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	<title>Comments for bayesianbiologist</title>
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	<link>http://bayesianbiologist.com</link>
	<description>Corey Chivers on P(A&#124;B) ∝P(B&#124;A)P(A)</description>
	<lastBuildDate>Thu, 23 May 2013 14:29:11 +0000</lastBuildDate>
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		<title>Comment on Uncertainty in markov chains: fun with snakes and ladders by Generating a Markov chain vs. computing the transition matrix &#124; Freakonometrics</title>
		<link>http://bayesianbiologist.com/2011/12/31/uncertainty-in-markov-chains-fun-with-snakes-and-ladders/#comment-1110</link>
		<dc:creator><![CDATA[Generating a Markov chain vs. computing the transition matrix &#124; Freakonometrics]]></dc:creator>
		<pubDate>Thu, 23 May 2013 14:29:11 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=144#comment-1110</guid>
		<description><![CDATA[[&#8230;] blog, about snakes and ladders (see http://kbroman.wordpress.com/&#8230;) with Karl and Corey (see http://bayesianbiologist.com/&#8230;.), and the use of Markov Chain. I do believe that this application is truly awesome: the example is [&#8230;]]]></description>
		<content:encoded><![CDATA[<p>[&#8230;] blog, about snakes and ladders (see <a href="http://kbroman.wordpress.com/&#038;#8230" rel="nofollow">http://kbroman.wordpress.com/&#038;#8230</a> <img src='http://s1.wp.com/wp-includes/images/smilies/icon_wink.gif' alt=';)' class='wp-smiley' />  with Karl and Corey (see <a href="http://bayesianbiologist.com/&#038;#8230" rel="nofollow">http://bayesianbiologist.com/&#038;#8230</a>;.), and the use of Markov Chain. I do believe that this application is truly awesome: the example is [&#8230;]</p>
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		<title>Comment on Did the sun just explode? The last Dutch Book you&#8217;ll ever make by AlexandreAlexandre</title>
		<link>http://bayesianbiologist.com/2012/11/09/did-the-sun-just-explode-the-last-dutch-book-youll-ever-make/#comment-1105</link>
		<dc:creator><![CDATA[AlexandreAlexandre]]></dc:creator>
		<pubDate>Mon, 20 May 2013 16:05:32 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=690#comment-1105</guid>
		<description><![CDATA[Moreover, this test is inadmissible since it is based on an ancillary statistic.

What we have to keep in mind is that the classical modeling is so vast* and full of possibilities that many types of bizarre conclusions can arise when we are not concerned about optimal properties. We could restrict ourselves only to tests based on the likelihood ratio statistics or other optimal procedure. 

Notice that, Bayesians use the likelihood function and, in addition, represent prior information by probability distributions, so the set of possibilities to build a test is restrict. On the other hand, classical statisticians also have the option of using the likelihood function (but is not mandatory), they implicitly represent prior information by possibility distributions, so the set of possibilities to build a test is sensibly bigger than the Bayesian procedure.

*We can model by using likelihoods, pseudo-likelihoods, matching moments, estimating equations and so forth.]]></description>
		<content:encoded><![CDATA[<p>Moreover, this test is inadmissible since it is based on an ancillary statistic.</p>
<p>What we have to keep in mind is that the classical modeling is so vast* and full of possibilities that many types of bizarre conclusions can arise when we are not concerned about optimal properties. We could restrict ourselves only to tests based on the likelihood ratio statistics or other optimal procedure. </p>
<p>Notice that, Bayesians use the likelihood function and, in addition, represent prior information by probability distributions, so the set of possibilities to build a test is restrict. On the other hand, classical statisticians also have the option of using the likelihood function (but is not mandatory), they implicitly represent prior information by possibility distributions, so the set of possibilities to build a test is sensibly bigger than the Bayesian procedure.</p>
<p>*We can model by using likelihoods, pseudo-likelihoods, matching moments, estimating equations and so forth.</p>
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		<title>Comment on What is probabilistic truth? by fer_rabanal</title>
		<link>http://bayesianbiologist.com/2013/05/18/what-is-probabilistic-truth/#comment-1101</link>
		<dc:creator><![CDATA[fer_rabanal]]></dc:creator>
		<pubDate>Mon, 20 May 2013 09:08:46 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=917#comment-1101</guid>
		<description><![CDATA[Reblogged this on &lt;a href=&quot;http://easymlworld.wordpress.com/2013/05/20/what-is-probabilistic-truth/&quot; rel=&quot;nofollow&quot;&gt;Easy ML World&lt;/a&gt;.]]></description>
		<content:encoded><![CDATA[<p>Reblogged this on <a href="http://easymlworld.wordpress.com/2013/05/20/what-is-probabilistic-truth/" rel="nofollow">Easy ML World</a>.</p>
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		<title>Comment on Did the sun just explode? The last Dutch Book you&#8217;ll ever make by Alexandre</title>
		<link>http://bayesianbiologist.com/2012/11/09/did-the-sun-just-explode-the-last-dutch-book-youll-ever-make/#comment-1096</link>
		<dc:creator><![CDATA[Alexandre]]></dc:creator>
		<pubDate>Sun, 19 May 2013 04:02:49 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=690#comment-1096</guid>
		<description><![CDATA[The problem here is that the p-value for this problem is not 1/36. Notice that, we have the following two hypotheses, namely

