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	<title>Comments on: Richard Smith on PC Retention</title>
	<atom:link href="http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/feed/" rel="self" type="application/rss+xml" />
	<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/</link>
	<description>by Steve McIntyre</description>
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		<title>By: UC</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-298474</link>
		<dc:creator><![CDATA[UC]]></dc:creator>
		<pubDate>Sat, 16 Jul 2011 20:46:14 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-298474</guid>
		<description><![CDATA[Catching up a bit, the data set used in Kemp11, glhad_eiv_composite.mat is almost like glglfulhad_smxx, non-screened proxies with global temperature target. Here&#039;s where I am now with the replication:

&lt;img src=&quot;http://www.climateaudit.info/data/uc/Mann08_gl.png&quot; alt=&quot;a1&quot; /&gt;

I was confused by the use of  non-screened proxies, but Mann08 explains:


&lt;blockquote&gt;For the EIV approach, which does not require that proxy
data represent local temperature variations, results are compared
by using several alternative data-selection schemes, including one
that employs all available proxy records, another that employs only
proxy records contained within the target hemisphere, and another
that employs only the proxy data within that hemisphere that pass
the temperature-screening analysis mentioned above.
&lt;/blockquote&gt;

MAKEPROXY.m  &#039;screening on raw data  (old)&#039; would result a reconstruction that is sometimes outside the 2-sigma uncertainties of Kemp11 Fig. 4A, so that must be oldish, incorrect screening method. The glglhadfulsm20 that is used for no-Tiljander example in http://www.meteo.psu.edu/~mann/supplements/MultiproxyMeans07/ seems to be non-screened EIV result as well.]]></description>
		<content:encoded><![CDATA[<p>Catching up a bit, the data set used in Kemp11, glhad_eiv_composite.mat is almost like glglfulhad_smxx, non-screened proxies with global temperature target. Here&#8217;s where I am now with the replication:</p>
<p><img src="http://www.climateaudit.info/data/uc/Mann08_gl.png" alt="a1" /></p>
<p>I was confused by the use of  non-screened proxies, but Mann08 explains:</p>
<blockquote><p>For the EIV approach, which does not require that proxy<br />
data represent local temperature variations, results are compared<br />
by using several alternative data-selection schemes, including one<br />
that employs all available proxy records, another that employs only<br />
proxy records contained within the target hemisphere, and another<br />
that employs only the proxy data within that hemisphere that pass<br />
the temperature-screening analysis mentioned above.
</p></blockquote>
<p>MAKEPROXY.m  &#8216;screening on raw data  (old)&#8217; would result a reconstruction that is sometimes outside the 2-sigma uncertainties of Kemp11 Fig. 4A, so that must be oldish, incorrect screening method. The glglhadfulsm20 that is used for no-Tiljander example in <a href="http://www.meteo.psu.edu/~mann/supplements/MultiproxyMeans07/" rel="nofollow">http://www.meteo.psu.edu/~mann/supplements/MultiproxyMeans07/</a> seems to be non-screened EIV result as well.</p>
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		<title>By: Steve McIntyre</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-297351</link>
		<dc:creator><![CDATA[Steve McIntyre]]></dc:creator>
		<pubDate>Tue, 05 Jul 2011 22:41:32 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-297351</guid>
		<description><![CDATA[AMac, the most notorious infilling was spotted early - Mann et al deleted the post-1960 portion of the Briffa MXD data and infilled it, thus &quot;hide the decline&quot;.  No one in climate science seems to mind.]]></description>
		<content:encoded><![CDATA[<p>AMac, the most notorious infilling was spotted early &#8211; Mann et al deleted the post-1960 portion of the Briffa MXD data and infilled it, thus &#8220;hide the decline&#8221;.  No one in climate science seems to mind.</p>
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		<title>By: AMac</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-297344</link>
		<dc:creator><![CDATA[AMac]]></dc:creator>
		<pubDate>Tue, 05 Jul 2011 21:04:58 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-297344</guid>
		<description><![CDATA[I&#039;m afraid I am not much help here.  

If you want to visualize the proxies or retrieve the data as archived by Tiljander, check my blog for the relevant posts.

