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/set-up.Rmd:
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1 | ---
2 | title: "Set-up"
3 | output:
4 | html_document:
5 | toc: true
6 | include:
7 | before_body: header.html
8 | after_body: footer.html
9 | ---
10 |
11 | ```{r setup, include=FALSE}
12 | knitr::opts_chunk$set(echo = TRUE)
13 | ```
14 |
15 | The following will walk you through installing R, RStudio, and GitHub Desktop. Though the instructions are long, it hopefully will not take you long to get set up. You will need admin access on your laptop.
16 |
17 | If you run into trouble, you can post in the comment section at the bottom. Please, help each other out in the comments if you can solve someone's installation issues. I will check in periodically and try to help too.
18 |
19 | ## Get an account on GitHub
20 |
21 | If you don't already have an account on GitHub, go to [github.com](github.com) and click the "sign up" link near upper right
22 | of the page. It is pretty self-explanatory. Go ahead and get a **free** account.
23 |
24 | The free GitHub account does not have private repositories. Everything is public and viewable. You can upgrade (for money) and get private repositories. Or _if you are a student_, you can get private repositories from GitHub for free. Go to [https://education.github.com/pack](https://education.github.com/pack) to sign up for your free student pack. You will need to upload proof that you are a student or faculty.
25 |
26 | ## Install GitHub Desktop (Windows and Mac users)
27 |
28 | *Windows users: GitHub Desktop is only available for 64-bit*
29 |
30 | 1. Go to [desktop.github.com](https://desktop.github.com/) and install.
31 | 2. Open GitHub Desktop, go to 'GitHub Desktop > Preferences' menu.
32 | 3. Under 'Accounts', sign into your GitHub account.
33 | 3. Under 'Git', enter your name (or initials) and the email you used for your GitHub account.
34 |
35 | Linux users can install Git and interact with GitHub though RStudio. GitHub Desktop is not essential for the course, however it is a standard R Workflow that I will be demonstrating.
36 |
37 | You should not need to install Git as that comes with GitHub Desktop, however it is possible that you will need to to interact with RStudio. If so, download and install Git from [git-scm](https://git-scm.com/downloads).
38 |
39 | ## Install R and RStudio
40 |
41 | * **R:** Make sure you have the latest version of R.
42 | Go to [https://cran.r-project.org/](https://cran.r-project.org/) and find the download link for your computer system.
43 |
44 | * **RStudio:** Install the latest version of RStudio. Get it from [https://www.rstudio.com/products/rstudio/download](https://www.rstudio.com/products/rstudio/download) and install the appropriate one for your OS.
45 |
46 | ## Set up RStudio to use Git
47 |
48 | 1. Open RStudio
49 | 2. Go to Global Options (from the Tools menu)
50 | 3. Click Git/SVN
51 | 4. Click Enable version control interface for RStudio projects
52 |
53 | Linux users will need to install Git for this to work.
54 |
55 | Windows/Mac users: Git comes with GitHub Desktop. If RStudio complains that it cannot find Git: 1. Make sure you set your Preferences in GitHub Desktop. 2. Download and install Git from from [git-scm](https://git-scm.com/downloads).
56 |
57 | ## Install R packages
58 |
59 | *If you get an error saying that the repository cannot be found: 1. Check that you are online. 2. Run `chooseCRANmirror()` and choose a mirror. 3. Repeat until you find a mirror that has the up to date packages.*
60 |
61 | From the command line in R Studio
62 |
63 | 1. **bookdown:** package. Enter the following code at the command line (`>`).
64 |
65 | ```{r get-bd, eval=FALSE}
66 | install.packages("devtools")
67 | devtools::install_github("rstudio/bookdown")
68 | ```
69 |
70 | 2. Install **other packages** that we are going to be need. I have created a package on GitHub that will install the packages you need. This will probably take **awhile** as the first time you do it, many packages will be loaded.
71 |
72 | ```{r get-packages, eval=FALSE}
73 | devtools::install_github("RVerse-Tutorials/RWorkflowsetup")
74 | ```
75 |
76 | 3. If you do not have LaTeX installed, you can install the tinytex package. Run these commands. This will allow you to make PDF files from R Markdown files.
77 |
78 | ```
79 | install.packages('tinytex')
80 | tinytex::install_tinytex()
81 | ```
82 |
83 | ## Create a workshop folder
84 |
85 | Create a folder/directory on your computer for the workshop materials. You can create it anywhere you wish. Name it `RWorkflow` just so we all use the same folder name for the workshop.
86 |
87 | ## Disqus forum
88 |
89 | I have added a Disqus forum to the website. [Create an account](https://disqus.com/) if you would like to be able to add comments/questions. This will allow people to pose questions to the group and allow me (and others) to answer.
90 |
91 | ## Downloading repositories
92 |
93 | **In case we do not have internet access, I will provide the files on a thumb drive also.**
94 |
95 | You will need to fork (copy) repositories from [RVerse-Tutorials](https://github.com/RVerse-Tutorials) for many of the labs. You can also download zip files.
96 |
97 | 1. Log into GitHub.
98 | 2. Go to [RVerse-Tutorials/Test](https://github.com/RVerse-Tutorials/Test).
99 | 3. Click 'Fork' in the upper right corner of the repository. This will create a copy of Test-Website in your GitHub account.
100 | 4. Open RStudio. Click File > New Project > Version Control
101 | 5. Paste in the url of the repository you are copying---the **forked** repository in your GitHub account. For example, `https://github.com/
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/site_libs/font-awesome-5.0.13/css/fa-svg-with-js.css:
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1 | /*!
