-
Notifications
You must be signed in to change notification settings - Fork 13
/
Copy pathAppendices.html
695 lines (551 loc) · 29.5 KB
/
Appendices.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
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
<!DOCTYPE html>
<html lang="en" data-content_root="" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
<title>Vision: The reproducible science stack — FLINT Handbook documentation</title>
<script data-cfasync="false">
document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
</script>
<!-- Loaded before other Sphinx assets -->
<link href="_static/styles/theme.css?digest=5b4479735964841361fd" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=5b4479735964841361fd" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=5b4479735964841361fd" rel="stylesheet" />
<link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=5b4479735964841361fd" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" href="_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=5b4479735964841361fd" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd" />
<script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=5b4479735964841361fd"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
<script>DOCUMENTATION_OPTIONS.pagename = 'Appendices';</script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Annex of FLINT Analysis" href="Reports.html" />
<link rel="prev" title="Conclusion" href="Conclusion.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
<body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
<a class="skip-link" href="#main-content">Skip to main content</a>
<div id="pst-scroll-pixel-helper"></div>
<button type="button" class="btn rounded-pill" id="pst-back-to-top">
<i class="fa-solid fa-arrow-up"></i>
Back to top
</button>
<input type="checkbox"
class="sidebar-toggle"
name="__primary"
id="__primary"/>
<label class="overlay overlay-primary" for="__primary"></label>
<input type="checkbox"
class="sidebar-toggle"
name="__secondary"
id="__secondary"/>
<label class="overlay overlay-secondary" for="__secondary"></label>
<div class="search-button__wrapper">
<div class="search-button__overlay"></div>
<div class="search-button__search-container">
<form class="bd-search d-flex align-items-center"
action="search.html"
method="get">
<i class="fa-solid fa-magnifying-glass"></i>
<input type="search"
class="form-control"
name="q"
id="search-input"
placeholder="Search..."
aria-label="Search..."
autocomplete="off"
autocorrect="off"
autocapitalize="off"
spellcheck="false"/>
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form></div>
</div>
<nav class="bd-header navbar navbar-expand-lg bd-navbar">
</nav>
<div class="bd-container">
<div class="bd-container__inner bd-page-width">
<div class="bd-sidebar-primary bd-sidebar">
<div class="sidebar-header-items sidebar-primary__section">
</div>
<div class="sidebar-primary-items__start sidebar-primary__section">
<div class="sidebar-primary-item">
<a class="navbar-brand logo" href="index.html">
<p class="title logo__title">FLINT Handbook documentation</p>
</a></div>
<div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
<div class="bd-toc-item navbar-nav active">
<ul class="current nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter1/index.html">Chapter 1: Understanding Climate Science and Carbon Models</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter1/section_one.html">The Organisations behind the Climate Mitigation Steps</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter1/section_two.html">How does FLINT help solve issues arising from Climate Change</a></li>
</ul>
</li>
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter2/index.html">Chapter 2: Introduction to the Full Lands Integration Tool</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter2/section_one.html">Modules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter2/section_two.html">Inputs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter2/section_three.html">Outputs</a></li>
</ul>
</li>
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter3/index.html">Chapter 3: Introduction to Generic Carbon Budget Model</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter3/section_one.html">End-to-end workflow for the GCBM Analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter3/section_two.html">Post-processing</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter3/section_three.html">What is the effect of running the model without disturbance?</a></li>
</ul>
</li>
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter4/index.html">Chapter 4: The Work DVC Plays in the Land Sector Repo</a><input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-4"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter4/section_one.html">How to create a reproducible pipeline with Moja Global Dataset.</a></li>
