264
237 | 2.21685985212682,-3.44789485328259,"B",25.6926711372672
238 | 1.85695085395875,-1.45185309403686,"B",34.9659933952443
239 | 2.7057829413052,-2.21561300532335,"B",33.544180957847
240 | 1.86287314838049,-2.2997095902998,"B",26.1830518789973
241 | 2.21383669750785,-2.93422120101716,"B",30.352568920066
242 | 1.90818460864456,-2.64563595364073,"B",27.2123742444245
243 | 1.10568552977735,-1.29116649851881,"B",27.6236118891273
244 | 3.11780518222904,-2.31124688607303,"B",26.9337109724889
245 | 1.03752379642514,-2.13957748487073,"B",30.4261748360558
246 | 2.62714089022837,-2.09275139506549,"B",29.9945796223486
247 | 2.01371932341697,-3.6344907909836,"B",22.7318815063131
248 | 1.39514502515317,-2.21763324909486,"B",32.3853190103913
249 | 0.908507835001625,-4.36269869500337,"B",37.598229899389
250 | 2.01125147915871,-2.96013226206139,"B",27.6039007826305
251 | -0.359677626454198,-3.36305854220979,"B",34.9331703908154
252 | 2.63394748320767,0.0203738131914135,"B",31.5365402902041
253 | 2.12013933187301,-3.10456622910097,"B",31.2910395475057
254 | 2.80200640754404,-1.00843159102324,"B",33.3266411450311
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1987 | 11.6341762088754,-8.41148968710637,"J",27.9771056524638
1988 | 10.037800450872,-10.0936499087369,"J",33.4945922145746
1989 | 10.2817924192465,-7.63814249196294,"J",25.1131670926581
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1996 | 11.169643020964,-8.61739862715028,"J",24.2522684574462
1997 | 10.4305513718222,-9.23669765301099,"J",28.9915162935082
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2000 | 10.4221293203204,-8.52713825956083,"J",27.1219986188433
2001 | 10.6935339108403,-10.3630845853815,"J",31.65131023314
2002 |
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/figures/1_plot_density-1.pdf:
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/figures/1_plot_scatter_basic-1.pdf:
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/figures/1_plot_scatter_basic-1.png:
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/figures/2_plot_model-1.pdf:
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/figures/demo.gif:
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/index.Rmd:
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1 | ---
2 | title: '**Results Template**'
3 | subtitle: A Subtitle
4 | output:
5 | html_document:
6 | theme: cerulean
7 | highlight: pygments
8 | toc: yes
9 | toc_depth: 3
10 | toc_float: yes
11 | number_sections: no
12 | df_print: kable
13 | code_folding: hide
14 | code_download: yes
15 | word_document:
16 | reference_docx: utils/Template_Word.docx
17 | highlight: pygments
18 | toc: no
19 | toc_depth: 3
20 | df_print: kable
21 | number_sections: yes
22 | rmarkdown::html_vignette:
23 | toc: yes
24 | toc_depth: 3
25 | pdf_document:
26 | toc: yes
27 | toc_depth: '2'
28 | latex_engine: xelatex
29 | editor_options:
30 | chunk_output_type: console
31 | bibliography: utils/bibliography.bib
32 | csl: utils/apa.csl
33 | ---
34 |
35 |
36 |
39 |
40 | ```{r setup, warning=FALSE, message=TRUE, include=FALSE}
41 | # Set up the environment (or use local alternative `source("utils/config.R")`)
42 | source("https://raw.githubusercontent.com/RealityBending/TemplateResults/main/utils/config.R")
43 |
44 | fast <- FALSE # Make this false to skip the chunks
45 | ```
46 |
47 | # Introduction
48 |
49 | ```{r badges, echo=FALSE, message=TRUE, warning=FALSE, results='asis'}
50 | # This chunk is a bit complex so don't worry about it: it's made to add badges to the HTML versions
51 | # NOTE: You have to replace the links accordingly to have working "buttons" on the HTML versions
52 | if (!knitr::is_latex_output() && knitr::is_html_output()) {
53 | cat("
54 | [](https://github.com/RealityBending/TemplateResults)
55 | [](https://realitybending.github.io/TemplateResults/)
56 | [](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
57 | [](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)")
58 | }
59 | ```
60 |
61 | This is a template for a data analysis folder that can be easily exported as a [**webpage**](https://realitybending.github.io/TemplateResults/) or as **Supplementary Materials** (e.g., as a [**Word document**](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx) or a [**PDF**](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)).
