-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
259 lines (211 loc) · 7.72 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
<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Using cutting edge open-source tools to drill into clinical safety data</title>
<meta charset="utf-8" />
<meta name="author" content="Eli Miller, Atorus Research" />
<script src="libs/header-attrs-2.13/header-attrs.js"></script>
<link href="libs/remark-css-0.0.1/fc.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/fc-fonts.css" rel="stylesheet" />
<link rel="stylesheet" href="styles.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: bottom, left, title-slide
.title[
# Using cutting edge open-source tools to drill into clinical safety data
]
.subtitle[
## A look into recent developments in Tplyr and safetyGraphics
]
.author[
### Eli Miller, Atorus Research
]
.date[
### 4/13/2022
]
---
## What is "metadata" in Tplyr?
.two-column[
.left-col[
`get_meta_result`
Get the value of a cell with the row_id and column
`get_meta_subset`
Get the dataset filtered based on the row and column selected.
`build(metadata = TRUE)`
Build a Tplyr table with metadata build in.
]
.right-col[
### What does this help us do?
- Traceability from summary to data - We don't lose the context when we create the table
- Interface for interactive elements - If you are building widgets or interactive elements, you can now know what data a user is trying to interact with
- Logic for filtering and relevant variables - Helper functions for extracting results and filtering data
]
]
---
## Why are you using safetyGraphics?
.center[
- A prebuilt framework for loading and mapping data - safetyGraphics has built in mapping options, but can be used to load data in any format
- Filtering widgets built in - Data can be filtered on the fly
- Extensible built in - Watch out for this to be included in the new release of Tplyr
- Under active development - Multiple teams are developing and improving graphics
]
---
## An example demo table
<iframe src="https://atorus-connect.eastus2.cloudapp.azure.com/content/72595d82-f89d-4e97-ab72-da70d490e9f8", height=85%, width=100%/>
---
## An example AE table
<iframe src="https://atorus-connect.eastus2.cloudapp.azure.com/content/e7b9c342-7f7f-4869-a9d3-03108704373b", height=85%, width=100%/>
---
## An example Renal Table
<iframe src="https://atorus-connect.eastus2.cloudapp.azure.com/content/011dfee9-97d7-4305-83c6-2c138b2f9cb7", height=85%, width=100%/>
---
## Now What?
.center[
1. Make the charts prettier and check with clinicians to make sure they are useful
2. Configure Tplyr so these charts ship by default and data can be swapped in
3. Send Tplyr off to CRAN
4. Get feedback from *you*
]
---
## Thank you to...
.center[
- Jeremy Wildfire (safetyGraphics)
- Matt Kumar (Proof-of-concept)
- Mike Stackhouse (Tplyr Metadata)
]
</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",
"slideNumberFormat": "%current%",
"highlightLines": true,
"countIncrementalSlides": false,
"ratio": "16:9"
});
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;
});
})();
// add `data-at-shortcutkeys` attribute to <body> to resolve conflicts with JAWS
// screen reader (see PR #262)
(function(d) {
let res = {};
d.querySelectorAll('.remark-help-content table tr').forEach(tr => {
const t = tr.querySelector('td:nth-child(2)').innerText;
tr.querySelectorAll('td:first-child .key').forEach(key => {
const k = key.innerText;
if (/^[a-z]$/.test(k)) res[k] = t; // must be a single letter (key)
});
});
d.body.setAttribute('data-at-shortcutkeys', JSON.stringify(res));
})(document);
(function() {
"use strict"
// Replace <script> tags in slides area to make them executable
var scripts = document.querySelectorAll(
'.remark-slides-area .remark-slide-container script'
);
if (!scripts.length) return;
for (var i = 0; i < scripts.length; i++) {
var s = document.createElement('script');
var code = document.createTextNode(scripts[i].textContent);
s.appendChild(code);
var scriptAttrs = scripts[i].attributes;
for (var j = 0; j < scriptAttrs.length; j++) {
s.setAttribute(scriptAttrs[j].name, scriptAttrs[j].value);
}
scripts[i].parentElement.replaceChild(s, scripts[i]);
}
})();
(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';
}
}
})();
// adds .remark-code-has-line-highlighted class to <pre> parent elements
// of code chunks containing highlighted lines with class .remark-code-line-highlighted
(function(d) {
const hlines = d.querySelectorAll('.remark-code-line-highlighted');
const preParents = [];
const findPreParent = function(line, p = 0) {
if (p > 1) return null; // traverse up no further than grandparent
const el = line.parentElement;
return el.tagName === "PRE" ? el : findPreParent(el, ++p);
};
for (let line of hlines) {
let pre = findPreParent(line);
if (pre && !preParents.includes(pre)) preParents.push(pre);
}
preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
})(document);</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>