</ul>
</li>
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter5/index.html">Chapter 5: Running a GCBM Simulation</a><input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-5"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter5/section_one.html">Project structure and directory hierarchy overview</a></li>
<li class="toctree-l2 has-children"><a class="reference internal" href="Chapter5/section_two.html">Setting up our GCBM environment</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l3"><a class="reference internal" href="Chapter5/section_two_a.html">Installing Python</a></li>
<li class="toctree-l3"><a class="reference internal" href="Chapter5/section_two_b.html">Installing Microsoft Access Database Driver</a></li>
<li class="toctree-l3"><a class="reference internal" href="Chapter5/section_two_c.html">Installing Visual C++ Redistributable Packages</a></li>
<li class="toctree-l3"><a class="reference internal" href="Chapter5/section_two_d.html">Update GCBM Run Script</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="Chapter5/section_three.html">Spatial data preparation(jupyter notebook)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter5/section_four.html">Tiler Configuration</a></li>
</ul>
</li>
<li class="toctree-l1 has-children"><a class="reference internal" href="Chapter6/index.html">Chapter 6: Climate Projections</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-7"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="Chapter6/section_one.html">How do we expect our world to change?</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter6/section_two.html">What does the increase in CO2 mean for forests?</a></li>
<li class="toctree-l2"><a class="reference internal" href="Chapter6/section_three.html">Changing Patterns</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Conclusion.html">Conclusion</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Vision: The reproducible science stack</a></li>
<li class="toctree-l1"><a class="reference internal" href="Reports.html">Annex of FLINT Analysis</a></li>
</ul>
</div>
</nav></div>
</div>
<div class="sidebar-primary-items__end sidebar-primary__section">
</div>
<div id="rtd-footer-container"></div>
</div>
<main id="main-content" class="bd-main">
<div class="sbt-scroll-pixel-helper"></div>
<div class="bd-content">
<div class="bd-article-container">
<div class="bd-header-article">
<div class="header-article-items header-article__inner">
<div class="header-article-items__start">
<div class="header-article-item"><label class="sidebar-toggle primary-toggle btn btn-sm" for="__primary" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-bars"></span>
</label></div>
</div>
<div class="header-article-items__end">
<div class="header-article-item">
<div class="article-header-buttons">
<div class="dropdown dropdown-download-buttons">
<button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Download this page">
<i class="fas fa-download"></i>
</button>
<ul class="dropdown-menu">
<li><a href="_sources/Appendices.rst" target="_blank"
class="btn btn-sm btn-download-source-button dropdown-item"
title="Download source file"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-file"></i>
</span>
<span class="btn__text-container">.rst</span>
</a>
</li>
<li>
<button onclick="window.print()"
class="btn btn-sm btn-download-pdf-button dropdown-item"
title="Print to PDF"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-file-pdf"></i>
</span>
<span class="btn__text-container">.pdf</span>
</button>
</li>
</ul>
</div>
<button onclick="toggleFullScreen()"
class="btn btn-sm btn-fullscreen-button"
title="Fullscreen mode"
data-bs-placement="bottom" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-expand"></i>
</span>
</button>
<script>
document.write(`
<button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
</button>
`);
</script>
<script>
document.write(`
<button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass fa-lg"></i>
</button>
`);
</script>
<label class="sidebar-toggle secondary-toggle btn btn-sm" for="__secondary"title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-list"></span>
</label>
</div></div>
</div>
</div>
</div>
<div id="jb-print-docs-body" class="onlyprint">
<h1>Vision: The reproducible science stack</h1>
<!-- Table of contents -->
<div id="print-main-content">
<div id="jb-print-toc">
<div>
<h2> Contents </h2>
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#summary">Summary:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#components">Components:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#system-control-flow">System control flow:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#prior-art">Prior art:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#data-requirements">Data requirements:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#ensemble-assessment">Ensemble assessment:</a></li>