2 | * Font Awesome Free 5.0.13 by @fontawesome - https://fontawesome.com
3 | * License - https://fontawesome.com/license (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
4 | */
5 | svg:not(:root).svg-inline--fa {
6 | overflow: visible; }
7 |
8 | .svg-inline--fa {
9 | display: inline-block;
10 | font-size: inherit;
11 | height: 1em;
12 | overflow: visible;
13 | vertical-align: -.125em; }
14 | .svg-inline--fa.fa-lg {
15 | vertical-align: -.225em; }
16 | .svg-inline--fa.fa-w-1 {
17 | width: 0.0625em; }
18 | .svg-inline--fa.fa-w-2 {
19 | width: 0.125em; }
20 | .svg-inline--fa.fa-w-3 {
21 | width: 0.1875em; }
22 | .svg-inline--fa.fa-w-4 {
23 | width: 0.25em; }
24 | .svg-inline--fa.fa-w-5 {
25 | width: 0.3125em; }
26 | .svg-inline--fa.fa-w-6 {
27 | width: 0.375em; }
28 | .svg-inline--fa.fa-w-7 {
29 | width: 0.4375em; }
30 | .svg-inline--fa.fa-w-8 {
31 | width: 0.5em; }
32 | .svg-inline--fa.fa-w-9 {
33 | width: 0.5625em; }
34 | .svg-inline--fa.fa-w-10 {
35 | width: 0.625em; }
36 | .svg-inline--fa.fa-w-11 {
37 | width: 0.6875em; }
38 | .svg-inline--fa.fa-w-12 {
39 | width: 0.75em; }
40 | .svg-inline--fa.fa-w-13 {
41 | width: 0.8125em; }
42 | .svg-inline--fa.fa-w-14 {
43 | width: 0.875em; }
44 | .svg-inline--fa.fa-w-15 {
45 | width: 0.9375em; }
46 | .svg-inline--fa.fa-w-16 {
47 | width: 1em; }
48 | .svg-inline--fa.fa-w-17 {
49 | width: 1.0625em; }
50 | .svg-inline--fa.fa-w-18 {
51 | width: 1.125em; }
52 | .svg-inline--fa.fa-w-19 {
53 | width: 1.1875em; }
54 | .svg-inline--fa.fa-w-20 {
55 | width: 1.25em; }
56 | .svg-inline--fa.fa-pull-left {
57 | margin-right: .3em;
58 | width: auto; }
59 | .svg-inline--fa.fa-pull-right {
60 | margin-left: .3em;
61 | width: auto; }
62 | .svg-inline--fa.fa-border {
63 | height: 1.5em; }
64 | .svg-inline--fa.fa-li {
65 | width: 2em; }
66 | .svg-inline--fa.fa-fw {
67 | width: 1.25em; }
68 |
69 | .fa-layers svg.svg-inline--fa {
70 | bottom: 0;
71 | left: 0;
72 | margin: auto;
73 | position: absolute;
74 | right: 0;
75 | top: 0; }
76 |
77 | .fa-layers {
78 | display: inline-block;
79 | height: 1em;
80 | position: relative;
81 | text-align: center;
82 | vertical-align: -.125em;
83 | width: 1em; }
84 | .fa-layers svg.svg-inline--fa {
85 | -webkit-transform-origin: center center;
86 | transform-origin: center center; }
87 |
88 | .fa-layers-text, .fa-layers-counter {
89 | display: inline-block;
90 | position: absolute;
91 | text-align: center; }
92 |
93 | .fa-layers-text {
94 | left: 50%;
95 | top: 50%;
96 | -webkit-transform: translate(-50%, -50%);
97 | transform: translate(-50%, -50%);
98 | -webkit-transform-origin: center center;
99 | transform-origin: center center; }
100 |
101 | .fa-layers-counter {
102 | background-color: #ff253a;
103 | border-radius: 1em;
104 | -webkit-box-sizing: border-box;
105 | box-sizing: border-box;
106 | color: #fff;
107 | height: 1.5em;
108 | line-height: 1;
109 | max-width: 5em;
110 | min-width: 1.5em;
111 | overflow: hidden;
112 | padding: .25em;
113 | right: 0;
114 | text-overflow: ellipsis;
115 | top: 0;
116 | -webkit-transform: scale(0.25);
117 | transform: scale(0.25);
118 | -webkit-transform-origin: top right;
119 | transform-origin: top right; }
120 |
121 | .fa-layers-bottom-right {
122 | bottom: 0;
123 | right: 0;
124 | top: auto;
125 | -webkit-transform: scale(0.25);
126 | transform: scale(0.25);
127 | -webkit-transform-origin: bottom right;
128 | transform-origin: bottom right; }
129 |
130 | .fa-layers-bottom-left {
131 | bottom: 0;
132 | left: 0;
133 | right: auto;
134 | top: auto;
135 | -webkit-transform: scale(0.25);
136 | transform: scale(0.25);
137 | -webkit-transform-origin: bottom left;
138 | transform-origin: bottom left; }
139 |
140 | .fa-layers-top-right {
141 | right: 0;
142 | top: 0;
143 | -webkit-transform: scale(0.25);
144 | transform: scale(0.25);
145 | -webkit-transform-origin: top right;
146 | transform-origin: top right; }
147 |
148 | .fa-layers-top-left {
149 | left: 0;
150 | right: auto;
151 | top: 0;
152 | -webkit-transform: scale(0.25);
153 | transform: scale(0.25);
154 | -webkit-transform-origin: top left;
155 | transform-origin: top left; }
156 |
157 | .fa-lg {
158 | font-size: 1.33333em;
159 | line-height: 0.75em;
160 | vertical-align: -.0667em; }
161 |
162 | .fa-xs {
163 | font-size: .75em; }
164 |
165 | .fa-sm {
166 | font-size: .875em; }
167 |
168 | .fa-1x {
169 | font-size: 1em; }
170 |
171 | .fa-2x {
172 | font-size: 2em; }
173 |
174 | .fa-3x {
175 | font-size: 3em; }
176 |
177 | .fa-4x {
178 | font-size: 4em; }
179 |
180 | .fa-5x {
181 | font-size: 5em; }
182 |
183 | .fa-6x {
184 | font-size: 6em; }
185 |
186 | .fa-7x {
187 | font-size: 7em; }
188 |
189 | .fa-8x {
190 | font-size: 8em; }
191 |
192 | .fa-9x {
193 | font-size: 9em; }
194 |
195 | .fa-10x {
196 | font-size: 10em; }
197 |
198 | .fa-fw {
199 | text-align: center;
200 | width: 1.25em; }
201 |
202 | .fa-ul {
203 | list-style-type: none;
204 | margin-left: 2.5em;
205 | padding-left: 0; }
206 | .fa-ul > li {
207 | position: relative; }
208 |
209 | .fa-li {
210 | left: -2em;
211 | position: absolute;
212 | text-align: center;
213 | width: 2em;
214 | line-height: inherit; }
215 |
216 | .fa-border {
217 | border: solid 0.08em #eee;
218 | border-radius: .1em;
219 | padding: .2em .25em .15em; }
220 |
221 | .fa-pull-left {
222 | float: left; }
223 |
224 | .fa-pull-right {
225 | float: right; }
226 |
227 | .fa.fa-pull-left,
228 | .fas.fa-pull-left,
229 | .far.fa-pull-left,
230 | .fal.fa-pull-left,
231 | .fab.fa-pull-left {
232 | margin-right: .3em; }
233 |
234 | .fa.fa-pull-right,
235 | .fas.fa-pull-right,
236 | .far.fa-pull-right,
237 | .fal.fa-pull-right,
238 | .fab.fa-pull-right {
239 | margin-left: .3em; }
240 |
241 | .fa-spin {
242 | -webkit-animation: fa-spin 2s infinite linear;
243 | animation: fa-spin 2s infinite linear; }
244 |
245 | .fa-pulse {
246 | -webkit-animation: fa-spin 1s infinite steps(8);
247 | animation: fa-spin 1s infinite steps(8); }
248 |
249 | @-webkit-keyframes fa-spin {
250 | 0% {
251 | -webkit-transform: rotate(0deg);
252 | transform: rotate(0deg); }
