forked from USCbiostats/research-pipelines
-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
406 lines (303 loc) · 13 KB
/
index.html
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
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
<title>Research pipelines</title>
<meta charset="utf-8" />
<meta name="author" content="George G Vega Yon" />
<link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/default-fonts.css" rel="stylesheet" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# Research pipelines
### George G Vega Yon
### USC IMAGE project
### 2019/10/24
---
# Today's talk
## Reproducible Research
## Tools to eaze your work
We will spend most time looking at other people's work
---
background-image: url("http://giphygifs.s3.amazonaws.com/media/88VqLDyQttwpa/giphy.gif")
---
## Reproducible research (RR) (or how to avoid "it works on my computer!")
--
**A major new issue in sciences (overall)**
* Accessible Reproducible Research ([Mesirov, __Science__ 2010](http://science.sciencemag.org/content/327/5964/415))
* Again, and Again, and Again, ... ([Jasny et al., __Science__ 2011](http://science.sciencemag.org/content/334/6060/1225))
* Challenges in Irreproducible Research ([__nature__ topic](http://www.nature.com/news/reproducibility-1.17552))
* Reproducibility of computational workflows is automated using continuous analysis ([Beaulieu-Jones & Greene, __nature biotechnology__ 2017](https://www.nature.com/articles/nbt.3780?foxtrotcallback=true))
--
**A Major productivity problem for researchers**
* It is not only a good idea for science, but also for saving you time!
---
# Reproducible research
--
**Polished paper**
- Ready to be submitted
- Written using your fav doc editor
--
**Intermediate report**
- Not ready to be published
- Not necesarily using your fav doc editor
What do these two have in common?
---
background-image: url("http://www.phdcomics.com/comics/archive/phd012618s.gif")
class: center, top, inverse
... both should have pretty figures AND be
reproducible
---
# The minimum
**Data** people must have a way to get your data
- Include it with the paper.
- Put it on a repo online like [zenodo](https://zenodo.org) (see for example
the [Gene Ontology's profile](https://zenodo.org/communities/gene-ontology/?page=1&size=20)) .
- Include instructions about how to get the data (e.g. in an experimental
setting, how did you get the samples).
--
**Analysis** source code/steps of your analysis
- Include it with the paper
- Put it on a repo online like [Github](https://github.com) or [GitLab](https://gitlab.com)
--
**Pro tip:** *Avoid the "contact the corresponding author for..." lines.*
---
# Tiers of reproducibility
### ~~minimum~~ Basic
* **Data** Use public dataset (or at least shareable), or publish your dataset.
* **Analysis** source code/steps of your analysis.
### Plus
* **Tools** Use open source software (like R, python, etc.).
* **Decency** Write your code neatly (like Emil does)
* **Tidy** Organize your work in a structured way (folders+readme files,
[here](https://github.com/gvegayon/fctc) is one example)
### Premium
* **plug-n-play** Use a container (like [docker](https://www.docker.com/) or
[singularity](https://sylabs.io/))
---
class: center, middle
# Research Pipeline
Source: Diagram by [문건웅](https://www.linkedin.com/in/%EA%B1%B4%EC%9B%85-%EB%AC%B8-5ab72599/?locale=en_US) showed [here](https://www.slideshare.net/ssuser7e30b2/reproducible-research1)
---
class: center, bottom, inverse
background-image: url("https://media.giphy.com/media/wLtPSVuz0co5G/giphy.gif")
Now, a lot of it has to do with automatization...
---
class: middle
## Automatizing your research: automatic reports
- For quick reports use tools like [**rmarkdown**](https://cran.r-project.org/package=rmarkdown) which is based on
[**pandoc**](https://pandoc.org)
- Automate tabular outputs using [**kableExtra**](https://cran.r-project.org/package=kableExtra) or
[**pander**](https://cran.r-project.org/package=pander)
- Automate tables: In R, you can use [**texreg**](https://cran.r-project.org/package=texreg), [**xtable**](https://cran.r-project.org/package=xtable)
---
## Automatizing your research: automatic reports (example)
.pull-left[
```r
data(anorexia, package = "MASS")
anorex.1 <- glm(
Postwt ~ Treat,
data = anorexia
)
anorex.2 <- glm(
Postwt ~ Prewt + Treat,
data = anorexia
)
library(texreg)
htmlreg(
list(anorex.1, anorex.2),
doctype = FALSE
)
```
]
<div style="font-size: small;" class="pull-right">
<table cellspacing="0" align="center" style="border: none;">
<caption align="bottom" style="margin-top:0.3em;">Statistical models</caption>
<tr>
<th style="text-align: left; border-top: 2px solid black; border-bottom: 1px solid black; padding-right: 12px;"><b></b></th>
<th style="text-align: left; border-top: 2px solid black; border-bottom: 1px solid black; padding-right: 12px;"><b>Model 1</b></th>
<th style="text-align: left; border-top: 2px solid black; border-bottom: 1px solid black; padding-right: 12px;"><b>Model 2</b></th>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">(Intercept)</td>
<td style="padding-right: 12px; border: none;">85.70<sup style="vertical-align: 0px;">***</sup></td>
<td style="padding-right: 12px; border: none;">49.77<sup style="vertical-align: 0px;">***</sup></td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;">(1.35)</td>
<td style="padding-right: 12px; border: none;">(13.39)</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">TreatCont</td>
<td style="padding-right: 12px; border: none;">-4.59<sup style="vertical-align: 0px;">*</sup></td>
