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rebuilt course website
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33 changes: 8 additions & 25 deletions docs/License.html
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<title>License</title>

<script src="site_libs/header-attrs-2.14/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<div id="license" class="section level1">
<h1>License</h1>
<p>This code was developed by United States federal government employees
as part of their official duties. As such, it is not subject to
copyright protection and is considered “public domain” (see 17 USC §
105). Public domain software can be used by anyone for any purpose, and
cannot be released under a copyright license.</p>
<p>Additionally, we waive copyright and related rights in the work
worldwide through the CC0 1.0 Universal public domain dedication.</p>
<p>This code was developed by United States federal government employees as part of their official duties. As such, it is not subject to copyright protection and is considered “public domain” (see 17 USC § 105). Public domain software can be used by anyone for any purpose, and cannot be released under a copyright license.</p>
<p>Additionally, we waive copyright and related rights in the work worldwide through the CC0 1.0 Universal public domain dedication.</p>
<div id="cc0-1.0-universal-summary" class="section level2">
<h2>CC0 1.0 Universal Summary</h2>
<p>This is a human-readable summary of the <a
href="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Legal
Code (read the full text)</a>.</p>
<p>This is a human-readable summary of the <a href="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Legal Code (read the full text)</a>.</p>
<div id="no-copyright" class="section level3">
<h3>No Copyright</h3>
<p>The person who associated a work with this deed has dedicated the
work to the public domain by waiving all of their rights to the work
worldwide under copyright law, including all related and neighboring
rights, to the extent allowed by law.</p>
<p>You can copy, modify, distribute, and perform the work, even for
commercial purposes, all without asking permission.</p>
<p>The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.</p>
<p>You can copy, modify, distribute, and perform the work, even for commercial purposes, all without asking permission.</p>
</div>
<div id="other-information" class="section level3">
<h3>Other Information</h3>
<p>In no way are the patent or trademark rights of any person affected
by CC0, nor are the rights that other persons may have in the work or in
how the work is used, such as publicity or privacy rights.</p>
<p>Unless expressly stated otherwise, the person who associated a work
with this deed makes no warranties about the work, and disclaims
liability for all uses of the work, to the fullest extent permitted by
applicable law. When using or citing the work, you should not imply
endorsement by the author or the affirmer.</p>
<p>In no way are the patent or trademark rights of any person affected by CC0, nor are the rights that other persons may have in the work or in how the work is used, such as publicity or privacy rights.</p>
<p>Unless expressly stated otherwise, the person who associated a work with this deed makes no warranties about the work, and disclaims liability for all uses of the work, to the fullest extent permitted by applicable law. When using or citing the work, you should not imply endorsement by the author or the affirmer.</p>
</div>
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46 changes: 15 additions & 31 deletions docs/asyllabus.html
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<title>2021 Schedule</title>

<script src="site_libs/header-attrs-2.14/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
Expand Down Expand Up @@ -337,8 +337,7 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
5 Jan
</td>
<td style="text-align:left;width: 27em; ">
Course overview <br>Properties of time series <br>Data transformations
<br>Time series decomposition <br>
Course overview <br>Properties of time series <br>Data transformations <br>Time series decomposition <br>
</td>
<td style="text-align:left;">
Matrices &amp; matrix algebra <br>(review on your own) <br>
Expand All @@ -352,13 +351,10 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
7 Jan
</td>
<td style="text-align:left;width: 27em; ">
Covariance &amp; correlation <br>Autocorrelation &amp; Partial
autocorrelation <br>Cross correlation <br>White noise <br>Random walks
<br>Differencing <br>
