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	<title>PCR&#039;s notepad &#187; science</title>
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	<link>http://notepad.patheticcockroach.com</link>
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		<title>Computing the standard normal cumulative distribution with R</title>
		<link>http://notepad.patheticcockroach.com/2414/computing-the-standard-normal-cumulative-distribution-with-r/</link>
		<comments>http://notepad.patheticcockroach.com/2414/computing-the-standard-normal-cumulative-distribution-with-r/#comments</comments>
		<pubDate>Mon, 21 Nov 2011 15:36:35 +0000</pubDate>
		<dc:creator>David Dernoncourt</dc:creator>
				<category><![CDATA[R (R-project)]]></category>
		<category><![CDATA[statistics]]></category>

		<guid isPermaLink="false">http://notepad.patheticcockroach.com/?p=2414</guid>
		<description><![CDATA[I recently had to compute the Bayes error for a Gaussian model. Let xi be a predictive variable, following a Gaussian distribution of variance 1 and mean Ti in a class, and -Ti in the other class. The Bayes error of the model is e=1-Φ(sqrt(sum(Ti^2)). In R, the standard normal cumulative distribution function is computed [...]]]></description>
			<content:encoded><![CDATA[<p>I recently had to compute the Bayes error for a Gaussian model.<br />
Let x<sub>i</sub> be a predictive variable, following a Gaussian distribution of variance 1 and mean T<sub>i</sub> in a class, and -T<sub>i</sub> in the other class.<br />
The Bayes error of the model is e=1-Φ(sqrt(sum(T<sub>i</sub>^2)).<br />
In R, the standard normal cumulative distribution function is computed using <strong>pnorm()</strong>.</p>
<p>So, here&#8217;s the Bayes error if for instance we have 10 variables with mean 0.5 in a class and -0.5 in the other class:<br />
<code>Bayes_error=1-pnorm(1*sqrt(10*0.5^2));</code></p>
<p>If we had more complicated things, like 5 variables with mean 0.5,0.6,0.7,0.8,0.9 in a class and -0.5,-0.6,-0.7,-0.8,-0.9 in the other, we could do something like:<br />
<code>mus=c(0.5,0.6,0.7,0.8,0.9);<br />
Bayes_error=1-pnorm(1*sqrt(t(mus)%*%mus));</code><br />
or not vectorized: <code>Bayes_error=1-pnorm(1*sqrt(sum(mus*mus)));</code></p>
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		<item>
		<title>How to restrict a PubMed search to PubMed&#8217;s main journals?</title>
		<link>http://notepad.patheticcockroach.com/1251/how-to-restrict-a-pubmed-search-to-pubmeds-main-journals/</link>
		<comments>http://notepad.patheticcockroach.com/1251/how-to-restrict-a-pubmed-search-to-pubmeds-main-journals/#comments</comments>
		<pubDate>Sat, 08 Jan 2011 16:08:38 +0000</pubDate>
		<dc:creator>David Dernoncourt</dc:creator>
				<category><![CDATA[science]]></category>

		<guid isPermaLink="false">http://notepad.patheticcockroach.com/?p=1251</guid>
		<description><![CDATA[This post in a one-word nutshell: jsubsetaim. Usually when I have such a simple question, I just type it into Google Scroogle and voilà. You know, standard Tech support cheat sheet algorithm. But this time it just didn&#8217;t work. Oddly enough, that basic question doesn&#8217;t seem to be answered anywhere. Or at least not clearly. [...]]]></description>
			<content:encoded><![CDATA[<p>This post in a one-word nutshell: <em>jsubsetaim</em>.</p>
<p>Usually when I have such a simple question, I just type it into <del>Google</del> Scroogle and voilà. You know, standard <a href="http://gal.patheticcockroach.com/humor/computers/tech_support_cheat_sheet">Tech support cheat sheet</a> algorithm. But this time it just didn&#8217;t work. Oddly enough, that basic question doesn&#8217;t seem to be answered anywhere. Or at least not clearly.<br />
Anyway, after searching a bit around the <a href="http://www.ncbi.nlm.nih.gov/pubmed/limits">PubMed search limits</a>, I eventually found the <em>Core clinical journals</em> subset. And those core clinical journals, aka Abridged Index Medicus (AIM) are just it: the &#8220;main&#8221; (&#8220;most important&#8221;) PubMed journals. Check out the <a href="http://www.nlm.nih.gov/bsd/aim.html">list</a>: Nature, Lancet, The New England journal of medicine, etc.<br />
So, to search among those titles only you can go to limits and select the <em>Core clinical journals</em> subset, or more simply you can just add <em>jsubsetaim</em> within your PubMed query.</p>
]]></content:encoded>
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		<item>
		<title>Quick statistics competence assessment</title>
		<link>http://notepad.patheticcockroach.com/527/quick-statistics-competence-assessment/</link>
		<comments>http://notepad.patheticcockroach.com/527/quick-statistics-competence-assessment/#comments</comments>
		<pubDate>Thu, 18 Mar 2010 16:32:58 +0000</pubDate>
		<dc:creator>David Dernoncourt</dc:creator>
				<category><![CDATA[funnies]]></category>
		<category><![CDATA[statistics]]></category>