62 |
63 | How does it look like? Just like this! The README page of this repository, alongside the [webpage](https://realitybending.github.io/TemplateResults/) and the word and PDF documents, were all created from the [index.Rmd](https://github.com/RealityBending/TemplateResults/blob/main/index.Rmd) file.
64 |
65 | This means you can easily **share your data analysis**, either by attaching the *PDF* or *Word* file to the publication (as **Supplementary Materials**), or by directly providing the URL of your GitHub repository: the readers can then enjoy your awesome open-access work in a convenient and transparent way.
66 |
67 | ## Features
68 |
69 | - [x] Automatically generates different types of document:
70 | - [**README page**](https://github.com/RealityBending/TemplateResults/blob/main/README.md)
71 | - [**Published website**](https://realitybending.github.io/TemplateResults/)
72 | - [**Word document**](https://github.com/RealityBending/TemplateResults/raw/main/word_and_pdf/SupplementaryMaterials.docx)
73 | - [**PDF document**](https://github.com/RealityBending/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)
74 | - [x] APA citations
75 | - [x] Automatic citations and [reference list](https://github.com/RealityBending/TemplateResults#package-references) for all packages
76 | - [x] Tidy organisation (separate files for independent analyses)
77 | - [x] Great default configuration
78 | - [x] And more!
79 |
80 | ```{r demo_gif, echo=FALSE, message=TRUE, warning=FALSE}
81 | # Let's include a demo GIF (this doesn't work in PDF documents)
82 | if (!knitr::is_latex_output()) {
83 | knitr::include_graphics("figures/demo.gif")
84 | }
85 | ```
86 |
87 |
88 | ## Installation
89 |
90 | - **What is this?**
91 |
92 | This repository is a template to set up a reproducible, convenient and shareable workflow for your data analysis. It consists of several [*Rmarkdown*](https://rmarkdown.rstudio.com/lesson-1.html) files (`.Rmd`), that allow you to have R code and text (markdown) in the same document. Importantly, these files can be transformed into other documents formats.
93 |
94 | - **How to use this template?**
95 |
96 | Download it ([**click here to download**](https://github.com/RealityBending/TemplateResults/archive/main.zip)), unzip it and edit.
97 | Alternatively, you click on the [**Use this template**](https://github.com/RealityBending/TemplateResults/generate) button at the top of this screen to create a GitHub repository with all the content copied (then you just need to clone the repo to your local machine).
98 |
99 | The main files you need to edit are the `.Rmd` files, that you can open with some editor (e.g., [Rstudio](https://rstudio.com/)), and edit the text and the R chunks of code.
100 |
101 |
102 | - **How to upload it to a website?**
103 |
104 | If your repo is not already connected to GitHub, then create a new repository and upload all the content (so that it looks like this repo). Then, go to settings of the repo and enable **GitHub pages** (i.e., that gives you a webpage from an html stored on GitHub), and select the `docs/` folder as the location of the webpage. Indeed, rendering (knitting) the files will generate an "index.html" file in the `/docs/` folder, which is used as the website. You can see an example at [https://realitybending.github.io/TemplateResults/](https://realitybending.github.io/TemplateResults/).
105 |
106 | - **To knit or not to knit**
107 |
108 | In this repo, with have set up a [GitHub action](https://github.com/RealityBending/TemplateResults/blob/main/.github/workflows/website.yml) that generates all the output files everytime someone commit to the repository. This means that the final documents here are always "up-to-date" with the *Rmds* (as shown by the green badge). That said, you can remove this GitHub action (just remove the `.github/workflows/website.yml` file) if you prefer to generate the documents manually only.
109 |
110 | - **But I don't want do upload all my data**
111 |
112 | In that case, you'll need to 1) deactivate (i.e., remove the action file) the automatic rendering by GitHub (as no data will be stored on GitHub) and 2) mark the **data** folder as "to be ignored" (so that it won't be uploaded). This can be done by adding `/data/` to the [**.gitignore**](https://github.com/RealityBending/TemplateResults/blob/main/.gitignore) file (that you can open with a notepad). This means that you can still store the data here locally, and generate the documents accordingly, but the data folder will be ignored by git and never uploaded to GitHub. This way, you can still have a cool website, an open-access script, but the data is safe with you. The only down side is that you have to build it manually (cannot use GitHub actions).
113 |
114 | - **How to add references?**
115 |
116 | References have to be added in `bib` format in the [*utils/bibliography.bib*](https://github.com/RealityBending/TemplateResults/blob/main/utils/bibliography.bib) file, and further referenced in the text like this `[@ludecke2019insight]` [@ludecke2019insight].