<td style="padding-right: 12px; border: none;">-4.10<sup style="vertical-align: 0px;">*</sup></td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;">(1.97)</td>
<td style="padding-right: 12px; border: none;">(1.89)</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">TreatFT</td>
<td style="padding-right: 12px; border: none;">4.80<sup style="vertical-align: 0px;">*</sup></td>
<td style="padding-right: 12px; border: none;">4.56<sup style="vertical-align: 0px;">*</sup></td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;">(2.23)</td>
<td style="padding-right: 12px; border: none;">(2.13)</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">Prewt</td>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;">0.43<sup style="vertical-align: 0px;">**</sup></td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;"></td>
<td style="padding-right: 12px; border: none;">(0.16)</td>
</tr>
<tr>
<td style="border-top: 1px solid black;">AIC</td>
<td style="border-top: 1px solid black;">495.28</td>
<td style="border-top: 1px solid black;">489.97</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">BIC</td>
<td style="padding-right: 12px; border: none;">504.39</td>
<td style="padding-right: 12px; border: none;">501.36</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">Log Likelihood</td>
<td style="padding-right: 12px; border: none;">-243.64</td>
<td style="padding-right: 12px; border: none;">-239.99</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;">Deviance</td>
<td style="padding-right: 12px; border: none;">3665.06</td>
<td style="padding-right: 12px; border: none;">3311.26</td>
</tr>
<tr>
<td style="border-bottom: 2px solid black;">Num. obs.</td>
<td style="border-bottom: 2px solid black;">72</td>
<td style="border-bottom: 2px solid black;">72</td>
</tr>
<tr>
<td style="padding-right: 12px; border: none;" colspan="4"><span style="font-size:0.8em"><sup style="vertical-align: 0px;">***</sup>p &lt; 0.001; <sup style="vertical-align: 0px;">**</sup>p &lt; 0.01; <sup style="vertical-align: 0px;">*</sup>p &lt; 0.05</span></td>
</tr>
</table>
</div>
--
Checkout the R CRAN Task View for [Reproducible Research](https://cran.r-project.org/web/views/ReproducibleResearch.html)
---
class: center, bottom, inverse
background-image: url("http://www.phdcomics.com/comics/archive/phd101212s.gif")
background-size: 40%
<!-- {style="width:50%" } -->
Version control to the rescue...
---
class: center, middle
# Git: The stupid version control system
<img src="fig/git.svg" width="600px" />
(Live demo now)
---
class: center, middle, inverse
# Thank you!
## Some other resources
rOpenSci's ["Reproduciblity in Science"](https://ropensci.github.io/reproducibility-guide/)
Karl Broman's ["Tools for Reproducible Research Spring, 2016"](http://kbroman.org/Tools4RR/)
The [**workflowr**](https://github.com/jdblischak/workflowr) package
Colin Fay's ["An introduction to Docker for R Users"](https://colinfay.me/docker-r-reproducibility/)
R packages that work with Docker/Singularity [**babelwhale**](https://cran.r-project.org/package=babelwhale) and
[**dockerfiler**](https://cran.r-project.org/package=dockerfiler)
</textarea>
<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
<script>var slideshow = remark.create({
"highlightStyle": "github",
"highlightLines": true,
"countIncrementalSlides": false
});
if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
window.dispatchEvent(new Event('resize'));
});
(function(d) {
var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
if (!r) return;
s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
d.head.appendChild(s);
})(document);
(function(d) {
var el = d.getElementsByClassName("remark-slides-area");
if (!el) return;
var slide, slides = slideshow.getSlides(), els = el[0].children;
for (var i = 1; i < slides.length; i++) {
slide = slides[i];
if (slide.properties.continued === "true" || slide.properties.count === "false") {
els[i - 1].className += ' has-continuation';
}
}
var s = d.createElement("style");
s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
d.head.appendChild(s);
})(document);
// delete the temporary CSS (for displaying all slides initially) when the user
// starts to view slides
(function() {
var deleted = false;
slideshow.on('beforeShowSlide', function(slide) {
if (deleted) return;
var sheets = document.styleSheets, node;
for (var i = 0; i < sheets.length; i++) {
node = sheets[i].ownerNode;
if (node.dataset["target"] !== "print-only") continue;
node.parentNode.removeChild(node);
}
deleted = true;
});
})();</script>
<script>
(function() {
var links = document.getElementsByTagName('a');
for (var i = 0; i < links.length; i++) {
if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
links[i].target = '_blank';
}
}
})();
</script>
<script>
slideshow._releaseMath = function(el) {
var i, text, code, codes = el.getElementsByTagName('code');
for (i = 0; i < codes.length;) {
code = codes[i];
if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
text = code.textContent;
if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
/^\$\$(.|\s)+\$\$$/.test(text) ||
/^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
code.outerHTML = code.innerHTML; // remove <code></code>
continue;
}
}
i++;
}
};
slideshow._releaseMath(document);
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement('script');
script.type = 'text/javascript';
script.src = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
if (location.protocol !== 'file:' && /^https?:/.test(script.src))
script.src = script.src.replace(/^https?:/, '');
document.getElementsByTagName('head')[0].appendChild(script);
})();
</script>
</body>
</html>