tadd scrollspy, change limits - cosmo - front and backend for Markov-Chain Monte Carlo inversion of cosmogenic nuclide concentrations
(HTM) git clone git://src.adamsgaard.dk/cosmo
(DIR) Log
(DIR) Files
(DIR) Refs
(DIR) README
(DIR) LICENSE
---
(DIR) commit 9e704f6e5c33a57dd9374eb1191af0864ab79570
(DIR) parent fdda8f0332e66e01af8b749793b176dc435ac16a
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Fri, 20 Nov 2015 12:16:53 +0100
add scrollspy, change limits
Diffstat:
M js/history-form-prefiller.js | 6 +++---
M matlab/generate_plots.m | 190 ++++++++++++++++++++++++++++++
M pages/methods.html | 124 +++++++++++++++++++------------
3 files changed, 270 insertions(+), 50 deletions(-)
---
(DIR) diff --git a/js/history-form-prefiller.js b/js/history-form-prefiller.js
t@@ -84,17 +84,17 @@ var PrefillMachine2 = {
$("#rock_density").val("2650");
- $("#epsilon_gla_min").val("1.0e-6");
+ $("#epsilon_gla_min").val("1.0e-5");
$("#epsilon_gla_max").val("1.0e-1");
- $("#epsilon_int_min").val("1.0e-6");
+ $("#epsilon_int_min").val("1.0e-5");
$("#epsilon_int_max").val("1.0e-1");
$("#t_degla_min").val("10000");
$("#t_degla_max").val("12000");
$("#record_threshold_min").val("3.7");
- $("#record_threshold_max").val("4.7");
+ $("#record_threshold_max").val("4.5");
}
}
(DIR) diff --git a/matlab/generate_plots.m b/matlab/generate_plots.m
t@@ -731,3 +731,193 @@ html = [html, ' </tbody>\n'...
fileID = fopen(filename,'w');
fprintf(fileID, html);
fclose(fileID);
+
+
+%% generate html table of input parameters
+filename = [save_file, '-input.html'];
+disp('Saving html table of input values')
+
+% header
+html = [...
+ '\n'...
+ '<table class="highlight">\n'...
+ ' <thead>\n'...
+ ' <tr>\n'...
+ ' <th data-field="param">Parameter</th>\n'...
+ ' <th data-field="param">Percentile</th>\n'];
+
+for i=1:Nwalkers
+ html = [html, ...
+ ' <th data-field="w1">Walker ', num2str(i), '</th>\n'];
+end
+
+% epsilon_int
+html = [html, ...
+ ' <th data-field="avg">Average</th>\n'...
+ ' </tr>\n'...
+ ' </thead>\n'...
+ ' <tbody>\n'...
+ ' <tr>\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">25%%</td>\n'];
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_int_25(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_int_25)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr>\n'...
+ ' <td align="center">ε<sub>int</sub> [m/Myr]</td>\n'...
+ ' <td align="center">50%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_int_50(i),3),'</td>\n'];
+end
+
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_int_50)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr style="border-bottom:1px solid #D0D0D0">\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">75%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_int_75(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_int_75)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'];
+
+
+% epsilon_gla
+html = [html, ...
+ ' <tr>\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">25%%</td>\n'];
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_gla_25(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_gla_25)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr>\n'...
+ ' <td align="center">ε<sub>gla</sub> [m/Myr]</td>\n'...
+ ' <td align="center">50%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_gla_50(i),3),'</td>\n'];
+end
+
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_gla_50)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr style="border-bottom:1px solid #D0D0D0">\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">75%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(epsilon_gla_75(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(epsilon_gla_75)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'];
+
+
+% record_threshold
+html = [html, ...
+ ' <tr>\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">25%%</td>\n'];
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(record_threshold_25(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(record_threshold_25)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr>\n'...
+ ' <td align="center">δ<sup>18</sup>O<sub>threshold</sub> [‰]</td>\n'...
+ ' <td align="center">50%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(record_threshold_50(i),3),'</td>\n'];
+end
+
+
+html = [html, ' <td>',...
+ num2str(sum(record_threshold_50)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr style="border-bottom:1px solid #D0D0D0">\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">75%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(record_threshold_75(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(record_threshold_75)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'];
+
+% E
+html = [html, ...
+ ' <tr>\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">25%%</td>\n'];
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(E_25(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(E_25)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr>\n'...
+ ' <td align="center">E [m]</td>\n'...
+ ' <td align="center">50%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(E_50(i),3),'</td>\n'];
+end
+
+
+html = [html, ' <td>',...
+ num2str(sum(E_50)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'...
+ ' <tr style="border-bottom:1px solid #D0D0D0">\n'...
+ ' <td> </td>\n'...
+ ' <td align="center">75%%</td>\n'];
+
+for i=1:Nwalkers
+ html = [html, ' <td>',...
+ num2str(E_75(i),3),'</td>\n'];
+end
+
+html = [html, ' <td>',...
+ num2str(sum(E_75)/Nwalkers,3),'</td>\n'...
+ ' </tr>\n'];
+
+
+% footer
+html = [html, ' </tbody>\n'...
+ '</table>\n'...
