--------------------------------------------------------------------------------------------------------------------------- name: log: C:\Users\dupontwd.VANDERBILT\Documents\Dropbox\OFFICE_desktop\ChoiFisherTest\Stata Program\ado\ForSubmission\c > hoi_lr_test\test.log log type: text opened on: 31 May 2016, 14:08:46 . * test.log . . * This program tests choi_lr_test.ado and choi_lr_testi.ado . * Ancillary files that are needed by these programs are . * nl_choi_support_interval.ado, choi_lr_support_interval.ado . * choi_lr_hypergeom.ado and choi_lr_hyperg_prog.ado. . . * These programs calculate statistics described in . * Choi et al. 2015. Elucidating the Foundations of Statistical Inference with 2 x 2 Tables. . * PLoS ONE 10(4): e0121263. doi:10.1371/journal.pone.0121263 . . * Output from this program may be checked against the Shiny app posted at . * http://statcomp2.vanderbilt.edu:37212/ProfileLikelihood/ . * or against the R program posted at . * https://cran.r-project.org/web/packages/ProfileLikelihood/index.html . . set more off . use testdata.dta . . * Test choi_lr_test program . choi_lr_test case exposed [fweight=patients] Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . . * Check scalars returned by the cc program . di r(p) .13057002 . di r(or) 5 . di r(lb_or) .40865859 . di r(ub_or) 75.971185 . di r(afe) .8 . di r(lb_afe) -1.4470304 . di r(ub_afe) .98683711 . di r(afp) .6 . di r(chi2) 2.2857143 . . * Check scalars calculated by the choi_lr_test program . di r(or_cond) 4.4742438 . di r(clr) 2.9944571 . di r(chi2_clr) 2.1935259 . di r(p_choi) .13859174 . di r(lr6pt8lsi_lb) .62397643 . di r(lr6pt8lsi_ub) 42.991698 . . choi_lr_test case exposed [fweight=patients], exact k(32) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- 1-sided Fisher's exact P = 0.1573 2-sided Fisher's exact P = 0.3147 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] 1/32 LSI for the OR = [.32148657, 109.60039] . * Check scalars returned by the cc program . di r(p1_exact) .15734266 . di r(p_exact) .31468531 . . * Check that extra LSIs are returned . di r(lrklsi_lb) .32148657 . di r(lrklsi_ub) 109.60039 . . choi_lr_test case exposed [fweight=patients], corn | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .6433784 38.07362 (Cornfield) Attr. frac. ex. | .8 | -.5542952 .9737351 (Cornfield) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . choi_lr_test case exposed [fweight=patients], woolf | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .5841514 42.79712 (Woolf) Attr. frac. ex. | .8 | -.7118849 .9766339 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . . * Check behavior for tables with larger sample sizes . replace patients = patients*12 (4 real changes made) . choi_lr_test case exposed [fweight=patients], woolf k(16) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 72 24 | 96 0.7500 Controls | 36 60 | 96 0.3750 -----------------+------------------------+------------------------ Total | 108 84 | 192 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 2.690274 9.292735 (Woolf) Attr. frac. ex. | .8 | .6282906 .8923891 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 27.43 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9539211 Likelihood ratio under the null hypothesis = 1213489.1 Likelihood ratio chi-squared statistic = 28.018021 P value for the null hypothesis that the OR equals 1 = 1.202e-07 1/6.825936 LSI for the OR = [2.7020791, 9.3208557] 1/16 LSI for the OR = [2.3971936, 10.628488] . . use testdata.dta, clear . replace patients = patients*30 (4 real changes made) . choi_lr_test case exposed [fweight=patients], woolf k(32) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 180 60 | 240 0.7500 Controls | 90 150 | 240 0.3750 -----------------+------------------------+------------------------ Total | 270 210 | 480 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 3.378545 7.399635 (Woolf) Attr. frac. ex. | .8 | .7040146 .8648582 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 68.57 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9815164 Likelihood ratio under the null hypothesis = 1.821e+15 Likelihood ratio chi-squared statistic = 70.276267 P value for the null hypothesis that the OR equals 1 = 5.155e-17 1/6.825936 LSI for the OR = [3.384192, 7.409481] 1/32 LSI for the OR = [2.9695546, 8.5152491] . . use testdata.dta, clear . replace patients = patients*100 (4 real changes made) . choi_lr_test case