117 |
118 | - **I don't like the Word (.docx) theme**
119 |
120 | The theme for the word document is defined in the [**Template_Word.docx](https://github.com/RealityBending/TemplateResults/tree/main/utils) file, in the `/utils/` folder. You need to edit the "styles" (not just the content, but the style itself) to your preference.
121 |
122 | - **I have Python code**
123 |
124 | Thanks to R's possibilities when it comes to integration with Python, it's super easy to enable it in your pipeline. Just uncomment the [Python installation line](https://github.com/RealityBending/TemplateResults/blob/main/utils/config.R#L24) in the `utils/config.R` file and you're ready to go!
125 |
126 | - **It doesn't work / I have questions / I have ideas**
127 |
128 | Just [**open an issue**](https://github.com/RealityBending/TemplateResults/issues) and we'll be happy to assist ☺
129 |
130 | ## Structure
131 |
132 | Most files that you'll need to create / edit will be written in [**rmarkdown**](https://rmarkdown.rstudio.com/lesson-1.html), which consists of a mix of markdown text and R chunks of code.
133 |
134 | The main file is named [**index.Rmd**](https://github.com/RealityBending/TemplateResults/blob/main/index.Rmd). However, to avoid having overly long files, the different (and independent) analyses parts are actually split in other documents. For instance, in this template example, the descriptive statistics section is in the [**1_descriptive.Rmd**](https://github.com/RealityBending/TemplateResults/blob/main/1_descriptive.Rmd) file. As you can [see in the index file](https://github.com/RealityBending/TemplateResults/blob/690f7947da0fc8ac85eaf6fb87fafeaa46fb3c50/index.Rmd#L89-L90), this file is then integrated as a child document (i.e., it is merged). This makes it very convenient to have a clear structure with well-organized files, that are put together only when merged.
135 |
136 | ## Render and Publish
137 |
138 | Importantly, in order to render all the files, do not Knit this document by pressing the 'Knit' button. If you do, it will create an output file (for instance `index.html`) in the root folder, alongside `index.Rmd`. This is **not what we want**, as we want to keep the output files tidy in separate folders (for instance, the html version should be in the `/docs/` folder, as this is where the website will look for).
139 |
140 | There an R script, [utils/render.R](https://github.com/RealityBending/TemplateResults/blob/main/utils/render.R), that contains the lines to render everything in its correct location. So, when you have the "index.Rmd" file opened (and your working directory is at its root), simply run **`source("utils/render.R")`** in the console (or the relevant lines in that file). This will run the rendering file and create all the files.
141 |
142 | ## Contribution
143 |
144 | Do not hesitate to improve this template by updating, documenting, or expanding it!
145 |
146 |
147 | # Packages & Data
148 |
149 | ## Packages
150 |
151 | This document was prepared on `r format(Sys.Date())`.
152 |
153 | ```{r warning=FALSE, message=TRUE, results='asis'}
154 | library(bayestestR)
155 | library(parameters)
156 | library(performance)
157 | library(report)
158 | library(see)
159 | library(ggplot2)
160 |
161 | summary(report::report(sessionInfo()))
162 | ```
163 |
164 |
165 | ## Data
166 |
167 | ```{r warning=FALSE, message=TRUE, results='asis'}
168 | df <- read.csv("data/data.csv")
169 |
170 | cat(paste("The data consists of",
171 | report::report_participants(df,
172 | participants = "Participant",
173 | age = "Age")))
174 | ```
175 |
176 |
177 |
178 | Note that the chunks generating figures in the code below have some arguments specified in their header, such as `fig.width` and `fig.height`, which controls the figure size. These were filled with an eponym argument defined in [`utils/config.R`](https://github.com/RealityBending/TemplateResults/blob/main/utils/config.R#L26-L27). We also set the resolution, i.e., `dpi`, to a low value so that the resulting file is lighter. But **don't forget to crank this value up** (to 300-600) to get nice-looking results.
179 |
180 |
181 | # Descriptive Stats {.tabset}
182 |
183 | Notice the `{.tabset}` tag after the section name. This will show the subsections as different tabs (in the [html version](https://realitybending.github.io/TemplateResults/#Descriptive_Stats) only, because the other formats are static).
184 |
185 |
186 | ```{r child=if (fast == FALSE) '1_descriptive.Rmd'}
187 | ```
188 |
189 | # Inferential Stats
190 |
191 | ```{r child=if (fast == FALSE) '2_inferential.Rmd'}
192 | ```
193 |
194 |
195 | # Full Code
196 |
197 | The full script of executive code contained in this document is reproduced here.