		<guid isPermaLink="false">http://notepad.patheticcockroach.com/?p=527</guid>
		<description><![CDATA[Do you understand the following comic? &#169; xkcdThis work is licensed under a Creative Commons Attribution-NonCommercial 2.5 License If you don&#8217;t, your statistical skills require an emergency treatment (unless you actually don&#8217;t use statistics) because you are likely to draw erroneous excessive conclusions. If you do, well, I can&#8217;t conclude.]]></description>
			<content:encoded><![CDATA[<p>Do you understand the following comic?<br />
<img src="http://img.patheticcockroach.com/01/xkcd_correlation.png" alt="Correlation vs causation" width="459" height="185"/></p>
<div style="text-align:center; font-size:x-small;">&copy; <a href="http://xkcd.com/552/">xkcd</a><br />This work is licensed under a <a href="http://creativecommons.org/licenses/by-nc/2.5/">Creative Commons Attribution-NonCommercial 2.5 License</a></div>
<p>If you don&#8217;t, your statistical skills require an emergency treatment (unless you actually don&#8217;t use statistics) because you are likely to draw <a href="http://www.sciencenews.org/view/feature/id/57091/title/Odds_Are,_Its_Wrong">erroneous excessive conclusions</a>.<br />
If you do, well, I can&#8217;t conclude.</p>
]]></content:encoded>
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		<item>
		<title>R-project Portable</title>
		<link>http://notepad.patheticcockroach.com/512/r-project-portable/</link>
		<comments>http://notepad.patheticcockroach.com/512/r-project-portable/#comments</comments>
		<pubDate>Thu, 21 Jan 2010 08:21:33 +0000</pubDate>
		<dc:creator>David Dernoncourt</dc:creator>
				<category><![CDATA[R (R-project)]]></category>
		<category><![CDATA[statistics]]></category>

		<guid isPermaLink="false">http://notepad.patheticcockroach.com/?p=512</guid>
		<description><![CDATA[The guys at R-project tell you that you can run R from a CD or USB drive (so it&#8217;s portable), but nowhere they provide you with a really portable version. I.e., you have to actually run the installer then you can make a portable copy of the R folder on your USB key. That&#8217;s not [...]]]></description>
			<content:encoded><![CDATA[<p>The guys at R-project tell you that you can <a href="http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-run-R-from-a-CD-or-USB-drive_003f">run R from a CD or USB drive</a> (so it&#8217;s portable), but nowhere they provide you with a really portable version. I.e., you have to actually run the installer then you can make a portable copy of the R folder on your USB key. That&#8217;s not exactly practical because if for instance you want to &#8220;install&#8221; it at work on a restricted computer where you can&#8217;t run an installer, you need to start with some homework first&#8230;<br />
So for the lazy like me, here is a <a href="http://www.megaupload.com/?d=57OV1VWC">portable version of R 2.10.1</a>. I made it from a custom installation (as far as I remember it&#8217;s like the standard installation without language packs and with only some of the manuals) and it&#8217;s in English, of course <img src='http://notepad.patheticcockroach.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
<p>Also, note that automatically installing additional packages should work fine on this portable version (I did so with my previous 2.10.0 portable, so no reason it wouldn&#8217;t work with that one).</p>
]]></content:encoded>
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		<slash:comments>4</slash:comments>
		</item>
		<item>
		<title>Calculating molar masses quickly and online</title>
		<link>http://notepad.patheticcockroach.com/435/calculating-molar-masses-quickly-and-online/</link>
		<comments>http://notepad.patheticcockroach.com/435/calculating-molar-masses-quickly-and-online/#comments</comments>
		<pubDate>Mon, 30 Nov 2009 10:19:39 +0000</pubDate>
		<dc:creator>David Dernoncourt</dc:creator>
				<category><![CDATA[chemistry]]></category>

		<guid isPermaLink="false">http://notepad.patheticcockroach.com/?p=435</guid>
		<description><![CDATA[Although I&#8217;m well aware and used to the fact that you can find anything on Internet, sometimes it still amazes me. Remember the time when you needed to fetch a periodic table of the chemical elements plus (optionally) a calculator to get a molar mass? Then came pieces of software that did it for you, [...]]]></description>
			<content:encoded><![CDATA[<p>Although I&#8217;m well aware and used to the fact that you can find anything on Internet, sometimes it still amazes me. Remember the time when you needed to fetch a periodic table of the chemical elements plus (optionally) a calculator to get a molar mass? Then came pieces of software that did it for you, but you still needed to fetch the software. Now, you can find the stuff anywhere on Internet, like at <a href="http://www.convertunits.com">convertunits.com</a>, where you can <a href="http://www.convertunits.com/molarmass.php?q=C6H2%28NO2%293CH3">calculate the molar mass of TNT</a> as easily as you can get the <a href="http://www.convertunits.com/molarmass.php?q=K">molar mass of potassium</a>. I personally found it when trying to compare the molar mass of sodium salt (58.44 g/mol) vs potassium salt (74.55 g/mol), which is the thing used in salt substitutes like LoSalt.</p>
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