exposed [fweight=patients], woolf k(8) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 600 200 | 800 0.7500 Controls | 300 500 | 800 0.3750 -----------------+------------------------+------------------------ Total | 900 700 | 1600 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 4.033904 6.19747 (Woolf) Attr. frac. ex. | .8 | .7521012 .8386438 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 228.57 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9944476 Likelihood ratio under the null hypothesis = 8.826e+50 Likelihood ratio chi-squared statistic = 234.6139 P value for the null hypothesis that the OR equals 1 = 5.877e-53 1/6.825936 LSI for the OR = [4.035843, 6.2001042] 1/8 LSI for the OR = [4.0014063, 6.2550805] . . use testdata.dta, clear . replace patients = patients*200 (4 real changes made) . choi_lr_test case exposed [fweight=patients], woolf k(8) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 1200 400 | 1600 0.7500 Controls | 600 1000 | 1600 0.3750 -----------------+------------------------+------------------------ Total | 1800 1400 | 3200 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 4.295722 5.819743 (Woolf) Attr. frac. ex. | .8 | .7672103 .8281711 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 457.14 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9972227 Likelihood ratio under the null hypothesis = 8.41e+101 Likelihood ratio chi-squared statistic = 469.38195 P value for the null hypothesis that the OR equals 1 = 4.37e-104 1/6.825936 LSI for the OR = [4.2967386, 5.8210048] 1/8 LSI for the OR = [4.2706733, 5.8572896] . . * Check if program handles 1 record per patient properly . use testdata.dta, clear . expand patients (12 observations created) . choi_lr_test case exposed Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . . * Check behavior for tables with 0 patients in some cells . use testdata.dta,clear . list +---------------------------+ | case exposed patients | |---------------------------| 1. | 0 0 5 | 2. | 0 1 3 | 3. | 1 0 2 | 4. | 1 1 6 | +---------------------------+ . replace patients =0 if _n==3 (1 real change made) . replace patients =0 if _n==4 (1 real change made) . choi_lr_test case exposed [fweight=patients] Too many empty cells to estimate OR Bad data input . replace patients =2 if _n==3 (1 real change made) . choi_lr_test case exposed [fweight=patients] , k(16) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 0 2 | 2 0.0000 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 3 7 | 10 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 0 | 0 4.841502 (Cornfield) Prev. frac. ex. | 1 | -3.841502 1 (Cornfield) Prev. frac. pop | . | +------------------------------------------------- chi2(1) = 1.07 Pr>chi2 = 0.3006 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 0 Likelihood ratio under the null hypothesis = 2.1428571 Likelihood ratio chi-squared statistic = 1.5242801 P value for the null hypothesis that the OR equals 1 = .21697293 1/6.825936 LSI for the OR = [0, 3.7822765] 1/16 LSI for the OR = [0, 7.3282039] . replace patients =2 if _n==1 (1 real change made) . replace patients =0 if _n==2 (1 real change made) . replace patients =5 if _n==3 (1 real change made) . replace patients =3 if _n==4 (1 real change made) . choi_lr_test case exposed [fweight=patients] , k(16) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 3 5 | 8 0.3750 Controls | 0 2 | 2 0.0000 -----------------+------------------------+------------------------ Total | 3 7 | 10 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | . | .2065475 . (Cornfield) Attr. frac. ex. | 1 | -3.841502 . (Cornfield) Attr. frac. pop | .375 | +------------------------------------------------- chi2(1) = 1.07 Pr>chi2 = 0.3006 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = infinity Likelihood ratio under the null hypothesis = 2.1428571 Likelihood ratio chi-squared statistic = 1.5242801 P value for the null hypothesis that the OR equals 1 = .21697293 1/6.825936 LSI for the OR = [.26439104, infinity] 1/16 LSI for the OR = [.13645908, infinity] . replace patients = patients*100 (3 real changes made) . choi_lr_test case exposed [fweight=patients] , k(8) | exposed | Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 300 500 | 800 0.3750 Controls | 0 200 | 200 0.0000 -----------------+------------------------+------------------------ Total | 300 700 | 1000 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | . | 31.2292 . (Cornfield) Attr. frac. ex. | 1 | .9679787 . (Cornfield) Attr. frac. pop | .375 | +------------------------------------------------- chi2(1) = 107.14 Pr>chi2 = 0.0000 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = infinity Likelihood ratio under the null hypothesis = 2.629e+35 Likelihood ratio chi-squared statistic = 163.11415 P value for the null hypothesis that the OR equals 1 = 2.362e-37 1/6.825936 LSI for the OR = [61.74006, infinity] 1/8 LSI for the OR = [56.981507, infinity] . * Test choi_lr_testi program . choi_lr_testi 6 2 3 5 Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . . * Check scalars returned by the cci program . di r(p) .13057002 . di r(or) 5 . di r(lb_or) .40865859 . di r(ub_or) 75.971185 . di r(afe) .8 . di r(lb_afe) -1.4470304 . di r(ub_afe) .98683711 . di r(afp) .6 . di r(chi2) 2.2857143 . . * Check scalars calculated and returned by the choi_lr_testi program . di r(or_cond) 4.4742438 . di r(clr) 2.9944571 . di r(chi2_clr) 2.1935259 . di r(p_choi) .13859174 . di r(lr6pt8lsi_lb) .62397643 . di r(lr6pt8lsi_ub) 42.991698 . . choi_lr_testi 6 2 3 5, exact k(8) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- 1-sided Fisher's exact P = 0.1573 2-sided Fisher's exact P = 0.3147 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] 1/8 LSI for the OR = [.57712034, 47.72445] . . * Check scalars returned by the cci program . di r(p1_exact) .15734266 . di r(p_exact) .31468531 . . * Check that extra LSIs are returned . di r(lrklsi_lb) .57712034 . di r(lrklsi_ub) 47.72445 . . choi_lr_testi 6 2 3 5, corn Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .6433784 38.07362 (Cornfield) Attr. frac. ex. | .8 | -.5542952 .9737351 (Cornfield) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] . choi_lr_testi 6 2 3 5, woolf k(16) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .5841514 42.79712 (Woolf) Attr. frac. ex. | .8 | -.7118849 .9766339 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 2.29 Pr>chi2 = 0.1306 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] 1/16 LSI for the OR = [.42305043, 73.372846] . choi_lr_testi 6 2 3 5, exact k(8) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 6 2 | 8 0.7500 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 9 7 | 16 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | .4086586 75.97119 (exact) Attr. frac. ex. | .8 | -1.44703 .9868371 (exact) Attr. frac. pop | .6 | +------------------------------------------------- 1-sided Fisher's exact P = 0.1573 2-sided Fisher's exact P = 0.3147 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.4742438 Likelihood ratio under the null hypothesis = 2.9944571 Likelihood ratio chi-squared statistic = 2.1935259 P value for the null hypothesis that the OR equals 1 = .13859174 1/6.825936 LSI for the OR = [.62397643, 42.991698] 1/8 LSI for the OR = [.57712034, 47.72445] . . * Check larger sample sizes . choi_lr_testi 72 24 36 60, k(8) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 72 24 | 96 0.7500 Controls | 36 60 | 96 0.3750 -----------------+------------------------+------------------------ Total | 108 84 | 192 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 2.576879 9.768128 (exact) Attr. frac. ex. | .8 | .6119337 .8976262 (exact) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 27.43 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9539211 Likelihood ratio under the null hypothesis = 1213489.1 Likelihood ratio chi-squared statistic = 28.018021 P value for the null hypothesis that the OR equals 1 = 1.202e-07 1/6.825936 LSI for the OR = [2.7020791, 9.3208557] 1/8 LSI for the OR = [2.6376818, 9.5689775] . choi_lr_testi 180 60 90 150, k(16) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 180 60 | 240 0.7500 Controls | 90 150 | 240 0.3750 -----------------+------------------------+------------------------ Total | 270 210 | 480 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 3.317747 7.54922 (exact) Attr. frac. ex. | .8 | .6985906 .867536 (exact) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 68.57 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9815164 Likelihood ratio under the null hypothesis = 1.821e+15 Likelihood ratio chi-squared statistic = 70.276267 P value for the null hypothesis that the OR equals 1 = 5.155e-17 1/6.825936 LSI for the OR = [3.384192, 7.409481] 1/16 LSI for the OR = [3.1339526, 8.0382116] . choi_lr_testi 600 200 300 500, woolf