253 | 100% {
254 | -webkit-transform: rotate(360deg);
255 | transform: rotate(360deg); } }
256 |
257 | @keyframes fa-spin {
258 | 0% {
259 | -webkit-transform: rotate(0deg);
260 | transform: rotate(0deg); }
261 | 100% {
262 | -webkit-transform: rotate(360deg);
263 | transform: rotate(360deg); } }
264 |
265 | .fa-rotate-90 {
266 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=1)";
267 | -webkit-transform: rotate(90deg);
268 | transform: rotate(90deg); }
269 |
270 | .fa-rotate-180 {
271 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2)";
272 | -webkit-transform: rotate(180deg);
273 | transform: rotate(180deg); }
274 |
275 | .fa-rotate-270 {
276 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=3)";
277 | -webkit-transform: rotate(270deg);
278 | transform: rotate(270deg); }
279 |
280 | .fa-flip-horizontal {
281 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1)";
282 | -webkit-transform: scale(-1, 1);
283 | transform: scale(-1, 1); }
284 |
285 | .fa-flip-vertical {
286 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1)";
287 | -webkit-transform: scale(1, -1);
288 | transform: scale(1, -1); }
289 |
290 | .fa-flip-horizontal.fa-flip-vertical {
291 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1)";
292 | -webkit-transform: scale(-1, -1);
293 | transform: scale(-1, -1); }
294 |
295 | :root .fa-rotate-90,
296 | :root .fa-rotate-180,
297 | :root .fa-rotate-270,
298 | :root .fa-flip-horizontal,
299 | :root .fa-flip-vertical {
300 | -webkit-filter: none;
301 | filter: none; }
302 |
303 | .fa-stack {
304 | display: inline-block;
305 | height: 2em;
306 | position: relative;
307 | width: 2em; }
308 |
309 | .fa-stack-1x,
310 | .fa-stack-2x {
311 | bottom: 0;
312 | left: 0;
313 | margin: auto;
314 | position: absolute;
315 | right: 0;
316 | top: 0; }
317 |
318 | .svg-inline--fa.fa-stack-1x {
319 | height: 1em;
320 | width: 1em; }
321 |
322 | .svg-inline--fa.fa-stack-2x {
323 | height: 2em;
324 | width: 2em; }
325 |
326 | .fa-inverse {
327 | color: #fff; }
328 |
329 | .sr-only {
330 | border: 0;
331 | clip: rect(0, 0, 0, 0);
332 | height: 1px;
333 | margin: -1px;
334 | overflow: hidden;
335 | padding: 0;
336 | position: absolute;
337 | width: 1px; }
338 |
339 | .sr-only-focusable:active, .sr-only-focusable:focus {
340 | clip: auto;
341 | height: auto;
342 | margin: 0;
343 | overflow: visible;
344 | position: static;
345 | width: auto; }
346 |
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258 | Welcome
251 |These are the Rmd files for the Welcome website:
252 |https://rverse-tutorials.github.io/Fish-Forecast-Training-Course/
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344 | Contact
340 | 341 |Eli Holmes
345 |National Marine Fisheries Service
346 |Northwest Fisheries Science Center
347 |2725 Montlake Blvd East
348 |Seattle, WA
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1 | /*! jQuery UI - v1.11.4 - 2016-01-05
2 | * http://jqueryui.com
3 | * Copyright jQuery Foundation and other contributors; Licensed MIT */
4 |
5 | .ui-helper-hidden{display:none}.ui-helper-hidden-accessible{border:0;clip:rect(0 0 0 0);height:1px;margin:-1px;overflow:hidden;padding:0;position:absolute;width:1px}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none}.ui-helper-clearfix:before,.ui-helper-clearfix:after{content:"";display:table;border-collapse:collapse}.ui-helper-clearfix:after{clear:both}.ui-helper-clearfix{min-height:0}.ui-helper-zfix{width:100%;height:100%;top:0;left:0;position:absolute;opacity:0;filter:Alpha(Opacity=0)}.ui-front{z-index:100}.ui-state-disabled{cursor:default!important}.ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat}.ui-widget-overlay{position:fixed;top:0;left:0;width:100%;height:100%}.ui-draggable-handle{-ms-touch-action:none;touch-action:none}.ui-resizable{position:relative}.ui-resizable-handle{position:absolute;font-size:0.1px;display:block;-ms-touch-action:none;touch-action:none}.ui-resizable-disabled .ui-resizable-handle,.ui-resizable-autohide 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344 | Data
340 | 341 |We will be modeling and forecasting catch data however you can use the techniques we will learn on any regularly spaced time data.
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389 | Data Format
348 |Your data should be in a simple csv (comma-separated) file with time (year, day, month, etc) and value:
349 |Year, metric.tons
350 | 1964, 5449.2
351 | 1965, 4263.5
352 | 1966, 5146.4
353 | 1967, 7271.5
354 | 1968, 6352.5If you have different locations or species, add that as a new column.
356 |Year, metric.tons, species
357 | 1964, 5449.2, Anchovy
358 | 1965, 4263.5, Anchovy
359 | 1966, 5146.4, Anchovy
360 | 1967, 7271.5, Anchovy
361 | 1968, 6352.5, Anchovy
362 | 1964, 5449.2, Sardine
363 | 1965, 4263.5, Sardine
364 | 1966, 5146.4, Sardine
365 | 1967, 7271.5, Sardine
366 | 1968, 6352.5, SardineHere is an example with species and location.
368 |Year, metric.tons, species, region
369 | 1964, 5449.2, Anchovy, North
370 | 1965, 4263.5, Anchovy, North
371 | 1966, 5146.4, Anchovy, North
372 | 1967, 7271.5, Anchovy, North
373 | 1968, 6352.5, Anchovy, North
374 | 1964, 5449.2, Sardine, North
375 | 1965, 4263.5, Sardine, North
376 | 1966, 5146.4, Sardine, North
377 | 1967, 7271.5, Sardine, North
378 | 1968, 6352.5, Sardine, North
379 | 1964, 5449.2, Sardine, South
380 | 1965, 4263.5, Sardine, South
381 | 1966, 5146.4, Sardine, South
382 | 1967, 7271.5, Sardine, South
383 | 1968, 6352.5, Sardine, South
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/nextsteps.html:
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344 | Fish Forecast Training Course
340 | 341 |Welcome to the training programme on “Fish-catch Time-Series Forecasting with R” organized by International Training Centre for Operational Oceanography (ITCOocean) ESSO-Indian National Centre for Ocean Information Services(INCOIS), Hyderabad, India. Course Announcement
345 |Instructor: Dr. Eli Holmes, NOAA Fisheries Service, Northwest Fisheries Science Center, Seattle, WA, USA.
