{"id":63055,"date":"2016-01-08T23:30:32","date_gmt":"2016-01-09T04:30:32","guid":{"rendered":"http:\/\/1boringoldman.com\/?p=63055"},"modified":"2016-01-09T13:53:32","modified_gmt":"2016-01-09T18:53:32","slug":"john-henrys-hammer-an-interim-summary","status":"publish","type":"post","link":"https:\/\/1boringoldman.com\/index.php\/2016\/01\/08\/john-henrys-hammer-an-interim-summary\/","title":{"rendered":"john henry&#8217;s hammer: an interim summary&#8230;"},"content":{"rendered":"\n<div align=\"justify\"><em><sup><font color=\"#200020\">In a way, what I&#8217;m trying to do here is at cross purposes with some of my own beliefs. Short term Randomized Clinical Trials [RCTs] can tell us whether a drug has the desired medicinal properties; something about the strength of those properties; the incidence of early adverse effects; and can identify some but certainly not all serious toxicity. Long term trials, the experience of practicing clinicians, and the reports of patients taking these drugs are a much more important source of ongoing information. Our system of drug development and patenting has created a situation where the early clinical trials are way overvalued during the in-patent period [even the &quot;good ones&quot;], and often the medication harms are suppressed until they emerge in legal actions late in the day &#8211; after the damage has already been done. In addition, the early RCTs are industry productions, and many of them have made mincemeat of the scientific method they&#8217;re meant to represent.&nbsp; So I&#8217;m focusing on the efficacy testing of short term RCTs when we all know that the most important thing is the long term harms. But I base that approach on the medical principles of preventive medicine, specifically secondary prevention &#8211; early detection and rapid intervention. I know that the ultimate answer is Data Transparency and Independent Trial Analysis, but until that happens, educating as many people as possible about how to evaluate these early trials seems an essential way to intervene in the present&#8230;<\/font><\/sup><\/em><\/div>\n<p>                   <\/p>\n<div align=\"justify\" class=\"big\"><u><strong><font color=\"#200020\">The <em>a priori<\/em> Protocol<\/font><\/strong><\/u>:<\/div>\n<div align=\"justify\" class=\"small\">A randomized, placebo controlled, double-blinded clinical trial [<font color=\"#200020\">RCT<\/font> for short] is not exploratory research. It&#8217;s more in the range of product testing. And its validity rests on a formal declaration of the details of how the study will be conducted and specifically what measurements will be taken, what will be the primary [and secondary] outcome variables, and how the data will be analyzed. The phrase <em><font color=\"#200020\">a priori<\/font><\/em> means <em><font color=\"#200020\">before the study begins<\/font><\/em>. We can never count on the sanctity of the blinding. People peek. But we can trust a formal Protocol filed before the study starts. So step one in evaluating a study is to get the Protocol, or as close to the Protocol as possible. That information should be in the article, but if it&#8217;s unclear, you can often get at it from the information on <a href=\"https:\/\/clinicaltrials.gov\/\" target=\"_blank\">clinicaltrials.gov<\/a>. I&#8217;ve yet to see a study where the Protocol was changed in midstream that didn&#8217;t smell like three day old fish. Likewise, if you can&#8217;t figure out what the Primary and Secondary Outcome Variables are, be suspicious of the whole enterprise.