Covariance &amp; correlation <br>Autocorrelation &amp; Partial autocorrelation <br>Cross correlation <br>White noise <br>Random walks <br>Differencing <br>
</td>
<td style="text-align:left;">
Writing models in matrix form (through section 2.5) <br>Basic time
series functions <br>Autocorrelation <br>
Writing models in matrix form (through section 2.5) <br>Basic time series functions <br>Autocorrelation <br>
</td>
<td style="text-align:left;">
linear regression in matrix form <br>Optional <br>
Expand All @@ -369,9 +365,7 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
12 Jan
</td>
<td style="text-align:left;width: 27em; ">
Autoregressive (AR) models <br>Moving average (MA) models <br>Stationary
AR models <br>Invertible MA models <br>Using ACF &amp; PACF for model ID
<br>
Autoregressive (AR) models <br>Moving average (MA) models <br>Stationary AR models <br>Invertible MA models <br>Using ACF &amp; PACF for model ID <br>
</td>
<td style="text-align:left;">
<br>
Expand All @@ -385,16 +379,13 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
14 Jan
</td>
<td style="text-align:left;width: 27em; ">
Box-Jenkins method <br>Fitting ARIMA models with R <br>Forecasting with
ARIMA models <br>Seasonal ARIMA models <br>
Box-Jenkins method <br>Fitting ARIMA models with R <br>Forecasting with ARIMA models <br>Seasonal ARIMA models <br>
</td>
<td style="text-align:left;">
Simulating ARMA models <br>Fitting ARIMA models <br>Forecasting with
ARIMA models <br>Box-Jenkins Methods <br>
Simulating ARMA models <br>Fitting ARIMA models <br>Forecasting with ARIMA models <br>Box-Jenkins Methods <br>
</td>
<td style="text-align:left;">
ARIMA models <br>Due next Thurs 11:59 PM PST; email to instructor(s) for
lab <br>
ARIMA models <br>Due next Thurs 11:59 PM PST; email to instructor(s) for lab <br>
</td>
</tr>
<tr>
Expand Down Expand Up @@ -444,15 +435,13 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
28 Jan
</td>
<td style="text-align:left;width: 27em; ">
Regression with autocorrelated errors <br>Dynamic factor analysis (DFA)
<br>
Regression with autocorrelated errors <br>Dynamic factor analysis (DFA) <br>
</td>
<td style="text-align:left;">
Fitting DFA models <br>
</td>
<td style="text-align:left;">
Dynamic Factor Analysis <br>Due next Thurs 11:59 PM PST; email to Mark
<br>
Dynamic Factor Analysis <br>Due next Thurs 11:59 PM PST; email to Mark <br>
</td>
</tr>
<tr>
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Fitting DLMs <br>
</td>
<td style="text-align:left;">
Dynamic Linear Models <br>Due next Thurs 11:59 PM PST; email to
instructor(s) for lab <br>
Dynamic Linear Models <br>Due next Thurs 11:59 PM PST; email to instructor(s) for lab <br>
</td>
</tr>
<tr>
Expand All @@ -503,8 +491,7 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
11 Feb
</td>
<td style="text-align:left;width: 27em; ">
MAP estimation <br>Multivariate models <br>DFA <br>Writing Bayesian
models in Stan <br>
MAP estimation <br>Multivariate models <br>DFA <br>Writing Bayesian models in Stan <br>
</td>
<td style="text-align:left;">
Bayesian estimation <br>STAN <br>
Expand All @@ -518,8 +505,7 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
16 Feb
</td>
<td style="text-align:left;width: 27em; ">
Multi-model inference and selection <br>Information criteria
<br>Cross-validation &amp; LOOIC <br>
Multi-model inference and selection <br>Information criteria <br>Cross-validation &amp; LOOIC <br>
</td>
<td style="text-align:left;">
<br>
Expand All @@ -533,8 +519,7 @@ <h1 class="title toc-ignore">2021 Schedule</h1>
18 Feb
</td>
<td style="text-align:left;width: 27em; ">
AR(p) Models <br>Estimating interaction strengths <br>Gompertz models
<br>Stability metrics <br>
AR(p) Models <br>Estimating interaction strengths <br>Gompertz models <br>Stability metrics <br>
</td>
<td style="text-align:left;">
Interactions <br>Stability <br>B matrix <br>
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25 Feb
</td>
<td style="text-align:left;width: 27em; ">
Frequency domain <br>Fourier transforms <br>Spectral analysis
<br>Wavelet analysis <br>
Frequency domain <br>Fourier transforms <br>Spectral analysis <br>Wavelet analysis <br>
</td>
<td style="text-align:left;">
Fitting EDM models <br>
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<title>Computer Labs</title>

<script src="site_libs/header-attrs-2.14/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
Expand Down Expand Up @@ -317,11 +317,9 @@ <h3>Meeting days &amp; times</h3>
</div>
<div id="lab-book" class="section level3">
<h3>Lab book</h3>