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366 | Course Description
348 |
This short course will be divided into a morning session on creating forecasting models for catch data and an afternoon session on Report-writing and Code documentation with R.
350 |The course will consist of short lectures and many practical labs where you will work with R to model data and prepare forecasts. You are encouraged to bring your own time-series data, for example yearly or monthly catch or count data, so that you can begin to model it during the course.
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In the afternoon, you will learn to write reports and websites with R and R Markdown so that you can easily share your work and document your work. You will learn how to easily prepare online books, reports and websites that integrate R and text.
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1 | /*!
2 | * Font Awesome Free 5.0.13 by @fontawesome - https://fontawesome.com
3 | * License - https://fontawesome.com/license (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
4 | */
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y"],["object-group","far",null],["object-ungroup","far",null],["sticky-note-o","far","sticky-note"],["cc-jcb","fab",null],["cc-diners-club","fab",null],["clone","far",null],["hourglass-o","far","hourglass"],["hourglass-1",null,"hourglass-start"],["hourglass-2",null,"hourglass-half"],["hourglass-3",null,"hourglass-end"],["hand-rock-o","far","hand-rock"],["hand-grab-o","far","hand-rock"],["hand-paper-o","far","hand-paper"],["hand-stop-o","far","hand-paper"],["hand-scissors-o","far","hand-scissors"],["hand-lizard-o","far","hand-lizard"],["hand-spock-o","far","hand-spock"],["hand-pointer-o","far","hand-pointer"],["hand-peace-o","far","hand-peace"],["registered","far",null],["creative-commons","fab",null],["gg","fab",null],["gg-circle","fab",null],["tripadvisor","fab",null],["odnoklassniki","fab",null],["odnoklassniki-square","fab",null],["get-pocket","fab",null],["wikipedia-w","fab",null],["safari","fab",null],["chrome","fab",null],["firefox","fab",null],["opera","fab",null],["internet-explorer","fab",null],["television",null,"tv"],["contao","fab",null],["500px","fab",null],["amazon","fab",null],["calendar-plus-o","far","calendar-plus"],["calendar-minus-o","far","calendar-minus"],["calendar-times-o","far","calendar-times"],["calendar-check-o","far","calendar-check"],["map-o","far","map"],["commenting","far","comment-dots"],["commenting-o","far","comment-dots"],["houzz","fab",null],["vimeo","fab","vimeo-v"],["black-tie","fab",null],["fonticons","fab",null],["reddit-alien","fab",null],["edge","fab",null],["credit-card-alt",null,"credit-card"],["codiepie","fab",null],["modx","fab",null],["fort-awesome","fab",null],["usb","fab",null],["product-hunt","fab",null],["mixcloud","fab",null],["scribd","fab",null],["pause-circle-o","far","pause-circle"],["stop-circle-o","far","stop-circle"],["bluetooth","fab",null],["bluetooth-b","fab",null],["gitlab","fab",null],["wpbeginner","fab",null],["wpforms","fab",null],["envira","fab",null],["wheelchair-alt","fab","accessible-icon"],["question-circle-o","far","question-circle"],["volume-control-phone",null,"phone-volume"],["asl-interpreting",null,"american-sign-language-interpreting"],["deafness",null,"deaf"],["hard-of-hearing",null,"deaf"],["glide","fab",null],["glide-g","fab",null],["signing",null,"sign-language"],["viadeo","fab",null],["viadeo-square","fab",null],["snapchat","fab",null],["snapchat-ghost","fab",null],["snapchat-square","fab",null],["pied-piper","fab",null],["first-order","fab",null],["yoast","fab",null],["themeisle","fab",null],["google-plus-official","fab","google-plus"],["google-plus-circle","fab","google-plus"],["font-awesome","fab",null],["fa","fab","font-awesome"],["handshake-o","far","handshake"],["envelope-open-o","far","envelope-open"],["linode","fab",null],["address-book-o","far","address-book"],["vcard",null,"address-card"],["address-card-o","far","address-card"],["vcard-o","far","address-card"],["user-circle-o","far","user-circle"],["user-o","far","user"],["id-badge","far",null],["drivers-license",null,"id-card"],["id-card-o","far","id-card"],["drivers-license-o","far","id-card"],["quora","fab",null],["free-code-camp","fab",null],["telegram","fab",null],["thermometer-4",null,"thermometer-full"],["thermometer",null,"thermometer-full"],["thermometer-3",null,"thermometer-three-quarters"],["thermometer-2",null,"thermometer-half"],["thermometer-1",null,"thermometer-quarter"],["thermometer-0",null,"thermometer-empty"],["bathtub",null,"bath"],["s15",null,"bath"],["window-maximize","far",null],["window-restore","far",null],["times-rectangle",null,"window-close"],["window-close-o","far","window-close"],["times-rectangle-o","far","window-close"],["bandcamp","fab",null],["grav","fab",null],["etsy","fab",null],["imdb","fab",null],["ravelry","fab",null],["eercast","fab","sellcast"],["snowflake-o","far","snowflake"],["superpowers","fab",null],["wpexplorer","fab",null],["spotify","fab",null]];return 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344 | Continuing your learning
340 | 341 |Here are resources for continuing your learning of the topics that you studied this week:
345 |
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354 | Intro to R
347 |-
348 |
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Data Camp free tutorial. Takes about 4 hours.
350 | You can also learn R straight from within R using the swirl package. This doesn’t require internet access except to install the package.
351 | Basic R introduction from ComputerWorld.
352 |
355 |
361 | More R Workflow
356 |-
357 |
Software Carpenter has a course that covers some of more advanced topics I did not cover on R workflow: data wrangling with dplyr, tidyverse, and more on RStudio projects. Reproducible Research with R
358 | Eric Anderson produced a couple online courses on R workflow while with NOAA Fisheries. R Reproducible Research 2015 and Reproducible Research 2017
359 |
362 |
365 | Forecasting and Exponential Smoothing Models
363 |Rob J Hyndman (lead on the forecast package) and George Athanasopoulos have an excellent online text on practical forecasting and exponential smoothing.
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373 | Shiny Apps
367 |Start with RStudio’s online tutorial for shiny apps.
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344 | Notes
340 | 341 |
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362 | Thursday
346 |For building a package with roxygen documentation (the part that makes the help files for you), you need to tell RStudio to build that documentation when you click ‘Build and Reload’.
347 |Go to Tools > Project Options > Build Tools Then click the box that says the build documentation with roxygen. A pop-up window should appear. Click the box at the bottom that says to remake documentation when you click ‘Build and Reload’.
348 |349 |
Seasonal data. If you have seasonal data that you would like to analyze, please put in this format:
350 | Year Month metric.tons
351 | 2018 1 1
352 | 2018 2 2
353 | 2018 3 3
354 | ...