</ul>
</nav>
</div>
</div>
</div>
<div id="searchbox"></div>
<article class="bd-article" role="main">
<section id="vision-the-reproducible-science-stack">
<h1>Vision: The reproducible science stack<a class="headerlink" href="#vision-the-reproducible-science-stack" title="Permalink to this heading">#</a></h1>
<p><em>Author: Andrew O’Reilly Nugent</em></p>
<ul class="simple">
<li><p>Iterative</p>
<ul>
<li><p>A model representing simulations at a given location will be run
and re-run many times. The collective behavior of model
simulations (an ensemble) is summarised to assess the quality of
the results</p></li>
</ul>
</li>
<li><p>Containerized</p>
<ul>
<li><p>Models have a single defined operating environment that can be run
on a virtualized machine.</p></li>
</ul>
</li>
<li><p>Traceable</p>
<ul>
<li><p>All data and sources are given identifiers that can be used to
trace the provenance of a result</p></li>
</ul>
</li>
<li><p>Learning</p>
<ul>
<li><p>The simulated system may be better described by an altered
representation of important model processes. The composition of
ensembles will change as improved models rise and fall in
popularity.</p></li>
</ul>
</li>
</ul>
<section id="summary">
<h2>Summary:<a class="headerlink" href="#summary" title="Permalink to this heading">#</a></h2>
<p>A version-controlled reporting framework that works with any FLINT-based
workflow and enables the comparison of findings (in the same location)
between a variety of models and datasets. The FLINT Science Comparison
(FSC) Working Group will be able to evaluate the effectiveness of open
science models and produce incremental model modifications over time
thanks to this versioning and comparison.</p>
<p>At a high level, this looks simple:</p>
<ul class="simple">
<li><p>FSC Working Group will deploy and maintain an open-source science
model.</p></li>
<li><p>Open and closed datasets will be configured and maintained over time.</p></li>
<li><p>The science community is invited to review the science model and the
simulation reports</p></li>
<li><p>Suggestions are made to improve the quality of the simulation over
time. <img alt="image1" src="https://lh4.googleusercontent.com/ylR-w6DFrkRO0JG0ABoFj6aInfhoLpbNc7Et9sgn-Ivyz0IHWmHkVOJWPnZ2yOxlAUSY9VzjTGuHgj7SxmV8uYvAyNjln9nnEeV1kh3yZNMpWF3FEgoFk8do-kgaxJeW73Ys-qV6FpLYAAZ_pOj2qCEKne8qwyKHnYkwE-2DbN5HliVBENBHFpQS3lqlsQ" /></p></li>
</ul>
<p>However, making the FSC assessment system last over time is a challenge.
Models are frequently created for a particular report and then forgotten
about. The likelihood that we will be able to provide an accurate
judgment of the natural world is reduced by this long-term memory loss.
We can recall a simulation at any point in the future by enlivening
models using a distributed reproducibility system. Simulations that are
repeated help us learn</p>
</section>
<section id="components">
<h2>Components:<a class="headerlink" href="#components" title="Permalink to this heading">#</a></h2>
<ul class="simple">
<li><p>The FLINT computational engine runs landscape scale simulations of
land use and land use change, including forest growth, harvest, and
carbon flux. The FLINT can be run on local workstations, in a
(commercially) managed environment, or on user-hosted cloud
resources.</p></li>
<li><p>The GCBM modules are one example of an open science forest model. The
model requires information on forest areas, such as age, rainfall,
temperature, growth rates, harvest, and disturbance records.</p></li>
<li><p>Open datasets include the <a class="reference external" href="https://developers.google.com/earth-engine/datasets/catalog/UMD_hansen_global_forest_change_2021_v1_9">Hansen Forest cover
dataset</a>
and the <a class="reference external" href="https://www.worldclim.org/data/bioclim.html">WorldClim BioClimatic
datasets</a>. Growth
rates are available for some regions. Closed datasets include the
site-specific growth rates and harvest and disturbance records.
Forest managers typically best report forest locations/boundaries and
forest age.</p></li>
<li><p>An MLOps versioning system called Data Version Control (DVC). DVC
records the exact model compilation and datasets used to create a
specific report. It is independent of the hardware, model, or
platform that created the result. DVC records ensure reproducibility,
which means that the same results can be shown for an equivalent
model with equivalent input data</p></li>
<li><p>An ensemble is the collection of multiple reports, e.g., from
different data sources or different science models, for a given