k(32) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 600 200 | 800 0.7500 Controls | 300 500 | 800 0.3750 -----------------+------------------------+------------------------ Total | 900 700 | 1600 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 4.033904 6.19747 (Woolf) Attr. frac. ex. | .8 | .7521012 .8386438 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 228.57 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9944476 Likelihood ratio under the null hypothesis = 8.826e+50 Likelihood ratio chi-squared statistic = 234.6139 P value for the null hypothesis that the OR equals 1 = 5.877e-53 1/6.825936 LSI for the OR = [4.035843, 6.2001042] 1/32 LSI for the OR = [3.7536033, 6.6831072] . choi_lr_testi 1200 400 600 1000, woolf k(32) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 1200 400 | 1600 0.7500 Controls | 600 1000 | 1600 0.3750 -----------------+------------------------+------------------------ Total | 1800 1400 | 3200 0.5625 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 5 | 4.295722 5.819743 (Woolf) Attr. frac. ex. | .8 | .7672103 .8281711 (Woolf) Attr. frac. pop | .6 | +------------------------------------------------- chi2(1) = 457.14 Pr>chi2 = 0.0000 Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 4.9972227 Likelihood ratio under the null hypothesis = 8.41e+101 Likelihood ratio chi-squared statistic = 469.38195 P value for the null hypothesis that the OR equals 1 = 4.37e-104 1/6.825936 LSI for the OR = [4.2967386, 5.8210048] 1/32 LSI for the OR = [4.0810354, 6.1363946] . . * Check behavior with empty cells . choi_lr_testi 0 2 3 5 Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 0 2 | 2 0.0000 Controls | 3 5 | 8 0.3750 -----------------+------------------------+------------------------ Total | 3 7 | 10 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | 0 | 0 4.841502 (Cornfield) Prev. frac. ex. | 1 | -3.841502 1 (Cornfield) Prev. frac. pop | . | +------------------------------------------------- chi2(1) = 1.07 Pr>chi2 = 0.3006 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = 0 Likelihood ratio under the null hypothesis = 2.1428571 Likelihood ratio chi-squared statistic = 1.5242801 P value for the null hypothesis that the OR equals 1 = .21697293 1/6.825936 LSI for the OR = [0, 3.7822765] . choi_lr_testi 3 5 0 2, k(8) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 3 5 | 8 0.3750 Controls | 0 2 | 2 0.0000 -----------------+------------------------+------------------------ Total | 3 7 | 10 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | . | .2065475 . (Cornfield) Attr. frac. ex. | 1 | -3.841502 . (Cornfield) Attr. frac. pop | .375 | +------------------------------------------------- chi2(1) = 1.07 Pr>chi2 = 0.3006 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = infinity Likelihood ratio under the null hypothesis = 2.1428571 Likelihood ratio chi-squared statistic = 1.5242801 P value for the null hypothesis that the OR equals 1 = .21697293 1/6.825936 LSI for the OR = [.26439104, infinity] 1/8 LSI for the OR = [.23114771, infinity] . choi_lr_testi 300 500 0 200, k(16) Proportion | Exposed Unexposed | Total Exposed -----------------+------------------------+------------------------ Cases | 300 500 | 800 0.3750 Controls | 0 200 | 200 0.0000 -----------------+------------------------+------------------------ Total | 300 700 | 1000 0.3000 | | | Point estimate | [95% Conf. Interval] |------------------------+------------------------ Odds ratio | . | 31.2292 . (Cornfield) Attr. frac. ex. | 1 | .9679787 . (Cornfield) Attr. frac. pop | .375 | +------------------------------------------------- chi2(1) = 107.14 Pr>chi2 = 0.0000 Note: Exact confidence levels not possible with zero count cells. Likelihood ratio statistics conditioned on the marginal exposure rate Maximum likelihood estimate (MLE) of odds ratio = infinity Likelihood ratio under the null hypothesis = 2.629e+35 Likelihood ratio chi-squared statistic = 163.11415 P value for the null hypothesis that the OR equals 1 = 2.362e-37 1/6.825936 LSI for the OR = [61.74006, infinity] 1/16 LSI for the OR = [42.585057, infinity] . . log close name: log: C:\Users\dupontwd.VANDERBILT\Documents\Dropbox\OFFICE_desktop\ChoiFisherTest\Stata Program\ado\ForSubmission\c > hoi_lr_test\test.log log type: text closed on: 31 May 2016, 14:09:09 ---------------------------------------------------------------------------------------------------------------------------