355 | 2019 1 4
356 | 2019 2 6
357 | 2019 3 NARead in with this code:
359 |test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
360 | save(test, file="test.RData")
363 |
371 | Wednesday
364 |To save data in R to a .csv file use the following:
365 |write.csv(landings, file="test.csv", row.names=FALSE, quote=FALSE)This works for data.frames, like landings, and also matrices:
367 |mat <- matrix(rnorm(10),5,2)
368 | colnames(mat) <- c("number 1", "number 2")
369 | write.csv(landings, file="test.csv", row.names=FALSE, quote=FALSE)
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433 | Tuesday
373 |The bookdown-demo repository has been edited so that it does not try to make a PDF. If you want that, there are instructions in the README.md file.
374 |375 |
Read in simple csv file named test.csv that looks like this
Year Species metric.tons
377 | 1 2018 Fish1 1
378 | 2 2019 Fish1 2
379 | 3 2018 Fish2 3
380 | 4 2019 Fish2 4
381 | 5 2018 Fish3 6
382 | 6 2019 Fish4 NAwith this code:
384 |test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
385 | save(test, file="test.RData")387 |
Read in a file where the data are in columns. If your data (test.csv) look like this with each species (or site) across the columns:
388 |Year,Anchovy,Sardine,Chub mackerel,Horse mackerel,Mackerel,Jack Mackerel
389 | 1964,5449.2,12984.4,1720.7,4022.4,NA,NA
390 | 1965,4263.5,10611.1,1278.5,4158.3,NA,NA
391 | 1966,5146.4,11437.8,802.6,3012.1,NA,NAUse this code:
393 |library(reshape2)
394 | test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
395 | melt(test, id="Year", value.name="metric.tons", variable.name="Species")
396 | save(test, file="test.RData")If your data also have, say, a month (or qtr) column, use this code:
398 |library(reshape2)
399 | test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
400 | melt(test, id=c("Year","Month"), value.name="metric.tons", variable.name="Species")
401 | save(test, file="test.RData")403 |
If you have a response variable and multiple explanatory variables:
404 |Year, Anchovy, SST, Mackerel
405 | 1964, 5449.2, 24.4, 1720.7
406 | 1965, 4263.5, 30.1, 1278.5
407 | 1966, 5146.4, 23.8, 802.6Use this code:
409 |test <- read.csv("Data/test.csv", stringsAsFactors = FALSE)
410 | save(test, file="test.RData")Use this lm() model (or gam() etc):
fit <- lm(Anchovy ~ SST + Mackerel, data=test)414 |
What is a list? It is a object with multiple other types of objects ‘tied’ together.
415 |a <- list(ar=c(.8,.3), name="model", years=1:10)
416 | a## $ar
418 | ## [1] 0.8 0.3
419 | ##
420 | ## $name
421 | ## [1] "model"
422 | ##
423 | ## $years
424 | ## [1] 1 2 3 4 5 6 7 8 9 10You can now reference the different objects in a.
a$ar## [1] 0.8 0.3a$name## [1] "model"431 |
Why is the arima.sim throwing an error sometimes? You must specify a stationary model and if you just randomly chose the \(\beta\)’s (AR parameters) and \(\theta\)’s (MA parameters) then you might be specifying a non-stationary model.
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458 | Monday
435 |Please install the rmarkdown package. I forgot to include that.
436 |install.packages("rmarkdown")438 |
If you do not have LaTeX installed, you can install the tinytex package. Run these commands. This will allow you to make PDF files from R Markdown files. Some of you installed tinytex, but you need to run the 2nd command also to install LiveTeX.
439 |install.packages('tinytex')
440 | tinytex::install_tinytex()442 |
If your get an error saying package or repository unavailable when you are trying to install packages, try the following:
443 |-
444 |
- Make sure you are online. 445 |
- Run
chooseCRANmirror()from the command line. Pick any mirror.
446 | - Try installing package again. Repeat with a different mirror if it doesn’t work. 447 |
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1 | /*!
2 | * jQuery UI CSS Framework 1.11.4
3 | * http://jqueryui.com
4 | *
5 | * Copyright jQuery Foundation and other contributors
6 | * Released under the MIT license.
7 | * http://jquery.org/license
8 | *
9 | * http://api.jqueryui.com/category/theming/
10 | */
11 |
12 | /* Layout helpers
13 | ----------------------------------*/
14 | .ui-helper-hidden {
15 | display: none;
16 | }
17 | .ui-helper-hidden-accessible {
18 | border: 0;
19 | clip: rect(0 0 0 0);
20 | height: 1px;
21 | margin: -1px;
22 | overflow: hidden;
23 | padding: 0;
24 | position: absolute;
25 | width: 1px;
26 | }
27 | .ui-helper-reset {
28 | margin: 0;
29 | padding: 0;
30 | border: 0;
31 | outline: 0;
32 | line-height: 1.3;
33 | text-decoration: none;
34 | font-size: 100%;
35 | list-style: none;
36 | }
37 | .ui-helper-clearfix:before,
38 | .ui-helper-clearfix:after {
39 | content: "";
40 | display: table;
41 | border-collapse: collapse;
42 | }
43 | .ui-helper-clearfix:after {
44 | clear: both;
45 | }
46 | .ui-helper-clearfix {
47 | min-height: 0; /* support: IE7 */
48 | }
49 | .ui-helper-zfix {
50 | width: 100%;
51 | height: 100%;
52 | top: 0;
53 | left: 0;
54 | position: absolute;
55 | opacity: 0;
56 | filter:Alpha(Opacity=0); /* support: IE8 */
57 | }
58 |
59 | .ui-front {
60 | z-index: 100;
61 | }
62 |
63 |
64 | /* Interaction Cues
65 | ----------------------------------*/
66 | .ui-state-disabled {
67 | cursor: default !important;
68 | }
69 |
70 |
71 | /* Icons
72 | ----------------------------------*/
73 |
74 | /* states and images */
75 | .ui-icon {
76 | display: block;
77 | text-indent: -99999px;
78 | overflow: hidden;
79 | background-repeat: no-repeat;
80 | }
81 |
82 |
83 | /* Misc visuals
84 | ----------------------------------*/