location. Ensemble results can be assessed for agreement or coherence
without needing access to the underlying data or computational
platform that generated the result. Ensembles that agree tend to
engender higher credibility than ensembles that do not agree.</p></li>
<li><p>Data scientists may use local systems to execute these models. As an
alternative, the generation of DVC-compliant reports can be automated
using a continuous integration system (like Github Actions) whenever
changes are made to the underlying dataset, such as when new data is
collected. This has the potential to operate a FLINT-based open
science model sustainably and efficiently. GitHub Actions can command
cloud-hosted FLINT instances operating within protected environments,
with access to otherwise closed data. Data does not leave the
protected environment, however, a simulation record can be reported
back to the open-source community for review.</p></li>
<li><p>Data can be stored on cloud storage or in managed databases. Data
storage may be open (e.g., Google Drive), open access, but the user
pays to support hosting costs or closed. Spatially explicit data,
like area boundaries and forest cover time series, are typically best
stored in object storage (e.g., as files on S3). Alternatively,
spatially referenced data, like harvest records for a specific forest
stand (sometimes referred to as a forest coupe), can be stored in
tabular databases or spreadsheets.</p></li>
</ul>
</section>
<section id="system-control-flow">
<h2>System control flow:<a class="headerlink" href="#system-control-flow" title="Permalink to this heading">#</a></h2>
<img alt="https://lh5.googleusercontent.com/6VgMqGMIPFOlgg4IKGIxHpjnDL7CWug9VKW0YwawYPPUL3aJeg4dL5hrQDosJisaB6T5plCF4eyXTIkx209hVzHIPlX6rNSIKHa2KgADwpOZ41bEYRkkNPO6F7cSHhvnNUB25PeAEbvOEd1jucadX0keuYW85h3xmEnhH9-X9fV1Gnq7e__bfxtsfiujKg" src="https://lh5.googleusercontent.com/6VgMqGMIPFOlgg4IKGIxHpjnDL7CWug9VKW0YwawYPPUL3aJeg4dL5hrQDosJisaB6T5plCF4eyXTIkx209hVzHIPlX6rNSIKHa2KgADwpOZ41bEYRkkNPO6F7cSHhvnNUB25PeAEbvOEd1jucadX0keuYW85h3xmEnhH9-X9fV1Gnq7e__bfxtsfiujKg" />
<p>An overview of the steps <em>(from top to bottom)</em></p>
<ul class="simple">
<li><p>A data science workflow is defined to compile simulation input</p></li>
<li><p>Datasets are hosted on remote storage and indexed by DVC</p></li>
<li><p>A standard report template is configured for each simulation, indexed
by location</p>
<ul>
<li><p>GCBM.Belize, GCBM.Colombia, GCBM.Chile</p></li>
</ul>
</li>
<li><p>The automated integration system detects changes and re-runs the
simulation</p></li>
<li><p>Monitoring and observability services store a log of the new results</p></li>
<li><p>The simulation report is publicly available from GitHub.</p></li>
</ul>
</section>
<section id="prior-art">
<h2>Prior art:<a class="headerlink" href="#prior-art" title="Permalink to this heading">#</a></h2>
<ul class="simple">
<li><p>a DVC Pipeline for the GCBM Science Model
(<a class="reference external" href="https://github.com/radistoubalidis/GCBM.Belize/pull/1">link</a>)</p>
<ul>
<li><p>metadata and version control</p></li>
</ul>
</li>
<li><p>a GitHub Action for the GCBM Science Model
(<a class="reference external" href="https://github.com/moja-global/FLINT.Cloud/blob/b3152f842e6d1d8e591e2cb0136d9a7d3db27c5a/.github/workflows/cml-report.yml">link</a>)</p>
<ul>
<li><p>automating integration when data/models are updated</p></li>
</ul>
</li>
<li><p>the GCBM Science Model in Belize using open, global data
(<a class="reference external" href="https://docs.google.com/presentation/d/10bP6wk5YWMXBchPyff8ZMexlsbmVtuGq5mQzltflPvw/edit?usp=sharing">slides</a>)</p>
<ul>
<li><p>broad strokes template that should be globally applicable</p></li>
</ul>
</li>
<li><p>the GCBM Science Model in Chile using closed, local data
(<a class="reference external" href="https://www.researchgate.net/publication/341041237_Modelling_forest_carbon_dynamics_for_REDD_using_the_Generic_Carbon_Budget_Model_GCBM_Pilot_Project_Los_Rios_Region_-_Chile">report</a>)</p>
<ul>
<li><p>the report shows how models can be customized to increase accuracy</p></li>
</ul>
</li>
</ul>
</section>
<section id="data-requirements">
<h2>Data requirements:<a class="headerlink" href="#data-requirements" title="Permalink to this heading">#</a></h2>
<ul class="simple">
<li><p>Regionally appropriate growth and turnover parameters for Canada,
Amazon, Scandinavia, Baltics, and Russia, and South East Asia</p>
<ul>
<li><p>Where growth is measured in cubic meters, an appropriate volume to
biomass conversion is required</p></li>
</ul>
</li>
<li><p>Forest cover maps, potentially including one or more of</p>
<ul>
<li><p>Hansen et al. <a class="reference external" href="https://glad.earthengine.app/view/global-forest-change">Global Forest
Change</a></p></li>