Jeff Id of the Air Vent did a bunch of Mann08 reconstruction emulations.  Perhaps it would be useful to email him, or check his 2009/10 archives.

By the way, the post-1985 Tiljander numbers as used by Mann08 weren&#039;t archived by Tiljander -- those files only went to 1895.  So Mann08 &quot;infilled&quot; the 1986-1995 data with RegEM.  I am hazy on this, but as far as I can tell, &quot;infilling&quot; meant &quot;extrapolating&quot;.

Generating reasonable-looking data to fill in gaps in the reconstruction period doesn&#039;t seem like a good idea.  But generating data for use in one of the ends of the calibration period seems much riskier, to my unschooled eye.]]></description>
		<content:encoded><![CDATA[<p>I&#8217;m afraid I am not much help here.  </p>
<p>If you want to visualize the proxies or retrieve the data as archived by Tiljander, check my blog for the relevant posts.</p>
<p>Jeff Id of the Air Vent did a bunch of Mann08 reconstruction emulations.  Perhaps it would be useful to email him, or check his 2009/10 archives.</p>
<p>By the way, the post-1985 Tiljander numbers as used by Mann08 weren&#8217;t archived by Tiljander &#8212; those files only went to 1895.  So Mann08 &#8220;infilled&#8221; the 1986-1995 data with RegEM.  I am hazy on this, but as far as I can tell, &#8220;infilling&#8221; meant &#8220;extrapolating&#8221;.</p>
<p>Generating reasonable-looking data to fill in gaps in the reconstruction period doesn&#8217;t seem like a good idea.  But generating data for use in one of the ends of the calibration period seems much riskier, to my unschooled eye.</p>
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		<title>By: UC</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-297333</link>
		<dc:creator><![CDATA[UC]]></dc:creator>
		<pubDate>Tue, 05 Jul 2011 19:22:16 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-297333</guid>
		<description><![CDATA[AMac
 

&lt;blockquote&gt;For some analyses, “all four” proxies appear to be in the count, while for others, the count of proxies that have passed validation is used. That would be these three Tiljanders.

So maybe “10 minus 3 Tiljanders is 7? is what you are looking for?
&lt;/blockquote&gt;

Takes some time to figure out what screening I used. But the figure above ( http://www.climateaudit.info/data/uc/notilj.png ) shows step19 result without the following
proxies (in red):
 
 proxy19 1 : tiljander_2003_darksum
 proxy19 2 : tiljander_2003_lightsum
 proxy19 3 : tiljander_2003_thicknessmm
 proxy19 4 : tiljander_2003_xraydenseave
 
 That is not a real hockey stick, because regEM practically gives the calibration mean as the reconstruction (the reason seems to be that there is no good correlation add all with the target). If you add Tiljanders, you get a hockey stick (as Hu observed above, even ICE-results can go outside the calibration range with some extreme proxy on board). But in my replication result there are 10 proxies in step 19. 10 minus 4 is 6, and this wouldn&#039;t pass the 7-threshold.]]></description>
		<content:encoded><![CDATA[<p>AMac</p>
<blockquote><p>For some analyses, “all four” proxies appear to be in the count, while for others, the count of proxies that have passed validation is used. That would be these three Tiljanders.</p>
<p>So maybe “10 minus 3 Tiljanders is 7? is what you are looking for?
</p></blockquote>
<p>Takes some time to figure out what screening I used. But the figure above ( <a href="http://www.climateaudit.info/data/uc/notilj.png" rel="nofollow">http://www.climateaudit.info/data/uc/notilj.png</a> ) shows step19 result without the following<br />
proxies (in red):</p>
<p> proxy19 1 : tiljander_2003_darksum<br />
 proxy19 2 : tiljander_2003_lightsum<br />
 proxy19 3 : tiljander_2003_thicknessmm<br />
 proxy19 4 : tiljander_2003_xraydenseave</p>
<p> That is not a real hockey stick, because regEM practically gives the calibration mean as the reconstruction (the reason seems to be that there is no good correlation add all with the target). If you add Tiljanders, you get a hockey stick (as Hu observed above, even ICE-results can go outside the calibration range with some extreme proxy on board). But in my replication result there are 10 proxies in step 19. 10 minus 4 is 6, and this wouldn&#8217;t pass the 7-threshold.</p>
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		<title>By: AMac</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-297310</link>
		<dc:creator><![CDATA[AMac]]></dc:creator>
		<pubDate>Tue, 05 Jul 2011 15:41:45 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-297310</guid>
		<description><![CDATA[Oh.  

