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Click to edit Master title style,*,*,Click to edit Master text styles,Second level,Third level,Fourth level,Fifth level,Examples and SAS introduction:,-Violations of the rare disease assumption -Use of Fishers exact test,January 14, 2004,1,1. When can the OR mislead?,2,When is the OR is a good approximation of the RR?,General Rule of Thumb:,“OR is a good approximation as long as the probability of the outcome in the unexposed is less than 10%”,3,Volume 340:618-626,February 25, 1999,From: “The Effect of Race and Sex on Physicians Recommendations for Cardiac Catheterization”,Study overview:,Researchers developed a computerized survey instrument to assess,physicians recommendations for managing chest pain.,Actors,portrayed patients with particular characteristics (race and sex) in scripted,interviews about their symptoms.,720 Physicians at,two national meetings viewed a recorded,interview and was given other data about a hypothetical patient.,He or she then made recommendations about that patients care.,4,Volume 340:618-626,February 25, 1999,From: “The Effect of Race and Sex on Physicians Recommendations for Cardiac Catheterization”,5,Their results,The Media Reports: “Doctors were only 60 percent as likely to order cardiac catheterization for women and blacks as for men and whites. For black women, the doctors were only 40 percent as likely to order catheterization.”,6,Media headlines on Feb 25,th, 1999,Wall Street Journal,: “Study suggests race, sex influence physicians care.”,New York Times,: Doctor bias may affect heart care, study finds.”,Los Angeles Times,: “Heart study points to race, sex bias.”,Washington Post,: “Georgetown University study finds disparity in heart care; doctors less likely to refer blacks, women for cardiac test.”,USA Today,: “Heart care reflects race and sex, not symptoms.” ABC News: “Health care and race”,7,A closer look at the data,The authors failed to report the risk ratios:,RR for women: .847/.906=.93,RR for black race: .847/.906=.93,Correct conclusion: Only a 7% decrease in chance of being offered correct treatment.,8,Lessons learned:,90% outcome is not rare!,OR is a poor approximation of the RR here, magnifying the observed effect almost 6-fold.,Beware! Even the,New England Journal,doesnt always get it right!,SAS automatically calculates both, so check how different the two values are even if the RR is not appropriate. If they are very different, you have to be very cautious in how you interpret the OR.,9,SAS code and outputfor generating OR/RR from 2x2 table,Cath,No Cath,Female,305,55,Male,326,34,360,360,10,data cath_data;,input IsFemale GotCath Freq;,datalines;,1 1 305,1 0 55,0 1 326,0 0 34,run;,data cath_data; *Fix quirky reversal of SAS 2x2 tables;,set cath_data;,IsFemale=1-IsFemale;,GotCath=1-GotCath;,run;,proc freq data=cath_data;,tables IsFemale*GotCath /measures;,weight freq; run;,11,SAS output,Statistics for Table of IsFemale by GotCath,Estimates of the Relative Risk (Row1/Row2),Type of Study Value 95% Confidence Limits,Case-Control (Odds Ratio),0.5784 0.3669 0.9118,Cohort (Col1 Risk),0.9356 0.8854 0.9886,Cohort (Col2 Risk) 1.6176 1.0823 2.4177,Sample Size = 720,12,Furthermorestratification shows,13,2. Example of Fishers Exact Test,14,Fishers “Tea-tasting experiment” (p. 40 Agresti),Claim:,Fishers colleague (call her “Cathy”) claimed that, when drinking tea, she could distinguish whether milk or tea was added to the cup first.,To test her claim, Fisher designed an experiment in which she tasted 8 cups of tea (4 cups had milk poured first, 4 had tea poured first).,Null hypothesis:,Cathys guessing abilities are no better than chance.,Alternatives hypotheses:,Right-tail: She guesses right more than expected by chance.,Left-tail: She guesses wrong more than expected by chance,15,Fishers “Tea-tasting experiment” (p. 40 Agresti),Experimental Results,:,Milk,Tea,Milk,3,1,Tea,1,3,Guess poured first,Poured First,4,4,16,Fishers Exact Test,Step 1:,Identify tables that are,as extreme or more extreme,than what actually happened:,Here she identified 3 out of 4 of the milk-poured-first teas correctly. Is that good luck or real talent?,The only way she could have done,better,is if she identified 4 of 4 correct.,Milk,Tea,Milk,3,1,Tea,1,3,Guess poured first,Poured First,4,4,Milk,Tea,Milk,4,0,Tea,0,4,Guess poured first,Poured First,4,4,17,Fishers Exact Test,Step 2: Calculate the probability of the tables (assuming fixed marginals),Milk,Tea,Milk,3,1,Tea,1,3,Guess poured first,Poured First,4,4,Milk,Tea,Milk,4,0,Tea,0,4,Guess poured first,Poured First,4,4,18,Step 3: to get the left tail and right-tail p-values, consider the probability mass function:,Probability mass function of X, where X= the number of correct identifications of the cups with milk-poured-first:,“right-hand tail probability”: p=.243,“left-hand tail probability” (testing the null hypothesis that shes systematically wrong): p=.986,19,SAS code and outputfor generating Fishers Exact statistics for 2x2 table,Milk,Tea,Milk,3,1,Tea,1,3,4,4,20,data tea;,input MilkFirst GuessedMilk Freq;,datalines;,1 1 3,1 0 1,0 1 1,0 0 3,run;,data tea; *Fix quirky reversal of SAS 2x2 tables;,set tea;,MilkFirst=1-MilkFirst;,GuessedMilk=1-GuessedMilk;run;,proc freq data=tea;,tables MilkFirst*GuessedMilk /exact;,weight freq;run;,21,SAS output,Statistics for Table of MilkFirst by GuessedMilk,Statistic DF Value Prob,Chi-Square 1 2.0000 0.1573,Likelihood Ratio Chi-Square 1 2.0930 0.1480,Continuity Adj. Chi-Square 1 0.5000 0.4795,Mantel-Haenszel Chi-Square 1 1.7500 0.1859,Phi Coefficient 0.5000,Contingency Coefficient 0.4472,Cramers V 0.5000,WARNING: 100% of the cells have expected counts less,than 5. Chi-Square may not be a valid test.,Fishers Exact Test,Cell (1,1) Frequency (F) 3,Left-sided Pr = F 0.2429,Table Probability (P) 0.2286,Two-sided Pr = P 0.4857,Sample Size = 8,22,
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