<\/div>\n<p>                 <\/p>\n<div align=\"justify\" class=\"big\"><a href=\"https:\/\/en.wikipedia.org\/wiki\/Continuous_and_discrete_variables\" target=\"_blank\">Continuous Variables:<\/a><\/div>\n<div align=\"justify\" class=\"small\">Since we don&#8217;t have the luxury of seeing the raw data, we have to rely on <font color=\"#200020\">Summary Data<\/font>. In the case of Continuous Variables, that includes the <font color=\"#200020\">MEAN<\/font>, either the <font color=\"#200020\">Standard Deviation<\/font> or the <font color=\"#200020\">Standard Error of the Mean<\/font>, and the <font color=\"#200020\">Number<\/font> of subjects [<strong><font color=\"#200020\">&mu;<\/font><\/strong>,<strong><font color=\"#200020\"> &sigma; <\/font><\/strong>or<strong><font color=\"#200020\"> sem<\/font><\/strong>, and<strong><font color=\"#200020\"> n<\/font><\/strong>]. In groups of sufficient size [&gt;30], those three parameters are a reasonable proxy for the datasets. If the <font color=\"#200020\">Summary Data<\/font> is provided in the article, the task of quickly vetting a <font color=\"#200020\">Continuous Variables<\/font> is straightforward. Again, if you can&#8217;t figure out what the <font color=\"#200020\">Summary Data <\/font>is, be suspicious of the whole enterprise:<\/div>\n<ul><span class=\"small\">                <\/p>\n<li>\n<div align=\"justify\"><strong><font color=\"#200020\">STEP 1: The OMNIBUS Statistic<\/font><\/strong>:<\/div>\n<div align=\"justify\">If there are more than two groups [eg placebo+several drugs, placebo+several doses of a drug, etc], the first order of business is&nbsp; to test the significance of the whole dataset with an analysis of variance [often called the Omnibus Statistic]. With <font color=\"#200020\">Summary Data<\/font>, one can use the Internet Calculator provided on John C. Pezzullo&rsquo;s <a href=\"http:\/\/statpages.org\/index.html\" target=\"_blank\">statpages<\/a> &ndash; <a href=\"http:\/\/statpages.org\/anova1sm.html\" target=\"_blank\">Analysis of Variance from Summary Data<\/a> [see <a href=\"http:\/\/1boringoldman.com\/index.php\/2016\/01\/06\/john-henrys-hammer-continuous-variables-ii\/\">john henry&rsquo;s hammer: continuous variables II&hellip;<\/a>]. If the result is not significant, that means that the group&#8217;s variances are not different from the whole dataset&#8217;s variance, and no further testing is required. The study is negative for the tested variable &#8211; end of story. Even if STEP 2 produces pairwise significance, it is meaningless. There are plenty of studies that skip this step [notably Paxil Study 329]. Off-hand, I can think of no valid reason to skip it.<\/div>\n<\/li>\n<li>\n<div align=\"justify\"><strong><font color=\"#200020\">STEP 2: SIGNIFICANCE testing<\/font><\/strong>:<\/div>\n<div align=\"justify\">With Summary Data, the Pairwise Comparisons [placebo vs drug1, placebo vs drug2, drug1 vs drug 2] is also straightforward. There are any number of Internet Calculators that produce the same results. I recommended <a target=\"_blank\" href=\"http:\/\/graphpad.com\/quickcalcs\/ttest1\/?Format=SEM\">GraphPad QuickCalcs<\/a> because I like the interface [see <a href=\"http:\/\/1boringoldman.com\/index.php\/2016\/01\/05\/john-henrys-hammer-continuous-variables-i\/\" target=\"_blank\">john henry&rsquo;s hammer: continuous variables I&hellip;<\/a>]. The p-values are also invariably given in the article. Remember that p, the probability, is <em><font color=\"#200020\">qualitative<\/font><\/em>. Comments like &quot;almost significant&quot;, &quot;very significant&quot;, &quot;just barely significant&quot; are common &#8211; and meaningless.<\/div>\n<\/li>\n<li>\n<div align=\"justify\"><strong><font color=\"#200020\">STEP 3: EFFECT SIZE testing<\/font><\/strong>:<\/div>\n<div align=\"justify\">The various EFFECT SIZES are mathematical indices aiming to <font color=\"#200020\">quantify<\/font> the effect of a drug &#8211; its <em><font color=\"#200020\">strength<\/font><\/em>. The most common index with Continuous Variables is <em><font color=\"#200020\">Cohen&#8217;s d<\/font><\/em> &#8211; the difference between the two Means expressed as a function of the Standard Deviation &#8211; also called the <em><font color=\"#200020\">Standardized Mean