85 |
86 | /* Overlays */
87 | .ui-widget-overlay {
88 | position: fixed;
89 | top: 0;
90 | left: 0;
91 | width: 100%;
92 | height: 100%;
93 | }
94 | .ui-draggable-handle {
95 | -ms-touch-action: none;
96 | touch-action: none;
97 | }
98 | .ui-resizable {
99 | position: relative;
100 | }
101 | .ui-resizable-handle {
102 | position: absolute;
103 | font-size: 0.1px;
104 | display: block;
105 | -ms-touch-action: none;
106 | touch-action: none;
107 | }
108 | .ui-resizable-disabled .ui-resizable-handle,
109 | .ui-resizable-autohide .ui-resizable-handle {
110 | display: none;
111 | }
112 | .ui-resizable-n {
113 | cursor: n-resize;
114 | height: 7px;
115 | width: 100%;
116 | top: -5px;
117 | left: 0;
118 | }
119 | .ui-resizable-s {
120 | cursor: s-resize;
121 | height: 7px;
122 | width: 100%;
123 | bottom: -5px;
124 | left: 0;
125 | }
126 | .ui-resizable-e {
127 | cursor: e-resize;
128 | width: 7px;
129 | right: -5px;
130 | top: 0;
131 | height: 100%;
132 | }
133 | .ui-resizable-w {
134 | cursor: w-resize;
135 | width: 7px;
136 | left: -5px;
137 | top: 0;
138 | height: 100%;
139 | }
140 | .ui-resizable-se {
141 | cursor: se-resize;
142 | width: 12px;
143 | height: 12px;
144 | right: 1px;
145 | bottom: 1px;
146 | }
147 | .ui-resizable-sw {
148 | cursor: sw-resize;
149 | width: 9px;
150 | height: 9px;
151 | left: -5px;
152 | bottom: -5px;
153 | }
154 | .ui-resizable-nw {
155 | cursor: nw-resize;
156 | width: 9px;
157 | height: 9px;
158 | left: -5px;
159 | top: -5px;
160 | }
161 | .ui-resizable-ne {
162 | cursor: ne-resize;
163 | width: 9px;
164 | height: 9px;
165 | right: -5px;
166 | top: -5px;
167 | }
168 | .ui-selectable {
169 | -ms-touch-action: none;
170 | touch-action: none;
171 | }
172 | .ui-selectable-helper {
173 | position: absolute;
174 | z-index: 100;
175 | border: 1px dotted black;
176 | }
177 | .ui-sortable-handle {
178 | -ms-touch-action: none;
179 | touch-action: none;
180 | }
181 | .ui-accordion .ui-accordion-header {
182 | display: block;
183 | cursor: pointer;
184 | position: relative;
185 | margin: 2px 0 0 0;
186 | padding: .5em .5em .5em .7em;
187 | min-height: 0; /* support: IE7 */
188 | font-size: 100%;
189 | }
190 | .ui-accordion .ui-accordion-icons {
191 | padding-left: 2.2em;
192 | }
193 | .ui-accordion .ui-accordion-icons .ui-accordion-icons {
194 | padding-left: 2.2em;
195 | }
196 | .ui-accordion .ui-accordion-header .ui-accordion-header-icon {
197 | position: absolute;
198 | left: .5em;
199 | top: 50%;
200 | margin-top: -8px;
201 | }
202 | .ui-accordion .ui-accordion-content {
203 | padding: 1em 2.2em;
204 | border-top: 0;
205 | overflow: auto;
206 | }
207 | .ui-autocomplete {
208 | position: absolute;
209 | top: 0;
210 | left: 0;
211 | cursor: default;
212 | }
213 | .ui-button {
214 | display: inline-block;
215 | position: relative;
216 | padding: 0;
217 | line-height: normal;
218 | margin-right: .1em;
219 | cursor: pointer;
220 | vertical-align: middle;
221 | text-align: center;
222 | overflow: visible; /* removes extra width in IE */
223 | }
224 | .ui-button,
225 | .ui-button:link,
226 | .ui-button:visited,
227 | .ui-button:hover,
228 | .ui-button:active {
229 | text-decoration: none;
230 | }
231 | /* to make room for the icon, a width needs to be set here */
232 | .ui-button-icon-only {
233 | width: 2.2em;
234 | }
235 | /* button elements seem to need a little more width */
236 | button.ui-button-icon-only {
237 | width: 2.4em;
238 | }
239 | .ui-button-icons-only {
240 | width: 3.4em;
241 | }
242 | button.ui-button-icons-only {
243 | width: 3.7em;
244 | }
245 |
246 | /* button text element */
247 | .ui-button .ui-button-text {
248 | display: block;
249 | line-height: normal;
250 | }
251 | .ui-button-text-only .ui-button-text {
252 | padding: .4em 1em;
253 | }
254 | .ui-button-icon-only .ui-button-text,
255 | .ui-button-icons-only .ui-button-text {
256 | padding: .4em;
257 | text-indent: -9999999px;
258 | }
259 | .ui-button-text-icon-primary .ui-button-text,
260 | .ui-button-text-icons .ui-button-text {
261 | padding: .4em 1em .4em 2.1em;
262 | }
263 | .ui-button-text-icon-secondary .ui-button-text,
264 | .ui-button-text-icons .ui-button-text {
265 | padding: .4em 2.1em .4em 1em;
266 | }
267 | .ui-button-text-icons .ui-button-text {
268 | padding-left: 2.1em;
269 | padding-right: 2.1em;
270 | }
271 | /* no icon support for input elements, provide padding by default */
272 | input.ui-button {
273 | padding: .4em 1em;
274 | }
275 |
276 | /* button icon element(s) */
277 | .ui-button-icon-only .ui-icon,
278 | .ui-button-text-icon-primary .ui-icon,
279 | .ui-button-text-icon-secondary .ui-icon,
280 | .ui-button-text-icons .ui-icon,
281 | .ui-button-icons-only .ui-icon {
282 | position: absolute;
283 | top: 50%;
284 | margin-top: -8px;
285 | }
286 | .ui-button-icon-only .ui-icon {
287 | left: 50%;
288 | margin-left: -8px;
289 | }
290 | .ui-button-text-icon-primary .ui-button-icon-primary,
291 | .ui-button-text-icons .ui-button-icon-primary,
292 | .ui-button-icons-only .ui-button-icon-primary {
293 | left: .5em;
294 | }
295 | .ui-button-text-icon-secondary .ui-button-icon-secondary,
296 | .ui-button-text-icons .ui-button-icon-secondary,
297 | .ui-button-icons-only .ui-button-icon-secondary {
298 | right: .5em;
299 | }
300 |
301 | /* button sets */
302 | .ui-buttonset {
303 | margin-right: 7px;
304 | }
305 | .ui-buttonset .ui-button {
306 | margin-left: 0;
307 | margin-right: -.3em;
308 | }
309 |
310 | /* workarounds */
311 | /* reset extra padding in Firefox, see h5bp.com/l */
312 | input.ui-button::-moz-focus-inner,