This might be relevant, then:  Tiljander&#039;s thicknessmm, lightsum, and darksum passed Mann08&#039;s validation test.  A statistical metric (R or R^2 IIRC) had to be above a certain threshold.  XRD did not pass.

For some analyses, &quot;all four&quot; proxies appear to be in the count, while for others, the count of proxies that have passed validation is used.  That would be these three Tiljanders.

So maybe &quot;10 minus 3 Tiljanders is 7&quot; is what you are looking for?]]></description>
		<content:encoded><![CDATA[<p>Oh.  </p>
<p>This might be relevant, then:  Tiljander&#8217;s thicknessmm, lightsum, and darksum passed Mann08&#8242;s validation test.  A statistical metric (R or R^2 IIRC) had to be above a certain threshold.  XRD did not pass.</p>
<p>For some analyses, &#8220;all four&#8221; proxies appear to be in the count, while for others, the count of proxies that have passed validation is used.  That would be these three Tiljanders.</p>
<p>So maybe &#8220;10 minus 3 Tiljanders is 7&#8243; is what you are looking for?</p>
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		<title>By: UC</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-297296</link>
		<dc:creator><![CDATA[UC]]></dc:creator>
		<pubDate>Tue, 05 Jul 2011 12:33:46 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-297296</guid>
		<description><![CDATA[&lt;blockquote&gt;I don’t know about the 7-threshold rule.&lt;/blockquote&gt;

I&#039;m trying to find a rational explanation. Hopefully it is not 
 

 &lt;em&gt;10 minus 4 Tiljanders is less than 7  &lt;/em&gt;]]></description>
		<content:encoded><![CDATA[<blockquote><p>I don’t know about the 7-threshold rule.</p></blockquote>
<p>I&#8217;m trying to find a rational explanation. Hopefully it is not </p>
<p> <em>10 minus 4 Tiljanders is less than 7  </em></p>
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		<title>By: AMac</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-295930</link>
		<dc:creator><![CDATA[AMac]]></dc:creator>
		<pubDate>Tue, 28 Jun 2011 22:39:23 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-295930</guid>
		<description><![CDATA[Yes, the Mann09 recons start at 500 AD.

I don&#039;t know about the 7-threshold rule.  The approach of Mann09 builds on Mann08, but does not appear to be identical.  Mann09&#039;s summary of their methods is
&lt;blockquote&gt;We employ the global proxy data set used by [Mann08] comprising more than a thousand treering, ice core, coral, sediment, and other assorted proxy records spanning the ocean and land regions of both hemispheres over the past 1500 years. The surface temperature field is reconstructed by calibrating the proxy network against the spatial information contained within the instrumental annual mean surface temperature field [Brohan et al, JGRA, 2006] over a modern period of overlap between proxy and instrumental data (1850 to 1995) using the RegEM CFR procedure [Mann et al, JGRA, 2007] with additional minor modifications.&lt;/blockquote&gt;
Links to Mann09 text and SI at the post linked in my prior comment.]]></description>
		<content:encoded><![CDATA[<p>Yes, the Mann09 recons start at 500 AD.</p>
<p>I don&#8217;t know about the 7-threshold rule.  The approach of Mann09 builds on Mann08, but does not appear to be identical.  Mann09&#8242;s summary of their methods is</p>
<blockquote><p>We employ the global proxy data set used by [Mann08] comprising more than a thousand treering, ice core, coral, sediment, and other assorted proxy records spanning the ocean and land regions of both hemispheres over the past 1500 years. The surface temperature field is reconstructed by calibrating the proxy network against the spatial information contained within the instrumental annual mean surface temperature field [Brohan et al, JGRA, 2006] over a modern period of overlap between proxy and instrumental data (1850 to 1995) using the RegEM CFR procedure [Mann et al, JGRA, 2007] with additional minor modifications.</p></blockquote>
<p>Links to Mann09 text and SI at the post linked in my prior comment.</p>
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		<title>By: UC</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-295906</link>
		<dc:creator><![CDATA[UC]]></dc:creator>
		<pubDate>Tue, 28 Jun 2011 21:23:55 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-295906</guid>
		<description><![CDATA[Interesting, haven&#039;t read Mann09 yet (takes about 5 years to replicate one Mann paper, still some small issues with MBH98). Mann09 S8 also starts at AD 500, same robust-7-threshold rule applies ?]]></description>
		<content:encoded><![CDATA[<p>Interesting, haven&#8217;t read Mann09 yet (takes about 5 years to replicate one Mann paper, still some small issues with MBH98). Mann09 S8 also starts at AD 500, same robust-7-threshold rule applies ?</p>
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		<title>By: AMac</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-295801</link>
		<dc:creator><![CDATA[AMac]]></dc:creator>
		<pubDate>Tue, 28 Jun 2011 16:09:23 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-295801</guid>
		<description><![CDATA[UC (Jun 28, 2011 at 10:52 AM) --