H0: The Sun didn&#039;t explode,
H1: The Sun exploded.

Then,

p-value = P(&quot;the machine returns yes&quot;, when the Sun didn&#039;t explode).

Now, note that the event

&quot;the machine returns yes&quot;

is equivalent to

&quot;the neutrino detector measures the Sun exploding AND tells the true result&quot; OR &quot;the neutrino detector does not measure the Sun exploding AND lies to us&quot;.

Assuming that the dice throwing is independent of the neutrino detector measurement, we can compute the p-value. First define:

p0 = P(&quot;the neutrino detector measures the Sun exploding&quot;, when the Sun didn&#039;t explode),

then the p-value is

p-value = p0*35/36 + (1-p0)*1/36

=&gt; p-value = (1/36)*(35*p0 + 1 - p0)

=&gt; p-value = (1/36)*(1+34*p0).

If p0 = 0, then we are considering that the detector machine will never measure that &quot;the Sun just exploded&quot;.  The value p0 is obviously incomputable, therefore, a classical statistician that knows how to compute a p-value would never say that the Sun just exploded. By the way, the cartoon is funny.]]></description>
		<content:encoded><![CDATA[<p>The problem here is that the p-value for this problem is not 1/36. Notice that, we have the following two hypotheses, namely</p>
<p>H0: The Sun didn&#8217;t explode,<br />
H1: The Sun exploded.</p>
<p>Then,</p>
<p>p-value = P(&#8220;the machine returns yes&#8221;, when the Sun didn&#8217;t explode).</p>
<p>Now, note that the event</p>
<p>&#8220;the machine returns yes&#8221;</p>
<p>is equivalent to</p>
<p>&#8220;the neutrino detector measures the Sun exploding AND tells the true result&#8221; OR &#8220;the neutrino detector does not measure the Sun exploding AND lies to us&#8221;.</p>
<p>Assuming that the dice throwing is independent of the neutrino detector measurement, we can compute the p-value. First define:</p>
<p>p0 = P(&#8220;the neutrino detector measures the Sun exploding&#8221;, when the Sun didn&#8217;t explode),</p>
<p>then the p-value is</p>
<p>p-value = p0*35/36 + (1-p0)*1/36</p>
<p>=&gt; p-value = (1/36)*(35*p0 + 1 &#8211; p0)</p>
<p>=&gt; p-value = (1/36)*(1+34*p0).</p>
<p>If p0 = 0, then we are considering that the detector machine will never measure that &#8220;the Sun just exploded&#8221;.  The value p0 is obviously incomputable, therefore, a classical statistician that knows how to compute a p-value would never say that the Sun just exploded. By the way, the cartoon is funny.</p>
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		<title>Comment on What is probabilistic truth? by Jan van Rongen (@MrOoijer)</title>
		<link>http://bayesianbiologist.com/2013/05/18/what-is-probabilistic-truth/#comment-1094</link>
		<dc:creator><![CDATA[Jan van Rongen (@MrOoijer)]]></dc:creator>
		<pubDate>Sat, 18 May 2013 17:20:56 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=917#comment-1094</guid>
		<description><![CDATA[Let T be the Threshold used and x(1) ... x(m)  and y(1) ... y(n) the values for the prediction function of the dependent variable that can take the two values x and y.

