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> <channel><title>Autarchy of the Private Cave &#187; statistics</title> <atom:link href="https://bogdan.org.ua/tags/statistics/feed" rel="self" type="application/rss+xml" /><link>https://bogdan.org.ua</link> <description>Tiny bits of bioinformatics, [web-]programming etc</description> <lastBuildDate>Wed, 28 Dec 2022 16:09:04 +0000</lastBuildDate> <language>en-US</language> <sy:updatePeriod>hourly</sy:updatePeriod> <sy:updateFrequency>1</sy:updateFrequency> <generator>https://wordpress.org/?v=3.8.27</generator> <item><title>R functions for regression analysis cheat sheet</title><link>https://bogdan.org.ua/2012/05/29/r-functions-for-regression-analysis-cheat-sheet.html</link> <comments>https://bogdan.org.ua/2012/05/29/r-functions-for-regression-analysis-cheat-sheet.html#comments</comments> <pubDate>Tue, 29 May 2012 13:11:48 +0000</pubDate> <dc:creator><![CDATA[Bogdan]]></dc:creator> <category><![CDATA[Bioinformatics]]></category> <category><![CDATA[Links]]></category> <category><![CDATA[Misc]]></category> <category><![CDATA[R]]></category> <category><![CDATA[statistics]]></category> <guid
isPermaLink="false">http://bogdan.org.ua/?p=1838</guid> <description><![CDATA[Original PDF. My local copy.]]></description> <content:encoded><![CDATA[<p>Original <a
href="http://cran.r-project.org/doc/contrib/Ricci-refcard-regression.pdf">PDF</a>.<br
/> My local <a
href='/wp-content/uploads/2012/05/Ricci-refcard-regression.pdf'>copy</a>.</p><p><a
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isPermaLink="false">http://bogdan.org.ua/?p=1831</guid> <description><![CDATA[Usually I&#8217;m using 10-fold (non-stratified) CV to measure the predictive power of the models: it gives consistent results, and is easy to perform (at least on smaller datasets). Just came across the Akaikeâ€™s InforÂ­maÂ­tion Criterion (AIC) and Schwarz Bayesian InforÂ­maÂ­tion Criterion (BIC). Citing robjhyndman, AsympÂ­totÂ­iÂ­cally, minÂ­iÂ­mizÂ­ing the AIC is equivÂ­aÂ­lent to minÂ­iÂ­mizÂ­ing the CV value. [&#8230;]]]></description> <content:encoded><![CDATA[<p>Usually I&#8217;m using 10-fold (non-stratified) <abbr
title="cross-validation">CV</abbr> to measure the predictive power of the models: it gives consistent results, and is easy to perform (at least on smaller datasets).</p><p>Just came across the Akaikeâ€™s InforÂ­maÂ­tion Criterion (AIC) and Schwarz Bayesian InforÂ­maÂ­tion Criterion (BIC). Citing <a
href="http://robjhyndman.com/researchtips/crossvalidation/">robjhyndman</a>,</p><blockquote><p> AsympÂ­totÂ­iÂ­cally, minÂ­iÂ­mizÂ­ing the AIC is equivÂ­aÂ­lent to minÂ­iÂ­mizÂ­ing the CV value. This is true for any model (<a
href="http://www.jstor.org/stable/2984877" class="vt-p broken_link" rel="nofollow">Stone 1977</a>), not just linÂ­ear modÂ­els. It is this propÂ­erty that makes the AIC so useÂ­ful in model selecÂ­tion when the purÂ­pose is prediction.<br
/> &#8230;<br
/> Because of the heavÂ­ier penalty, the model choÂ­sen by BIC is either the same as that choÂ­sen by AIC, or one with fewer terms. AsympÂ­totÂ­iÂ­cally, for linÂ­ear modÂ­els minÂ­iÂ­mizÂ­ing BIC is equivÂ­aÂ­lent to leaveâ€“vâ€“out cross-â€‹â€‹validation when v = n[1-1/(log(n)-1)] (<a
href="http://www3.stat.sinica.edu.tw/statistica/oldpdf/A7n21.pdf" class="vt-p">Shao 1997</a>).</p></blockquote><p>Want to try AIC and maybe BIC on my models. Conveniently, both functions exist in R.</p><p><a
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isPermaLink="false">http://bogdan.org.ua/?p=1015</guid> <description><![CDATA[R time series tutorial (2010, a website of the &#8220;Time Series Analysis and Its Applications: With R Examples&#8221; book) Statistics with R (2007) R for programmers PDF (2008, 104 pages, linked to from here) Brief R tutorial (2004) Statistical computing with R: a tutorial (2004) An introduction to R (from the official r-project website, should [&#8230;]]]></description> <content:encoded><![CDATA[<ul><li><a