Also see Mann&lt;i&gt;09&lt;/i&gt; SI Fig. S8, which shows both no-dendro/yes-Tilj (blue line) and no-dendro/no-Tilj (green line) EIV reconstructions.

The green line is dashed prior to 1500 AD, signifying that this recon failed Mann09&#039;s validation test at the 95% level.  Unfortunately, the trace is so faint that it is hard to visualize.  

In the third graphic at &lt;a href=&quot;http://amac1.blogspot.com/2011/06/voldemorts-question.html&quot; rel=&quot;nofollow&quot;&gt;this recent post&lt;/a&gt;, I overwrote the green dashes with a solid green line.  This makes it easy to contrast no-dendro/yes-Tilj and no-dendro/no-Tilj -- the most informative comparison, in my opinion.]]></description>
		<content:encoded><![CDATA[<p>UC (Jun 28, 2011 at 10:52 AM) &#8211;</p>
<p>Also see Mann<i>09</i> SI Fig. S8, which shows both no-dendro/yes-Tilj (blue line) and no-dendro/no-Tilj (green line) EIV reconstructions.</p>
<p>The green line is dashed prior to 1500 AD, signifying that this recon failed Mann09&#8242;s validation test at the 95% level.  Unfortunately, the trace is so faint that it is hard to visualize.  </p>
<p>In the third graphic at <a href="http://amac1.blogspot.com/2011/06/voldemorts-question.html" rel="nofollow">this recent post</a>, I overwrote the green dashes with a solid green line.  This makes it easy to contrast no-dendro/yes-Tilj and no-dendro/no-Tilj &#8212; the most informative comparison, in my opinion.</p>
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		<title>By: UC</title>
		<link>http://climateaudit.org/2011/06/09/richard-smith-on-pc-retention/#comment-295789</link>
		<dc:creator><![CDATA[UC]]></dc:creator>
		<pubDate>Tue, 28 Jun 2011 15:52:22 +0000</pubDate>
		<guid isPermaLink="false">http://climateaudit.org/?p=13816#comment-295789</guid>
		<description><![CDATA[&lt;blockquote&gt;Why Mann08 Fig. S8 b starts at year 500?
&lt;/blockquote&gt;

I forgot that Mann08 SI says


&lt;blockquote&gt;As a further safeguard against
potentially nonrobust results, a minimum of seven predictors in
a given hemisphere was required in implementing the EIV
procedure.
&lt;/blockquote&gt;

..and if I remove 4 Tiljanders there are only 6 predictors remaining for this step.]]></description>
		<content:encoded><![CDATA[<blockquote><p>Why Mann08 Fig. S8 b starts at year 500?
</p></blockquote>
<p>I forgot that Mann08 SI says</p>
<blockquote><p>As a further safeguard against<br />
potentially nonrobust results, a minimum of seven predictors in<br />
a given hemisphere was required in implementing the EIV<br />
procedure.
</p></blockquote>
<p>..and if I remove 4 Tiljanders there are only 6 predictors remaining for this step.</p>
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