313 | button.ui-button::-moz-focus-inner {
314 | border: 0;
315 | padding: 0;
316 | }
317 | .ui-dialog {
318 | overflow: hidden;
319 | position: absolute;
320 | top: 0;
321 | left: 0;
322 | padding: .2em;
323 | outline: 0;
324 | }
325 | .ui-dialog .ui-dialog-titlebar {
326 | padding: .4em 1em;
327 | position: relative;
328 | }
329 | .ui-dialog .ui-dialog-title {
330 | float: left;
331 | margin: .1em 0;
332 | white-space: nowrap;
333 | width: 90%;
334 | overflow: hidden;
335 | text-overflow: ellipsis;
336 | }
337 | .ui-dialog .ui-dialog-titlebar-close {
338 | position: absolute;
339 | right: .3em;
340 | top: 50%;
341 | width: 20px;
342 | margin: -10px 0 0 0;
343 | padding: 1px;
344 | height: 20px;
345 | }
346 | .ui-dialog .ui-dialog-content {
347 | position: relative;
348 | border: 0;
349 | padding: .5em 1em;
350 | background: none;
351 | overflow: auto;
352 | }
353 | .ui-dialog .ui-dialog-buttonpane {
354 | text-align: left;
355 | border-width: 1px 0 0 0;
356 | background-image: none;
357 | margin-top: .5em;
358 | padding: .3em 1em .5em .4em;
359 | }
360 | .ui-dialog .ui-dialog-buttonpane .ui-dialog-buttonset {
361 | float: right;
362 | }
363 | .ui-dialog .ui-dialog-buttonpane button {
364 | margin: .5em .4em .5em 0;
365 | cursor: pointer;
366 | }
367 | .ui-dialog .ui-resizable-se {
368 | width: 12px;
369 | height: 12px;
370 | right: -5px;
371 | bottom: -5px;
372 | background-position: 16px 16px;
373 | }
374 | .ui-draggable .ui-dialog-titlebar {
375 | cursor: move;
376 | }
377 | .ui-menu {
378 | list-style: none;
379 | padding: 0;
380 | margin: 0;
381 | display: block;
382 | outline: none;
383 | }
384 | .ui-menu .ui-menu {
385 | position: absolute;
386 | }
387 | .ui-menu .ui-menu-item {
388 | position: relative;
389 | margin: 0;
390 | padding: 3px 1em 3px .4em;
391 | cursor: pointer;
392 | min-height: 0; /* support: IE7 */
393 | /* support: IE10, see #8844 */
394 | list-style-image: url("data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7");
395 | }
396 | .ui-menu .ui-menu-divider {
397 | margin: 5px 0;
398 | height: 0;
399 | font-size: 0;
400 | line-height: 0;
401 | border-width: 1px 0 0 0;
402 | }
403 | .ui-menu .ui-state-focus,
404 | .ui-menu .ui-state-active {
405 | margin: -1px;
406 | }
407 |
408 | /* icon support */
409 | .ui-menu-icons {
410 | position: relative;
411 | }
412 | .ui-menu-icons .ui-menu-item {
413 | padding-left: 2em;
414 | }
415 |
416 | /* left-aligned */
417 | .ui-menu .ui-icon {
418 | position: absolute;
419 | top: 0;
420 | bottom: 0;
421 | left: .2em;
422 | margin: auto 0;
423 | }
424 |
425 | /* right-aligned */
426 | .ui-menu .ui-menu-icon {
427 | left: auto;
428 | right: 0;
429 | }
430 | .ui-progressbar {
431 | height: 2em;
432 | text-align: left;
433 | overflow: hidden;
434 | }
435 | .ui-progressbar .ui-progressbar-value {
436 | margin: -1px;
437 | height: 100%;
438 | }
439 | .ui-progressbar .ui-progressbar-overlay {
440 | background: url("data:image/gif;base64,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");
441 | height: 100%;
442 | filter: alpha(opacity=25); /* support: IE8 */
443 | opacity: 0.25;
444 | }
445 | .ui-progressbar-indeterminate .ui-progressbar-value {
446 | background-image: none;
447 | }
448 | .ui-selectmenu-menu {
449 | padding: 0;
450 | margin: 0;
451 | position: absolute;
452 | top: 0;
453 | left: 0;
454 | display: none;
455 | }
456 | .ui-selectmenu-menu .ui-menu {
457 | overflow: auto;
458 | /* Support: IE7 */
459 | overflow-x: hidden;
460 | padding-bottom: 1px;
461 | }
462 | .ui-selectmenu-menu .ui-menu .ui-selectmenu-optgroup {
463 | font-size: 1em;
464 | font-weight: bold;
465 | line-height: 1.5;
466 | padding: 2px 0.4em;
467 | margin: 0.5em 0 0 0;
468 | height: auto;
469 | border: 0;
470 | }
471 | .ui-selectmenu-open {
472 | display: block;
473 | }
474 | .ui-selectmenu-button {
475 | display: inline-block;
476 | overflow: hidden;
477 | position: relative;
478 | text-decoration: none;
479 | cursor: pointer;
480 | }
481 | .ui-selectmenu-button span.ui-icon {
482 | right: 0.5em;
483 | left: auto;
484 | margin-top: -8px;
485 | position: absolute;
486 | top: 50%;
487 | }
488 | .ui-selectmenu-button span.ui-selectmenu-text {
489 | text-align: left;
490 | padding: 0.4em 2.1em 0.4em 1em;
491 | display: block;
492 | line-height: 1.4;
493 | overflow: hidden;
494 | text-overflow: ellipsis;
495 | white-space: nowrap;
496 | }
497 | .ui-slider {
498 | position: relative;
499 | text-align: left;
500 | }
501 | .ui-slider .ui-slider-handle {
502 | position: absolute;
503 | z-index: 2;
504 | width: 1.2em;
505 | height: 1.2em;
506 | cursor: default;
507 | -ms-touch-action: none;
508 | touch-action: none;
509 | }
510 | .ui-slider .ui-slider-range {
511 | position: absolute;
512 | z-index: 1;
513 | font-size: .7em;
514 | display: block;
515 | border: 0;
516 | background-position: 0 0;
517 | }
518 |
519 | /* support: IE8 - See #6727 */
520 | .ui-slider.ui-state-disabled .ui-slider-handle,
521 | .ui-slider.ui-state-disabled .ui-slider-range {
522 | filter: inherit;
523 | }
524 |
525 | .ui-slider-horizontal {
526 | height: .8em;
527 | }
528 | .ui-slider-horizontal .ui-slider-handle {
529 | top: -.3em;
530 | margin-left: -.6em;
531 | }
532 | .ui-slider-horizontal .ui-slider-range {
533 | top: 0;
534 | height: 100%;
535 | }
536 | .ui-slider-horizontal .ui-slider-range-min {
537 | left: 0;
538 | }
539 | .ui-slider-horizontal .ui-slider-range-max {
540 | right: 0;
541 | }
542 |
543 | .ui-slider-vertical {
544 | width: .8em;
545 | height: 100px;
546 | }
547 | .ui-slider-vertical .ui-slider-handle {
548 | left: -.3em;