<li><p>Mapping by commercial remote sensing providers</p></li>
</ul>
</li>
<li><p>Average annual rainfall and temperature</p>
<ul>
<li><p>as described in <a class="reference external" href="https://www.worldclim.org/data/bioclim.html">Bioclimatic variables — WorldClim 1
documentation</a></p></li>
</ul>
</li>
<li><p>Clustering of eco-regions</p>
<ul>
<li><p>for example, using <a class="reference external" href="https://en.wikipedia.org/wiki/Holdridge_life_zones">Holdridge life zones -
Wikipedia</a></p></li>
</ul>
</li>
<li><p>Assessment of planting and harvest frequency</p>
<ul>
<li><p>Used to estimate initial stand age at the beginning of a
simulation</p></li>
<li><p>Where known, harvest regimes can be incorporated into the
simulation, otherwise, a long term means harvest frequency can be
used as a substitute.</p></li>
</ul>
</li>
<li><p>If used, an ecologically appropriate impact transition matrix</p>
<ul>
<li><p>This matrix describes the impact of management and disturbance on
forest carbon stores across multiple pools</p></li>
<li><p>For example, different harvesting techniques leave a varying
amount of non-merchantable biomass on site.</p></li>
<li><p>For example, fire can release biomass stored in post-harvest
residues to the atmosphere</p></li>
</ul>
</li>
</ul>
</section>
<section id="ensemble-assessment">
<h2>Ensemble assessment:<a class="headerlink" href="#ensemble-assessment" title="Permalink to this heading">#</a></h2>
<ul class="simple">
<li><p>Index spatially explicit simulation results by location (e.g., pixel,
polygon, region), cross-referencing reports</p>
<ul>
<li><p>Reference indices: <a class="reference external" href="http://s2geometry.io/">S2 Geometry</a> ,
<a class="reference external" href="https://h3geo.org/">H3</a></p></li>
</ul>
</li>
<li><p>Compare the diversity of inputs (e.g., climate, forest cover) to
compute the probability of the observed conditions relative to the
space of possible environments</p></li>
<li><p>Reward model improvements relative to simulation complexity</p>
<ul>
<li><p>Occam’s razor is given by the term 2^(−K(µ)), which weights the
models’ performance in each environment inversely proportional to
its complexity [Legg07; <a class="reference external" href="https://arxiv.org/abs/0712.3329">https://arxiv.org/abs/0712.3329</a>]</p></li>
</ul>
</li>
<li><p>Small sample ensembles are difficult to bootstrap into a useful
learning loop.</p>
<ul>
<li><p>The Optometrist algorithm [Baltz17] leverages human interpretation
to guide parameter search within a fixed simulation budget [ie.
<a class="reference external" href="https://openai.com/blog/deep-reinforcement-learning-from-human-preferences/">Learning from human
preferences</a>]</p></li>
<li><p>This approach is particularly aligned with existing international
land sector reporting frameworks, which rely heavily on expert
opinion and critique.</p></li>
</ul>
</li>
</ul>
</section>
</section>
</article>
<footer class="prev-next-footer">
<div class="prev-next-area">
<a class="left-prev"
href="Conclusion.html"
title="previous page">
<i class="fa-solid fa-angle-left"></i>
<div class="prev-next-info">
<p class="prev-next-subtitle">previous</p>
<p class="prev-next-title">Conclusion</p>
</div>
</a>
<a class="right-next"
href="Reports.html"
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Annex of FLINT Analysis</p>
</div>
<i class="fa-solid fa-angle-right"></i>
</a>
</div>
</footer>
</div>
<div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
<div class="sidebar-secondary-item">
<div class="page-toc tocsection onthispage">
<i class="fa-solid fa-list"></i> Contents
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#summary">Summary:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#components">Components:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#system-control-flow">System control flow:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#prior-art">Prior art:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#data-requirements">Data requirements:</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#ensemble-assessment">Ensemble assessment:</a></li>
</ul>
</nav></div>
</div></div>
</div>
<footer class="bd-footer-content">
<div class="bd-footer-content__inner container">
<div class="footer-item">
<p class="component-author">
By Amarachi Iheanacho
</p>
</div>
<div class="footer-item">
<p class="copyright">
© Copyright 2022, moja global.
<br/>
</p>
</div>
<div class="footer-item">
</div>
<div class="footer-item">
</div>
</div>
</footer>
</main>
</div>
</div>
<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="_static/scripts/bootstrap.js?digest=5b4479735964841361fd"></script>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd"></script>
<footer class="bd-footer">
</footer>
</body>
</html>