href="http://www.stat.pitt.edu/stoffer/tsa2/R_time_series_quick_fix.htm">R time series tutorial</a> (2010, a website of the &#8220;Time Series Analysis and Its Applications: With R Examples&#8221; book)</li><li><a
href="http://zoonek2.free.fr/UNIX/48_R/all.html">Statistics with R</a> (2007)</li><li><a
href="http://heather.cs.ucdavis.edu/~matloff/R/RProg.pdf">R for programmers</a> PDF (2008, 104 pages, linked to from <a
href="http://heather.cs.ucdavis.edu/~matloff/r.html">here</a>)</li><li><a
href="http://mercury.bio.uaf.edu/mercury/R/R.html" class="broken_link" rel="nofollow">Brief R tutorial</a> (2004)</li><li><a
href="http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html" class="broken_link" rel="nofollow">Statistical computing with R: a tutorial</a> (2004)</li><li><a
href="http://cran.r-project.org/doc/manuals/R-intro.html">An introduction to R</a> (from the official r-project website, should be always up-to-date)</li><li><a
href="http://www.cyclismo.org/tutorial/R/">R tutorial</a> (date unknown, definitely newer than 2005)</li></ul><p><a
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class="a2a_dd addtoany_share_save addtoany_share" href="https://www.addtoany.com/share#url=https%3A%2F%2Fbogdan.org.ua%2F2010%2F03%2F29%2Fr-tutorial-links.html&#038;title=R%20tutorial%20links" data-a2a-url="https://bogdan.org.ua/2010/03/29/r-tutorial-links.html" data-a2a-title="R tutorial links"><img
src="https://static.addtoany.com/buttons/share_save_120_16.png" alt="Share"></a></p>]]></content:encoded> <wfw:commentRss>https://bogdan.org.ua/2010/03/29/r-tutorial-links.html/feed</wfw:commentRss> <slash:comments>1</slash:comments> </item> <item><title>Standard deviation and variance in pictures</title><link>https://bogdan.org.ua/2010/01/24/standard-deviation-and-variance-in-pictures.html</link> <comments>https://bogdan.org.ua/2010/01/24/standard-deviation-and-variance-in-pictures.html#comments</comments> <pubDate>Sun, 24 Jan 2010 14:07:42 +0000</pubDate> <dc:creator><![CDATA[Bogdan]]></dc:creator> <category><![CDATA[Links]]></category> <category><![CDATA[math]]></category> <category><![CDATA[standard deviation]]></category> <category><![CDATA[statistics]]></category> <category><![CDATA[variance]]></category> <category><![CDATA[youngling]]></category> <guid
isPermaLink="false">http://bogdan.org.ua/?p=965</guid> <description><![CDATA[MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more. For example, there is a step-by-step instruction on calculating variance and standard deviation for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points within each [&#8230;]]]></description> <content:encoded><![CDATA[<p><a
href="http://www.mathsisfun.com/"><img
src="http://bogdan.org.ua/wp-content/uploads/2010/01/mif120_60.gif" alt="" title="MathIsFun" width="120" height="60" class="alignleft size-full wp-image-966" /></a>MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more.</p><p></p><p>For example, there is a <a
href="http://www.mathsisfun.com/standard-deviation.html" class="broken_link" rel="nofollow">step-by-step instruction on calculating variance and standard deviation</a> for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points <a
href="http://bogdan.org.ua/2006/09/14/mean-standard-deviation-and-stem-and-leaf-plot.html">within each sigma range</a> are not discussed, but that might as well be too much for a nice explanation. There are also animations, like this <a
href="http://www.mathsisfun.com/data/mean-machine.html">mean machine</a>. Overall, MathIsFun is a nice resource for younglings.<br
/> <img
src="http://bogdan.org.ua/wp-content/uploads/2010/01/statistics-standard-deviation-500x167.gif" alt="" title="one-sigma from mean" width="500" height="167" class="aligncenter size-medium wp-image-967" /></p><p><a