<p>You can find the electronic lab book <a
href="https://nwfsc-timeseries.github.io/atsa-labs">here</a>.</p>
<p>You can find the electronic lab book <a href="https://atsa-es.github.io/atsa-labs/">here</a>.</p>
<!-- first is PDF, 2nd PPT, 3rd Rmd -->
<div
style="border: 1px solid #ddd; padding: 0px; border-style: none;overflow-y: scroll; height:700px; ">
<div style="border: 1px solid #ddd; padding: 0px; border-style: none;overflow-y: scroll; height:700px; ">
<table class="table table-striped" style="width: auto !important; ">
<caption>
</caption>
Expand Down Expand Up @@ -365,25 +363,18 @@ <h3>Lab book</h3>
Matrices &amp; matrix algebra <br>(review on your own) <br>
</td>
<td style="text-align:center;">
<a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-basicmat.html">html
1</a><br><a
href="Labs/Week%200%20basic%20matrix/basic-matrix-math.pdf">PDF
1</a><br>
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-basicmat.html">html 1</a><br><a href="Labs/Week%200%20basic%20matrix/basic-matrix-math.pdf">PDF 1</a><br>
</td>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
Optional (not part of grade): Listed at end of
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-basicmat.html">Chapter
1</a> in the ATSA lab book. <br>
Optional (not part of grade): Listed at end of <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-basicmat.html">Chapter 1</a> in the ATSA lab book. <br>
</td>
<td style="text-align:center;">
Optional <br>
</td>
<td style="text-align:center;">
<a
href="Labs/Week%200%20basic%20matrix/basic-matrix-math-key.pdf">Key</a>
<a href="Labs/Week%200%20basic%20matrix/basic-matrix-math-key.pdf">Key</a>
</td>
</tr>
<tr>
Expand All @@ -394,22 +385,15 @@ <h3>Lab book</h3>
Eli/Mark <br>
</td>
<td style="text-align:left;">
Writing models in matrix form (through section 2.5) <br>Basic time
series functions <br>Autocorrelation <br>
Writing models in matrix form (through section 2.5) <br>Basic time series functions <br>Autocorrelation <br>
</td>
<td style="text-align:center;">
<a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mlr.html">html
1</a> <a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-ts.html">html
2</a><br><br>
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mlr.html">html 1</a> <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-ts.html">html 2</a><br><br>
</td>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
Optional (but important to understand course material): End of
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mlr.html">Chapter
2</a> in the ATSA lab book. <br>
Optional (but important to understand course material): End of <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mlr.html">Chapter 2</a> in the ATSA lab book. <br>
</td>
<td style="text-align:center;">
Optional <br>
Expand Down Expand Up @@ -450,31 +434,21 @@ <h3>Lab book</h3>
Mark &amp; Eli <br>
</td>
<td style="text-align:left;">
Simulating ARMA models <br>Fitting ARIMA models <br>Forecasting with
ARIMA models <br>Box-Jenkins Methods <br>
Simulating ARMA models <br>Fitting ARIMA models <br>Forecasting with ARIMA models <br>Box-Jenkins Methods <br>
</td>
<td style="text-align:center;">
<a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-tslab.html">html
1</a> <a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-boxjenkins-.html">html
2</a><br><br>
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-tslab.html">html 1</a> <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-boxjenkins-.html">html 2</a><br><br>
</td>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
Intro to ts: problems at end of
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-tslab.html">Chapter
4</a> in the ATSA lab book.<br>Fitting ARMA models: problems at end of
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-boxjenkins-.html">Chapter
5</a> in the ATSA lab book. <br>
Intro to ts: problems at end of <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-tslab.html">Chapter 4</a> in the ATSA lab book.<br>Fitting ARMA models: problems at end of <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-boxjenkins-.html">Chapter 5</a> in the ATSA lab book. <br>
</td>
<td style="text-align:center;">
Due next Thurs 11:59 PM PST; email to instructor(s) for lab <br>
</td>
<td style="text-align:center;">
<a href="Labs/Week%202/HW_2_ts_Key.html">Key 1</a> <a
href="Labs/Week%202/HW_2_box-jenkins_Key.html">Key 2</a>
<a href="Labs/Week%202/HW_2_ts_Key.html">Key 1</a> <a href="Labs/Week%202/HW_2_box-jenkins_Key.html">Key 2</a>
</td>
</tr>
<tr>
Expand Down Expand Up @@ -512,24 +486,12 @@ <h3>Lab book</h3>