Suppose x(1)&lt;.. &lt;x(m-1)&lt;T&lt;x(m)&lt;y(1)&lt; .. &lt;y(n), then AUC=1 but the prediction is not perfect. So yes, a perfect model has AUC=1 but not the other way around. Thus I wonder why we do not use RMSE or OOB that attain 100% only when the prediction is perfect.]]></description>
		<content:encoded><![CDATA[<p>Let T be the Threshold used and x(1) &#8230; x(m)  and y(1) &#8230; y(n) the values for the prediction function of the dependent variable that can take the two values x and y.</p>
<p>Suppose x(1)&lt;.. &lt;x(m-1)&lt;T&lt;x(m)&lt;y(1)&lt; .. &lt;y(n), then AUC=1 but the prediction is not perfect. So yes, a perfect model has AUC=1 but not the other way around. Thus I wonder why we do not use RMSE or OOB that attain 100% only when the prediction is perfect.</p>
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	<item>
		<title>Comment on P-value fallacy on More or Less by Another comment on p-values &#124; Mathematics in everyday life</title>
		<link>http://bayesianbiologist.com/2011/08/21/p-value-fallacy-on-more-or-less/#comment-995</link>
		<dc:creator><![CDATA[Another comment on p-values &#124; Mathematics in everyday life]]></dc:creator>
		<pubDate>Mon, 15 Apr 2013 15:49:37 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.wordpress.com/?p=52#comment-995</guid>
		<description><![CDATA[[...] know this issue has been brought up many times, but I just read this excellent post, and wanted to bring it up [...]]]></description>
		<content:encoded><![CDATA[<p>[...] know this issue has been brought up many times, but I just read this excellent post, and wanted to bring it up [...]</p>
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		<title>Comment on Mathematical abstraction and the robustness to assumptions by Ken Butler</title>
		<link>http://bayesianbiologist.com/2013/04/12/mathematical-abstraction-and-the-robustness-to-assumptions/#comment-990</link>
		<dc:creator><![CDATA[Ken Butler]]></dc:creator>
		<pubDate>Sun, 14 Apr 2013 01:29:55 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=895#comment-990</guid>
		<description><![CDATA[My feeling too: it would take a lot to change the 1/6-analysis enough to break the non-transitivity of the dice.

(I have a die with 2&#039;s on three faces and 5&#039;s on the other. I plan to roll this one for my big Stats class and see how long it takes for them to catch on....)]]></description>
		<content:encoded><![CDATA[<p>My feeling too: it would take a lot to change the 1/6-analysis enough to break the non-transitivity of the dice.</p>
<p>(I have a die with 2&#8242;s on three faces and 5&#8242;s on the other. I plan to roll this one for my big Stats class and see how long it takes for them to catch on&#8230;.)</p>
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		<title>Comment on A quick guide to non-transitive Grime Dice by Mathematical abstraction and the robustness to assumptions &#124; bayesianbiologist</title>
		<link>http://bayesianbiologist.com/2013/04/07/a-quick-guide-to-non-transitive-grime-dice/#comment-986</link>
		<dc:creator><![CDATA[Mathematical abstraction and the robustness to assumptions &#124; bayesianbiologist]]></dc:creator>
		<pubDate>Sat, 13 Apr 2013 01:43:03 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=868#comment-986</guid>
		<description><![CDATA[[...] &#8592; A quick guide to non-transitive Grime&#160;Dice    April 12, 2013 [...]]]></description>
		<content:encoded><![CDATA[<p>[...] &larr; A quick guide to non-transitive Grime&nbsp;Dice    April 12, 2013 [...]</p>
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		<title>Comment on A quick guide to non-transitive Grime Dice by Corey Chivers</title>
		<link>http://bayesianbiologist.com/2013/04/07/a-quick-guide-to-non-transitive-grime-dice/#comment-983</link>
		<dc:creator><![CDATA[Corey Chivers]]></dc:creator>
		<pubDate>Thu, 11 Apr 2013 20:17:04 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=868#comment-983</guid>
		<description><![CDATA[Ouch, nice catch. That was a typo. It should read: &quot;5/6 * 1/2 + 1/6 = 7/12&quot;. I&#039;ve corrected it above. Thanks!]]></description>
		<content:encoded><![CDATA[<p>Ouch, nice catch. That was a typo. It should read: &#8220;5/6 * 1/2 + 1/6 = 7/12&#8243;. I&#8217;ve corrected it above. Thanks!</p>
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		<title>Comment on A quick guide to non-transitive Grime Dice by nabash</title>
		<link>http://bayesianbiologist.com/2013/04/07/a-quick-guide-to-non-transitive-grime-dice/#comment-982</link>
		<dc:creator><![CDATA[nabash]]></dc:creator>
		<pubDate>Thu, 11 Apr 2013 18:54:37 +0000</pubDate>
		<guid isPermaLink="false">http://bayesianbiologist.com/?p=868#comment-982</guid>
		<description><![CDATA[For example, P(Red &gt; Blue) = 5/6 + 1/2, which is 7/12.
5/6 + 1/2 is not 7/12, I think.]]></description>
		<content:encoded><![CDATA[<p>For example, P(Red &gt; Blue) = 5/6 + 1/2, which is 7/12.<br />
5/6 + 1/2 is not 7/12, I think.</p>
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