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class="a2a_dd addtoany_share_save addtoany_share" href="https://www.addtoany.com/share#url=https%3A%2F%2Fbogdan.org.ua%2F2010%2F01%2F24%2Fstandard-deviation-and-variance-in-pictures.html&#038;title=Standard%20deviation%20and%20variance%20in%20pictures" data-a2a-url="https://bogdan.org.ua/2010/01/24/standard-deviation-and-variance-in-pictures.html" data-a2a-title="Standard deviation and variance in pictures"><img
src="https://static.addtoany.com/buttons/share_save_120_16.png" alt="Share"></a></p>]]></content:encoded> <wfw:commentRss>https://bogdan.org.ua/2010/01/24/standard-deviation-and-variance-in-pictures.html/feed</wfw:commentRss> <slash:comments>0</slash:comments> </item> <item><title>Mean, standard deviation, and stem-and-leaf plot</title><link>https://bogdan.org.ua/2006/09/14/mean-standard-deviation-and-stem-and-leaf-plot.html</link> <comments>https://bogdan.org.ua/2006/09/14/mean-standard-deviation-and-stem-and-leaf-plot.html#comments</comments> <pubDate>Thu, 14 Sep 2006 14:07:58 +0000</pubDate> <dc:creator><![CDATA[Bogdan]]></dc:creator> <category><![CDATA[Science]]></category> <category><![CDATA[book]]></category> <category><![CDATA[mean]]></category> <category><![CDATA[plot]]></category> <category><![CDATA[standard deviation]]></category> <category><![CDATA[statistics]]></category> <category><![CDATA[stem-and-leaf]]></category> <guid
isPermaLink="false">http://www.bogdan.org.ua/2006/09/14/mean-standard-deviation-and-stem-and-leaf-plot.html</guid> <description><![CDATA[I am doing some simple statistics now, and had to review some basic concepts like standard deviation. As a note to myself and anyone interested, here it stays. The mean is just a sum of all your numerical observations, divided by the number of observations. E.g., if you have measured how tall your 5 children [&#8230;]]]></description> <content:encoded><![CDATA[<p>I am doing some simple statistics now, and had to review some basic concepts like standard deviation.<br
/> As a note to myself and anyone interested, here it stays.</p><p>The <a
href="http://en.wikipedia.org/wiki/Mean">mean</a> is just a sum of all your numerical observations, divided by the number of observations. E.g., if you have measured how tall your 5 children are, and got the values 1.42, 1.56, 1.05, 1.89, 1.92, the &#8220;mean height&#8221; of your children will be <span
style="text-decoration:overline;">x</span> = (1.42 + 1.56 + 1.05 + 1.89 + 1.92) / 5, <span
style="text-decoration:overline;">x</span> = 7.84 / 5 = 1.568 (all values in metres).</p><p>The mean itself doesn&#8217;t tell you much, however. If you had this 1.568 mean available, you wouldn&#8217;t know even the range of heights.</p><p>The <a
href="http://en.wikipedia.org/wiki/Standard_deviation">standard deviation</a> helps with this. First of all, it is measured in the same units as initial data &#8211; i.e. metres in our example. Second, it gives you an idea of how strongly do the measured values differ in your sample &#8211; the bigger the deviation, the longer is the value range measured in the sample.<br
/> <span
id="more-28"></span><br
/> Calculating standard deviation is simple (image &copy; wikipedia):<br
/><center><img
src="http://bogdan.org.ua/wp-content/uploads/2006/09/sigma.png" alt="sigma = \sqrt{\frac{1}{N} \sum_{i=1}^N (x_i - \overline{x})^2}" /></center><br
/> Here: N &#8211; number of data points (=5 in our example), <span
style="text-decoration:overline;">x</span> &#8211; mean, x<sub>i</sub> &#8211; each data point.</p><p>If we calculate sigma (standard deviation) for the example above, we will get:</p><p>&sigma; = sqrt( ( (1.42-1.57)^2 + (1.56-1.57)^2 + (1.05-1.57)^2 + (1.89-1.57)^2 + (1.92-1.57)^2)  / 5)<br
/> &sigma; = sqrt( 0.023 + 0 + 0.27 + 0.102 + 0.122 / 5)<br