549 | margin-left: 0;
550 | margin-bottom: -.6em;
551 | }
552 | .ui-slider-vertical .ui-slider-range {
553 | left: 0;
554 | width: 100%;
555 | }
556 | .ui-slider-vertical .ui-slider-range-min {
557 | bottom: 0;
558 | }
559 | .ui-slider-vertical .ui-slider-range-max {
560 | top: 0;
561 | }
562 | .ui-spinner {
563 | position: relative;
564 | display: inline-block;
565 | overflow: hidden;
566 | padding: 0;
567 | vertical-align: middle;
568 | }
569 | .ui-spinner-input {
570 | border: none;
571 | background: none;
572 | color: inherit;
573 | padding: 0;
574 | margin: .2em 0;
575 | vertical-align: middle;
576 | margin-left: .4em;
577 | margin-right: 22px;
578 | }
579 | .ui-spinner-button {
580 | width: 16px;
581 | height: 50%;
582 | font-size: .5em;
583 | padding: 0;
584 | margin: 0;
585 | text-align: center;
586 | position: absolute;
587 | cursor: default;
588 | display: block;
589 | overflow: hidden;
590 | right: 0;
591 | }
592 | /* more specificity required here to override default borders */
593 | .ui-spinner a.ui-spinner-button {
594 | border-top: none;
595 | border-bottom: none;
596 | border-right: none;
597 | }
598 | /* vertically center icon */
599 | .ui-spinner .ui-icon {
600 | position: absolute;
601 | margin-top: -8px;
602 | top: 50%;
603 | left: 0;
604 | }
605 | .ui-spinner-up {
606 | top: 0;
607 | }
608 | .ui-spinner-down {
609 | bottom: 0;
610 | }
611 |
612 | /* TR overrides */
613 | .ui-spinner .ui-icon-triangle-1-s {
614 | /* need to fix icons sprite */
615 | background-position: -65px -16px;
616 | }
617 | .ui-tabs {
618 | position: relative;/* position: relative prevents IE scroll bug (element with position: relative inside container with overflow: auto appear as "fixed") */
619 | padding: .2em;
620 | }
621 | .ui-tabs .ui-tabs-nav {
622 | margin: 0;
623 | padding: .2em .2em 0;
624 | }
625 | .ui-tabs .ui-tabs-nav li {
626 | list-style: none;
627 | float: left;
628 | position: relative;
629 | top: 0;
630 | margin: 1px .2em 0 0;
631 | border-bottom-width: 0;
632 | padding: 0;
633 | white-space: nowrap;
634 | }
635 | .ui-tabs .ui-tabs-nav .ui-tabs-anchor {
636 | float: left;
637 | padding: .5em 1em;
638 | text-decoration: none;
639 | }
640 | .ui-tabs .ui-tabs-nav li.ui-tabs-active {
641 | margin-bottom: -1px;
642 | padding-bottom: 1px;
643 | }
644 | .ui-tabs .ui-tabs-nav li.ui-tabs-active .ui-tabs-anchor,
645 | .ui-tabs .ui-tabs-nav li.ui-state-disabled .ui-tabs-anchor,
646 | .ui-tabs .ui-tabs-nav li.ui-tabs-loading .ui-tabs-anchor {
647 | cursor: text;
648 | }
649 | .ui-tabs-collapsible .ui-tabs-nav li.ui-tabs-active .ui-tabs-anchor {
650 | cursor: pointer;
651 | }
652 | .ui-tabs .ui-tabs-panel {
653 | display: block;
654 | border-width: 0;
655 | padding: 1em 1.4em;
656 | background: none;
657 | }
658 | .ui-tooltip {
659 | padding: 8px;
660 | position: absolute;
661 | z-index: 9999;
662 | max-width: 300px;
663 | -webkit-box-shadow: 0 0 5px #aaa;
664 | box-shadow: 0 0 5px #aaa;
665 | }
666 | body .ui-tooltip {
667 | border-width: 2px;
668 | }
669 |
--------------------------------------------------------------------------------
337 |
583 |
584 |
338 |
341 |
342 |
339 |
340 |
343 |
344 |
345 |
346 |
347 |
415 |
416 |
417 |
582 |
418 |
419 |
420 |
421 |
424 |
425 |
426 | Syllabus
422 | 423 |
427 |
440 | Forecasting fisheries catch time series with R (Forenoon)
428 |
430 |
439 | Topics
431 |-
432 |
- Time-varying regression 433 |
- Box-Jenkins (ARMA) Models 434 |
- Exponential smoothing 435 |
- Modelling time series with seasonality 436 |
- Forecast diagnostics and accuracy metrics 437 |
441 |
456 | Report-writing and code documentation with R (Afternoon)
442 |
444 |
455 | Topics
445 |-
446 |
- Basic workflow using RStudio, Git and GitHub 447 |
- Intro to R Markdown 448 |
- Creating simple websites from RStudio 449 |
- Build an R package with RStudio 450 |
- Creating simple websites from R packages on GitHub 451 |
- Creating a book with R Markdown: Intro to Bookdown. 452 |
- Creating and publishing RShiny applications 453 |
457 |
578 |
579 |
580 |
581 | Catch Forecasting Lectures and Labs
458 | 466 |Introduction
467 |Time-Varying Regression
468 |
469 |
470 |
491 |
493 |
494 |
522 |
524 |
549 |
551 |
576 |
577 | | Lectures | 477 |Labs | 478 |
|---|---|
| 1 Introduction to time-varying regression | 483 |1 Fit TV regression models to catch data | 484 |
| 2 Forecasts with a time-varying regression model | 487 |2 Create time-varying regression forecasts | 488 |
ARMA Models
492 || Lectures | 496 |Labs | 497 |
|---|---|
| 1 Introduction to ARMA Models | 502 |1 Intro to ARMA models and diagnostic plots | 503 |
| 2 Stationarity | 506 |2 Test the Greek catch data for stationarity | 507 |
| 3 Selecting Model Structure | 510 |3 Fit ARMA Models to the Greek catch data | 511 |
| 4 Fitting ARMA Models | 514 |4 Create and test forecasts | 515 |
| 5 Create and test forecasts | 518 |519 | |
Exponential Smoothing Models
523 || Lectures | 531 |Labs | 532 |
|---|---|
| 1 Introduction to Exponential Smoothing Models | 537 |1 Fit exponential smoothing models to data | 538 |
| 2 Selecting Model Structure | 541 |2 Create forecasts with exponential smoothing models | 542 |
| 3 Forecasting with exponential smoothing models | 545 |3 Testing models | 546 |
Seasonality
550 || Lectures | 558 |Labs | 559 |
|---|---|
| 1 Introduction to seasonality and approaches | 564 |1 Creating time-series objects with seasonality in R | 565 |
| 2 Seasonal time-vaying regression models | 568 |2 Seasonal exponential smoothing models | 569 |
| 3 Seasonal exponential smoothing models | 572 |573 | |