198 |
199 | ```{r full_code, ref.label=knitr::all_labels(), eval=FALSE}
200 | ```
201 |
202 | # Package References
203 |
204 | ```{r warning=FALSE, message=FALSE, results='asis'}
205 | report::cite_packages(sessionInfo())
206 | ```
207 |
208 |
209 | # References
210 |
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/utils/Template_Word.docx:
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https://raw.githubusercontent.com/RealityBending/TemplateResults/fe5a345a542c1f3625af0cbe65cfbfcac421dab3/utils/Template_Word.docx
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/utils/apa.csl:
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1 |
2 |
1527 |
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/utils/bibliography.bib:
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1 | @article{ludecke2019insight,
2 | title={Insight: A unified interface to access information from model objects in R},
3 | author={L{\"u}decke, Daniel and Waggoner, Philip D and Makowski, Dominique},
4 | journal={Journal of Open Source Software},
5 | volume={4},
6 | number={38},
7 | pages={1412},
8 | year={2019}
9 | }
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/utils/config.R:
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1 | installed <- rownames(installed.packages())
2 |
3 | # Install packages
4 | for(pkg in c("knitr", "magrittr", "insight", "bayestestR", "parameters", "effectsize", "performance", "correlation", "modelbased", "see", "remotes", "ggplot2")){
5 | if (!pkg %in% installed){
6 | install.packages(pkg, repos = "http://cran.us.r-project.org")
7 | }
8 | }
9 | # Because report and easystats are not on CRAN
10 | if (!"report" %in% installed) remotes::install_github("easystats/report")
11 | # if (!"easystats" %in% installed) remotes::install_github("easystats/easystats")
12 |
13 |
14 |
15 |
16 | # Load packages silently
17 | for(pkg in c("tidyverse", "ggplot2", "easystats")){
18 | if (pkg %in% installed && !require(pkg, character.only=TRUE)) {
19 | suppressWarnings(suppressPackageStartupMessages(library(pkg, character.only=TRUE)))
20 | }
21 | }
22 |
23 | # Install Python
24 | # py_install(packages = c('numpy', 'pandas', 'scipy', 'seaborn', 'matplotlib'))
25 |
26 |
27 | # Options relative to figure size
28 | figheight <- 6
29 | figwidth <- 6 * see::golden_ratio()
30 |
31 | # General options
32 | options(knitr.kable.NA = "",
33 | digits = 2,
34 | tidyverse.quiet = TRUE)
35 |
36 | # Chunk options (see https://yihui.org/knitr/options/#chunk_options)
37 | knitr::opts_chunk$set(
38 | comment = ">", # The prefix to be added before each line of the text output.
39 | dpi = 600,
40 | fig.path = "figures/",
41 | fig.height=figheight,
42 | fig.width=figwidth
43 | # fig.align = "center"
44 | )
45 |
46 |
47 | # Set seed for reproducible results
48 | set.seed(333)
49 |
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/utils/render.R:
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1 | suppressWarnings(library(rmarkdown))
2 |
3 | # Try to find the correct working dir
4 | if(!file.exists("index.Rmd") && file.exists("../index.Rmd")) {
5 | setwd("../")
6 | }
7 |
8 | # Render as README
9 | rmarkdown::render('index.Rmd', output_format = rmarkdown::md_document(variant = "markdown_github"), output_file = "README")
10 |
11 | # Render HTML
12 | rmarkdown::render('index.Rmd', output_format = "html_document", output_dir = "docs/", output_file = "index")
13 |
14 | # Render Word
15 | rmarkdown::render('index.Rmd', output_format = "word_document", output_dir = "word_and_pdf/", output_file = "SupplementaryMaterials")
16 |
17 | # Render PDF
18 | rmarkdown::render('index.Rmd', output_format = "pdf_document", output_dir = "word_and_pdf/", output_file = "SupplementaryMaterials")
19 |
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/word_and_pdf/SupplementaryMaterials.docx:
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https://raw.githubusercontent.com/RealityBending/TemplateResults/fe5a345a542c1f3625af0cbe65cfbfcac421dab3/word_and_pdf/SupplementaryMaterials.docx
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/word_and_pdf/SupplementaryMaterials.pdf:
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https://raw.githubusercontent.com/RealityBending/TemplateResults/fe5a345a542c1f3625af0cbe65cfbfcac421dab3/word_and_pdf/SupplementaryMaterials.pdf
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