/> &sigma; = sqrt( 0.517 / 5 )<br
/> &sigma; = sqrt( 0.103 ) = 0.32 metres</p><p>So now, if you write you measurements like this:<br
/> height = 1.57<span
style="text-decoration:underline;">+</span>0.32<br
/> that will read like: &#8220;on average, my 5 children are 1.57 metres high, and most of them are from (1.57-0.32) to (1.57+0.32) metres high&#8221;. That &#8220;most&#8221; in the previous sentence actually means 68.2% of all data points (or children heights in this case) (image from <a
href="http://en.wikipedia.org/wiki/File:Standard_deviation_diagram.png">wikipedia</a>):<br
/><center><img
src="http://bogdan.org.ua/wp-content/uploads/2006/09/stddevdiag.png" alt="standard deviation diagram" /></center></p><p>(More comprehensive version of this help image exists <a
href="http://en.wikipedia.org/wiki/File:Normal_distribution_and_scales.gif">here</a>:<br
/><center><img
src="http://bogdan.org.ua/wp-content/uploads/2006/17/distribution_and_scales.gif" alt="distribution and scales" /></center><br
/> Get <a
href="http://bogdan.org.ua/wp-content/uploads/2006/17/Normal_distribution_and_scales.gif">larger version</a>)</p><p>So if you want to include 95% of children heights, that will be (1.57-0.32*2) to (1.57+0.32*2), where 0.32 is the standard deviation we calculated above.</p><p>Now to the stem-and-leaf plot. Reading a <a
href="http://www.amazon.com/gp/product/0727915525?ie=UTF8&#038;tag=bioua-20&#038;linkCode=as2&#038;camp=1789&#038;creative=9325&#038;creativeASIN=0727915525">book on statistics</a><img
src="http://www.assoc-amazon.com/e/ir?t=bioua-20&#038;l=as2&#038;o=1&#038;a=0727915525" width="1px" height="1px" border="0" alt="" style="border:none !important; margin:0px !important;" />, I came across a simple method to evaluate your (small) numeric dataset without calculating mean and sigma. I will follow the book and cite it extensively.</p><p>For example, a pediatric registrar in a district general hospital is investigating the amount of lead in the urine of children from a nearby housing estate. In a particular street there are 15 children whose ages range from 1 year to under 16, and in a preliminary study the registrar has found the following amounts of urinary lead (Î¼mol/24 h):<br
/> 0.6, 2.6, 0.1, 1.1, 0.4, 2.0, 0.8, 1.3, 1.2, 1.5, 3.2, 1.7, 1.9, 1.9, 2.2</p><p>A simple way to order, and also to display, the data is to use a stem and leaf plot. To do this we need to abbreviate the observations to two significant digits. In the case of the urinary concentration data, the digit to the left of the decimal point is the â€œstemâ€ and the digit to the right the â€œleaf â€. We first write the stems in order down the page. We then work along the data set, writing the leaves down â€œas they comeâ€. Thus, for the first data point, we write a 6 opposite the 0 stem, and so on:</p><p><center><img
src="http://bogdan.org.ua/wp-content/uploads/2006/09/stem1.png" alt="ordered stems, and leafs as they come graph" /></center></p><p>We then order the leaves:</p><p><center><img
src="http://bogdan.org.ua/wp-content/uploads/2006/09/stem1.png" alt="both stems and leafs ordered" /></center></p><p>The advantage of first setting the figures out in order of size and not simply feeding them straight from notes into a calculator (for example, to find their mean) is that the relation of each to the next can be looked at. Is there a steady progression, a noteworthy hump, a considerable gap? Simple inspection can disclose irregularities. Furthermore, a glance at the figures gives information on their range. The smallest value is 0.1 and the largest is 3.2 Î¼mol/24 h.</p><p>Hope this helps you.</p><p><script type="text/javascript" src="http://www.assoc-amazon.com/s/link-enhancer?tag=bioua-20&#038;o=1"></script></p> <noscript> <img
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