-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
301 lines (221 loc) · 8.44 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
<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>R for the Planet</title>
<meta charset="utf-8" />
<meta name="author" content="Alexa Fredston, PhD" />
<meta name="date" content="2021-09-09" />
<script src="index_files/header-attrs/header-attrs.js"></script>
<link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# R for the Planet
## New York R Conference
### Alexa Fredston, PhD
### September 9, 2021
---
<style>
.title-slide {
vertical-align: bottom !important;
text-align: left !important;
}
</style>
# About our impact on the planet ...
Yes, it's real.
Yes, it's bad.
Yes, it's us.
No, it's not too late.
No, it isn't just climate change.
---
# About our impact on the planet ...
### More on climate
[IPCC report](https://www.ipcc.ch/assessment-report/ar6/), [FAQs answered](https://www.nytimes.com/article/climate-change-global-warming-faq.html), a [docu-series](https://www.amazon.com/Years-Living-Dangerously-Complete-Showtime/dp/B00NDOXDJU), a [YouTube channel](https://www.youtube.com/channel/UCi6RkdaEqgRVKi3AzidF4ow), a [bunch](https://www.criticalfrequency.org/drilled) [of](https://www.hottakepod.com/) [podcasts](https://www.degreespod.com/)
--
###Climate scientists to follow
[Jonathan Foley](https://twitter.com/GlobalEcoGuy), [Ed Hawkins](https://twitter.com/ed_hawkins), [Katharine Hayhoe](https://twitter.com/KHayhoe), [Leah Stokes](https://twitter.com/leahstokes)
###Environmental journalists to follow
[Juliet Eilperin](https://twitter.com/eilperin), [Robinson Meyer](https://twitter.com/yayitsrob), [Kendra Pierre-Louis](https://twitter.com/KendraWrites), [Hiroko Tabuchi](https://twitter.com/HirokoTabuchi)
---
# What I do
---
# Why R?
Really good at statistics
Facilitates transparency and reproducibility
The R ecosystem (R + RStudio + GitHub + RMarkdown + ...) enables us to [do better science in less time](https://www.nature.com/articles/s41559-017-0160) (*email me for a PDF*)
---
# Species on the move
<video height="450">
<source src="black seabass.mp4" type="video/mp4">
</video>
Source: [OceanAdapt](https://oceanadapt.rutgers.edu)
---
# Species on the move
## 2022?
---
# Species on the move
Explaining the past `\(\neq\)` predicting the future
Ecosystems are very, very complex
---
# My work
**Goal:** simulating near-term shifts in species' distributions in response to temperature
--
**Problem:** our only data are annual surveys of where fish were found, and how many
--
**Solution:** fit mechanistic models to historical data to estimate process rates and simulate the future
---
# The finer details
Fitted as a hierarchical Bayesian model using [Stan](https://mc-stan.org/)
Packages: [rstan](https://mc-stan.org/users/interfaces/rstan), [rstanarm](https://mc-stan.org/rstanarm/), [tidybayes](http://mjskay.github.io/tidybayes/)
Core model features
* Spatially structured: 1° patches along a coastline
* Age structured: adults reproduce, cohorts move through ages
* Most process rates estimated in model
* One process rate (reproduction, movement, or mortality) is temperature-dependent
* *Only fitted to historical data on abundance and distribution*
* Fitting 1972-2005, testing 2006-2015
* Competing annual forecast against different model types
---
# Bayesian network
---
# Fitting models to data
---
# R, the planet, and you
Data about issues that matter to you is [at your fingertips](https://ropensci.org/packages/data-access/)...
--
... **But use it with caution!**
Domain knowledge matters
We're friendly. Just ask!
---
class: center, middle
# Thanks!
Slides created via the R packages:
[xaringan](https://github.com/yihui/xaringan) and [xaringanthemer](https://github.com/gadenbuie/xaringanthemer)
## Contact Information
[www.alexafredston.com](https://www.alexafredston.com/)<br>
[[email protected]](mailto:[email protected])<br>
[@AFredston](https://twitter.com/AFredston)
</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({
"slideNumberFormat": "%current%",
"highlightStyle": "github",
"highlightLines": true,
"ratio": "16:9",
"countIncrementalSlides": true
});
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;
});
})();
(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>