Difference <\/font><\/em>[<em><font color=\"#200020\">SMD<\/font><\/em>]. It is usually reported with its <em><font color=\"#200020\">95% Confidence Interval<\/font><\/em>. I recommended using <a href=\"http:\/\/www.psychometrica.de\" target=\"_blank\">Psychometrica<\/a>&#8216;s <a href=\"http:\/\/www.psychometrica.de\/effect_size.html#cohenb\" target=\"_blank\">Comparison of groups with different sample size (Cohen&rsquo;s d, Hedges&rsquo; g)<\/a>. While one uses the same parameters as those used for significance testing, the Effect Size estimates add a <em><font color=\"#200020\">quantitative<\/font><\/em> dimension to the results. This is often omitted from published papers. So at the end of STEPs 1-3, you will have a table that looks like this &#8211; plenty enough information for an informed opinion:<\/div>\n<table cellspacing=\"0\" cellpadding=\"0\" border=\"0\" align=\"center\">\n<tr>\n<td align=\"center\" colspan=\"11\"><sup><strong><font color=\"#200020\">BREXPIPRAZOLE Trials in Schizophrenia<\/font><\/strong>                                          <\/p>\n<hr size=\"1\" \/><\/sup><\/td>\n<\/tr>\n<tr>\n<td width=\"45\" align=\"center\"><strong><font color=\"#200020\"><sup>STUDY<\/sup><\/font><\/strong><\/td>\n<td width=\"45\" align=\"center\"><strong><font color=\"#200020\"><sup>DRUG<\/sup><\/font><\/strong><\/td>\n<td width=\"45\" align=\"center\"><strong><font color=\"#200020\"><sup>MEAN<\/sup><\/font><\/strong><\/td>\n<td width=\"35\" align=\"center\"><strong><font color=\"#200020\"><sup>SEM<\/sup><\/font><\/strong><\/td>\n<td width=\"35\" align=\"center\"><strong><font color=\"#200020\"><sup>&sigma;<\/sup><\/font><\/strong><\/td>\n<td width=\"25\" align=\"center\"><strong><font color=\"#200020\"><sup>n<\/sup><\/font><\/strong><\/td>\n<td width=\"55\" align=\"center\"><strong><font color=\"#200020\"><sup>p<\/sup><\/font><\/strong><\/td>\n<td width=\"35\" align=\"center\"><strong><font color=\"#200020\"><sup>d<\/sup><\/font><\/strong><\/td>\n<td width=\"40\" align=\"center\"><strong><font color=\"#200020\"><sup>lower<\/sup><\/font><\/strong><\/td>\n<td width=\"35\" align=\"center\"><strong><font color=\"#200020\"><sup>upper<\/sup><\/font><\/strong><\/td>\n<td width=\"45\" align=\"center\"><strong><font color=\"#200020\"><sup>anova p <\/sup><\/font><\/strong><\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" rowspan=\"4\"><sup>Correll<br \/>                      et al<\/sup><\/td>\n<td align=\"right\"><sup>placebo<\/sup><\/td>\n<td align=\"center\"><sup>-12.01<\/sup><\/td>\n<td align=\"center\"><sup>1.60<\/sup><\/td>\n<td align=\"center\"><sup>21.35<\/sup><\/td>\n<td align=\"right\"><sup>178<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td valign=\"middle\" align=\"center\" rowspan=\"4\"><sup>0.0002      <\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>0.25mg<\/sup><\/td>\n<td align=\"center\"><sup>-14.90<\/sup><\/td>\n<td align=\"center\"><sup>2.23<\/sup><\/td>\n<td align=\"center\"><sup>20.80<\/sup><\/td>\n<td align=\"right\"><sup>87<\/sup><\/td>\n<td align=\"center\"><sup>0.3<\/sup><\/td>\n<td align=\"center\"><sup>0.14<\/sup><\/td>\n<td align=\"center\"><sup>-0.120<\/sup><\/td>\n<td align=\"center\"><sup>0.393<\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>2mg<\/sup><\/td>\n<td align=\"center\"><sup>-20.73<\/sup><\/td>\n<td align=\"center\"><sup>1.55<\/sup><\/td>\n<td align=\"center\"><sup>20.80<\/sup><\/td>\n<td align=\"right\"><sup>180<\/sup><\/td>\n<td align=\"center\"><sup>&lt;0.0001<\/sup><\/td>\n<td align=\"center\"><sup>0.41<\/sup><\/td>\n<td align=\"center\"><sup>0.204<\/sup><\/td>\n<td align=\"center\"><sup>0.623<\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>4mg<\/sup><\/td>\n<td align=\"center\"><sup>-19.65<\/sup><\/td>\n<td align=\"center\"><sup>1.54<\/sup><\/td>\n<td align=\"center\"><sup>20.55<\/sup><\/td>\n<td align=\"right\"><sup>178<\/sup><\/td>\n<td align=\"center\"><sup>0.0006<\/sup><\/td>\n<td