+ ];
+fileID = fopen(filename,'w');
+fprintf(fileID, html);
+fclose(fileID);
(DIR) diff --git a/pages/methods.html b/pages/methods.html
t@@ -1,57 +1,76 @@
<div class="section no-pad-bot" id="index-banner">
<div class="container">
+
<br><br>
- <!-- page header -->
- <h1 class="header center orange-text">Methods</h1>
- <!-- page subheader
- <div class="row center">
- <h5 class="header col s12 light">Markov-Chain Monte Carlo inversion
- of exposure age or erosion rates</h5> </div>-->
+ <div class="row">
+ <div class="col s12 m9 l10">
- <p>
- Cosmogenic nuclides are typically used to either constrain an
- exposure age, a burial age, or an erosion rate. Constraining the
- landscape history and past erosion rates in previously glaciated
- terrains is, however, notoriously difficult because it involves a
- large number of unknowns. The potential use of cosmogenic nuclides
- in landscapes with a complex history of exposure and erosion is
- therefore often quite limited. Here, we present a novel
- multi-nuclide approach based on the Markov Chain Monte Carlo (MCMC)
- technique. The model framework currently incorporates any
- combination of the following nuclides <sup>10</sup>Be,
- <sup>26</sup>Al, <sup>14</sup>C, and <sup>21</sup>Ne, and is highly
- flexible.
- </p>
+ <h1 class="header center orange-text">Methods</h1>
- <h3 class="header blue-text">Markov-Chain Monte Carlo (MCMC) basics</h3>
- <p>bla bla</p>
+ <div id="introduction" class="section scrollspy">
+ <h3 class="header blue-text">Introduction</h3>
+ <p>
+ Cosmogenic nuclides are typically used to either constrain
+ an exposure age, a burial age, or an erosion rate.
+ Constraining the landscape history and past erosion rates in
+ previously glaciated terrains is, however, notoriously
+ difficult because it involves a large number of unknowns.
+ The potential use of cosmogenic nuclides in landscapes with
+ a complex history of exposure and erosion is therefore often
+ quite limited. Here, we present a novel multi-nuclide
+ approach based on the Markov Chain Monte Carlo (MCMC)
+ technique. The model framework currently incorporates any
+ combination of the following nuclides <sup>10</sup>Be,
+ <sup>26</sup>Al, <sup>14</sup>C, and <sup>21</sup>Ne, and is
+ highly flexible.
+ </p>
- <h4 class="header blue-text light">What is a MCMC walker?</h4>
- <p>bla bla</p>
+ <p>In the following we give a basic overview of the applied
+ methods and their application. For a full description see
+ the open-access publication by <a
+ href="http://www.sciencedirect.com/science/article/pii/S1871101415300558">Knudsen
+ et al. (2015)</a>.</p>
+ </div>
- <h3 class="header blue-text">Two-stage glacial-interglacial model</h3>
- <p>bla bla</p>
+ <div id="mcmc" class="section scrollspy">
+ <h3 class="header blue-text">
+ Markov-Chain Monte Carlo (MCMC) basics</h3>
+ <p>bla bla</p>
+ </div>
- <p>For a full description of the methods and application possibilities,
- see the open-access publication by <a
- href="http://www.sciencedirect.com/science/article/pii/S1871101415300558">Knudsen
- et al. (2015)</a>.
+ <div id="mcmcwalker" class="subsection scrollspy">
+ <h4 class="header blue-text light">
+ What is a MCMC walker?</h4>
+ <p>bla bla</p>
+ </div>
- <h3 class="header blue-text">Citing the MCMC cosmo calculator</h3>
- If you use the results generated by this tool in a
- scientific publication, please acknowledge this fact by citing:</p>
- <blockquote>
- Knudsen, M.F., Egholm, D.L., Jacobsen, B.H., Larsen, N.K., Jansen,
- J.D., Andersen, J.L., Linge, H.C., 2015.<br>
- <b>A multi-nuclide approach to constrain landscape evolution and
- past erosion rates in previously glaciated terrains.</b></br>
- Quaternary Geochronology 30, 100-113,
- doi:10.1016/j.quageo.2015.08.004.
- </blockquote>
- <p>You may use the following BibTeX entry:</p>
- <div class="row">
- <pre><code class="language-markup col s12"> @article{Knudsen2015,
+ <div id="twostage" class="section scrollspy">
+ <h3 class="header blue-text">
+ Two-stage glacial-interglacial model</h3>
+ <p>bla bla</p>
+ </div>
+
+
+ <div id="citing" class="section scrollspy">
+ <h3 class="header blue-text">
+ Citing the MCMC cosmo calculator</h3>
+
+ <p>If you use the results generated by this tool in a
+ scientific publication, please acknowledge this fact by
+ citing:</p>
+ <blockquote>
+ Knudsen, M.F., Egholm, D.L., Jacobsen, B.H., Larsen, N.K., Jansen,
+ J.D., Andersen, J.L., Linge, H.C., 2015.<br>
+ <b>A multi-nuclide approach to constrain landscape evolution and
+ past erosion rates in previously glaciated terrains.</b></br>
+ Quaternary Geochronology 30, 100-113,
+ doi:10.1016/j.quageo.2015.08.004.
+ </blockquote>
+
+ <p>You may use the following BibTeX entry:</p>
+ <div class="row">
+ <pre><code class="language-markup col s12"> @article{Knudsen2015,
author = "Knudsen, M. F. and Egholm, D. L. and Jacobsen, B. H.
and Larsen, N. K. and Jansen, J. D. and Andersen, J. L.
and Linge, H. C.",
t@@ -67,10 +86,21 @@
issn = "1871-1014",
doi = "http://dx.doi.org/10.1016/j.quageo.2015.08.004",
}
- </code></pre>
- </div>
-
+ </code></pre>
+ </div>
+ </div>
+ </div>
+ <div class="col hide-on-small-only m3 l2">
+ <ul class="section table-of-contents">
+ <li><a href="#introduction">Introduction</a></li>
+ <li><a href="#mcmc">Markov-Chain Monte Carlo</a></li>
+ <li><a href="#mcmcwalker">MCMC walkers</a></li>
+ <li><a href="#twostage">Two-stage model</a></li>
+ <li><a href="#citing">Citing</a></li>
+ </ul>
+ </div>
+ </div>
</div>
</div>