Fitting univariate and mulitvariate state-space models <br>
</td>
<td style="text-align:center;">
<a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-univariate-state-space.html">html
1</a> <a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mss.html">html
2</a><br><br>
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-univariate-state-space.html">html 1</a> <a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-mss.html">html 2</a><br><br>
</td>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
HW #2 questions and data: <a
href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-NO2.Rmd">Rmd</a>,
<a
href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-NO2.html">html</a>,
<a
href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/ECNNO2.RData">data</a>,
<a
href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-Tips.html">Tips</a>
<br>
HW #2 questions and data: <a href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-NO2.Rmd">Rmd</a>, <a href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-NO2.html">html</a>, <a href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/ECNNO2.RData">data</a>, <a href="https://nwfsc-timeseries.github.io/atsa/Labs/Week%203/NO2Lab/HW2-Tips.html">Tips</a> <br>
</td>
<td style="text-align:center;">
Due Sat Jan 30 11:59 PM PST; email to Eli <br>
Expand Down Expand Up @@ -622,8 +584,7 @@ <h3>Lab book</h3>
Fitting DLMs <br>
</td>
<td style="text-align:center;">
<a href="Labs/Week%205/intro-to-dlms.html">html 1</a><br><br><a
href="Labs/Week%205/intro-to-dlms.Rmd">Rmd 1</a>
<a href="Labs/Week%205/intro-to-dlms.html">html 1</a><br><br><a href="Labs/Week%205/intro-to-dlms.Rmd">Rmd 1</a>
</td>
<td style="text-align:center;">
<a href="https://youtu.be/KpBgTqcsqNg">Video</a>
Expand Down Expand Up @@ -673,11 +634,7 @@ <h3>Lab book</h3>
Bayesian estimation <br>STAN <br>
</td>
<td style="text-align:center;">
<a
href="https://nwfsc-timeseries.github.io/atsa-labs/chap-stan.html">html
1</a><br><br><a
href="https://nwfsc-timeseries.github.io/atsa-labs/Rmds/fitting-models-with-stan.Rmd">Rmd
1</a>
<a href="https://nwfsc-timeseries.github.io/atsa-labs/chap-stan.html">html 1</a><br><br><a href="https://nwfsc-timeseries.github.io/atsa-labs/Rmds/fitting-models-with-stan.Rmd">Rmd 1</a>
</td>
<td style="text-align:center;">
</td>
Expand Down Expand Up @@ -730,21 +687,13 @@ <h3>Lab book</h3>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
HW #6: HMM/Bayesian State space models. <a
href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6.Rmd">Rmd</a>,
<a
href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6.html">html</a>,
<a
href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6-part2-JAGS.Rmd">Rmd
Part 2 JAGS</a>, <a href="https://rstudio.cloud/project/2228346">Part 2
Online</a> <br>
HW #6: HMM/Bayesian State space models. <a href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6.Rmd">Rmd</a>, <a href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6.html">html</a>, <a href="https://nwfsc-timeseries.github.io/atsa/Labs/HW6/HW6-part2-JAGS.Rmd">Rmd Part 2 JAGS</a>, <a href="https://rstudio.cloud/project/2228346">Part 2 Online</a> <br>
</td>
<td style="text-align:center;">
Due Monday Mar 1 11:59 PM PST; email to Eric &amp; Eli <br>
</td>
<td style="text-align:center;">
<a href="Labs/HW6/HW6-key-part1.html">Key 1</a> <a
href="Labs/HW6/HW6-key-part2.html">Key 2</a>
<a href="Labs/HW6/HW6-key-part1.html">Key 1</a> <a href="Labs/HW6/HW6-key-part2.html">Key 2</a>
</td>
</tr>
<tr>
Expand Down Expand Up @@ -782,8 +731,7 @@ <h3>Lab book</h3>
Fitting EDM models <br>
</td>
<td style="text-align:center;">
<a href="Labs/EDM%20Lab/EDM-Lab.html">html 1</a><br><br><a
href="Labs/EDM%20Lab/EDM-Lab.Rmd">Rmd 1</a>
<a href="Labs/EDM%20Lab/EDM-Lab.html">html 1</a><br><br><a href="Labs/EDM%20Lab/EDM-Lab.Rmd">Rmd 1</a>
</td>
<td style="text-align:center;">
</td>
Expand Down Expand Up @@ -837,10 +785,7 @@ <h3>Lab book</h3>
<td style="text-align:center;">
</td>
<td style="text-align:center;">
No homework; Datasets for in class lab <a
href="Labs/Week%209/SNOTEL_metadata.csv">Data1</a>, <a
href="Labs/Week%209/SNOTEL_Washington_1981_2013.csv">Data2</a>, <a
href="Labs/Week%209/tck_longform.Rdata">Data3</a> <br>
No homework; Datasets for in class lab <a href="Labs/Week%209/SNOTEL_metadata.csv">Data1</a>, <a href="Labs/Week%209/SNOTEL_Washington_1981_2013.csv">Data2</a>, <a href="Labs/Week%209/tck_longform.Rdata">Data3</a> <br>
</td>
<td style="text-align:center;">
work on projects <br>
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