align=\"center\"><sup>0.36<\/sup><\/td>\n<td align=\"center\"><sup>0.155<\/sup><\/td>\n<td align=\"center\"><sup>0.574<\/sup><\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" rowspan=\"4\"><sup>Kane<br \/>                      et al<\/sup><\/td>\n<td align=\"right\"><sup>placebo<\/sup><\/td>\n<td align=\"center\"><sup>-13.53<\/sup><\/td>\n<td align=\"center\"><sup>1.52<\/sup><\/td>\n<td align=\"center\"><sup>20.39<\/sup><\/td>\n<td align=\"right\"><sup>180<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td align=\"center\"><sup>&#8211;<\/sup><\/td>\n<td valign=\"middle\" align=\"center\" rowspan=\"4\"><sup>0.0025      <\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>1mg<\/sup><\/td>\n<td align=\"center\"><sup>-16.90<\/sup><\/td>\n<td align=\"center\"><sup>1.86<\/sup><\/td>\n<td align=\"center\"><sup>20.12<\/sup><\/td>\n<td align=\"right\"><sup>117<\/sup><\/td>\n<td align=\"center\"><sup>0.1588<\/sup><\/td>\n<td align=\"center\"><sup>0.166<\/sup><\/td>\n<td align=\"center\"><sup>-0.067<\/sup><\/td>\n<td align=\"center\"><sup>0.399<\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>2mg<\/sup><\/td>\n<td align=\"center\"><sup>-16.61<\/sup><\/td>\n<td align=\"center\"><sup>1.49<\/sup><\/td>\n<td align=\"center\"><sup>19.93<\/sup><\/td>\n<td align=\"right\"><sup>179<\/sup><\/td>\n<td align=\"center\"><sup>0.1488<\/sup><\/td>\n<td align=\"center\"><sup>0.153<\/sup><\/td>\n<td align=\"center\"><sup>-0.054<\/sup><\/td>\n<td align=\"center\"><sup>0.360<\/sup><\/td>\n<\/tr>\n<tr>\n<td align=\"right\"><sup>4mg<\/sup><\/td>\n<td align=\"center\"><sup>-20.00<\/sup><\/td>\n<td align=\"center\"><sup>1.48<\/sup><\/td>\n<td align=\"center\"><sup>19.91<\/sup><\/td>\n<td align=\"right\"><sup>181<\/sup><\/td>\n<td align=\"center\"><sup>0.0022<\/sup><\/td>\n<td align=\"center\"><sup>0.321<\/sup><\/td>\n<td align=\"center\"><sup>0.113<\/sup><\/td>\n<td align=\"center\"><sup>0.529<\/sup><\/td>\n<\/tr>\n<\/table>\n<\/li>\n<li>\n<div align=\"justify\"><strong><font color=\"#200020\">STEP 2 and 3: SPREADSHEET shortcut<\/font><\/strong>:<\/div>\n<div align=\"justify\">I made a simple spreadsheet that creates this table <span class=\"small\">[except for STEP 1]<\/span> just by entering the Summary Data to speeds things up a bit. It&#8217;s downloadable <a href=\"http:\/\/1boringoldman.com\/images\/1BOM-SPREADSHEET-1.xls\" target=\"_blank\">here<\/a>.         <\/div>\n<\/li>\n<p>               <\/span> <\/ul>\n<p align=\"justify\" class=\"small\">If the Summary Data isn&#8217;t provided, but the paper has the sample sizes and a p-value [<strong><font color=\"#200020\">p<\/font><\/strong>, <strong><font color=\"#200020\">n<sub>1<\/sub><\/font><\/strong>, and <strong><font color=\"#200020\">n<sub>2<\/sub><\/font><\/strong>], there is a way to extract the EFFECT SIZES. That shouldn&#8217;t happen, but it does. The procedure involves two Internet Calculators. The first converts the p-value into it&#8217;s z-score. You have to divide the p-value you&#8217;re given by two and then enter the result into John Walker&#8217;s <a href=\"https:\/\/www.fourmilab.ch\/rpkp\/experiments\/analysis\/zCalc.html\" target=\"_blank\">Internet Calculator<\/a> to extract the <em><font color=\"#200020\">z-score<\/font><\/em> &#8211; then enter that <font color=\"#200020\"><em>z-score<\/em><\/font> and the sum of the sizes of the groups being compared into <a target=\"_blank\" href=\"http:\/\/www.psychometrica.de\/effect_size.html\">Psychometrica<\/a>&#8216;s <a target=\"_blank\" href=\"http:\/\/www.psychometrica.de\/effect_size.html#transform2\">Computation of the effect sizes d, r and &eta;2 from &chi;2- and z test statistics<\/a>. And out comes <em><font color=\"#200020\">Cohen&#8217;s d<\/font><\/em> as if by magic! The Confidence Intervals can be generated with <strong><font color=\"#200020\">d<\/font><\/strong>, <strong><font color=\"#200020\">n<sub>1<\/sub><\/font><\/strong>, and <strong><font color=\"#200020\">n<sub>2<\/sub><\/font><\/strong> and a ponderous formula:<\/p>\n<p align=\"center\" class=\"small\"><strong><font color=\"#200020\">CI<sub>[95%]<\/sub>=d&plusmn;1.96&times;&radic;(((n<sub>1<\/sub>+n<sub>2<\/sub>)&divide;(n<sub>1<\/sub>&times;n<sub>2<\/sub>))+d&sup2;&divide;(2 &times;(n<sub>1<\/sub>+n<sub>2<\/sub>)))<\/font><\/strong><\/p>\n<p align=\"justify\" class=\"small\">[see <a target=\"_blank\" href=\"http:\/\/1boringoldman.com\/index.php\/2016\/01\/07\/john-henrys-hammer-continuous-variables-iii\/\">john henry&rsquo;s hammer: continuous variables III&hellip;<\/a>]. I expect this ponderous formula will be automated on a spreadsheet coming soon to a blog near you. Thus ends my summary of the discussion of Continuous Variables. How to interpret that table comes at the end of this series. On to the Categorical Variables&#8230;  <\/p>\n<div align=\"justify\"><em><font color=\"#200020\"><sup>In spite of an earlier career in hard science and a lot of statistical training and experience in a Jurassic Era, when I retired in 2003, I didn&#8217;t know how to do any of this. Worse, I didn&#8217;t even know it was there to do. I had moved in other directions and was a practicing psychotherapist by the time the IBM PC came along, or the Internet. I spent a lot of time with both, but it wasn&#8217;t doing this kind of thing. This looking at RCTs came after retirement and required a lot of catching up and pestering some very patient teachers to whom I will be eternally grateful. Back in the day, before I left Academia in the wake of the DSM-III, I had a job I loved &#8211; one I would&#8217;ve gladly done until retirement. I directed a Residency Training Program in Psychiatry. Having done three training programs myself, I know you never learn as much as you do in those first few years, and I loved being a part of that process and teaching the residents. It was a real loss to leave it. I guess I must still be at it in a way, because that&#8217;s where these posts are aimed. I&#8217;m trying to put together the collection of basic skills and simple tools that I wish I&#8217;d had in training or taught my residents. Back then, I would never have imagined that I would need to know how to spot deceit, sleight of hand, or sophisticated spin in the medical literature on a regular basis. But that&#8217;s the modern reality. And so that&#8217;s what I&#8217;m trying to work out in these posts. What does the new trainee need to learn out of the gate to prevent this kind of thing being perpetuated or repeated?&nbsp; Any and all help with that or suggestions appreciated&#8230; <\/sup><\/font><\/em><\/div>\n","protected":false},"excerpt":{"rendered":"<p>In a way, what I&#8217;m trying to do here is at cross purposes with some of my own beliefs. Short term Randomized Clinical Trials [RCTs] can tell us whether a drug has the desired medicinal properties; something about the strength of those properties; the incidence of early adverse effects; and can identify some but certainly [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[5],"tags":[],"class_list":["post-63055","post","type-post","status-publish","format-standard","hentry","category-opinion"],"_links":{"self":[{"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/posts\/63055","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/comments?post=63055"}],"version-history":[{"count":25,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/posts\/63055\/revisions"}],"predecessor-version":[{"id":63101,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/posts\/63055\/revisions\/63101"}],"wp:attachment":[{"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/media?parent=63055"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/categories?post=63055"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/1boringoldman.com\/index.php\/wp-json\/wp\/v2\/tags?post=63055"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}