Dear R users: In the example of meta-analysis (cochrane, package rmeta), I can not found the p-value of Test for overall effect, and some other indices (Z, I, weight and et al). How can I get the these indices listed?> library(rmeta) > data(cochrane) > cochranename ev.trt n.trt ev.ctrl n.ctrl 1 Auckland 36 532 60 538 2 Block 1 69 5 61 3 Doran 4 81 11 63 4 Gamsu 14 131 20 137 5 Morrison 3 67 7 59 6 Papageorgiou 1 71 7 75 7 Tauesch 8 56 10 71> a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) > summary(a)Fixed effects ( Mantel-Haenszel ) meta-analysis Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = ev.ctrl, names = name, data = cochrane) ------------------------------------ OR (lower 95% upper) Auckland 0.58 0.38 0.89 Block 0.16 0.02 1.45 Doran 0.25 0.07 0.81 Gamsu 0.70 0.34 1.45 Morrison 0.35 0.09 1.41 Papageorgiou 0.14 0.02 1.16 Tauesch 1.02 0.37 2.77 ------------------------------------ Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p-value ?) Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) Thanks Yours Ping Zhang [[alternative HTML version deleted]]
Le samedi 27 juin 2009 ? 13:02 +0800, sdzhangping a ?crit :> Dear R users: > > In the example of meta-analysis (cochrane, package rmeta), I can not > found the p-value of Test for overall effect, and some other indices > (Z, I, weight and et al). How can I get the these indices listed? > > library(rmeta) > > data(cochrane) > > cochrane > name ev.trt n.trt ev.ctrl n.ctrl > 1 Auckland 36 532 60 538 > 2 Block 1 69 5 61 > 3 Doran 4 81 11 63 > 4 Gamsu 14 131 20 137 > 5 Morrison 3 67 7 59 > 6 Papageorgiou 1 71 7 75 > 7 Tauesch 8 56 10 71 > > a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) > > summary(a) > Fixed effects ( Mantel-Haenszel ) meta-analysis > Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl > ev.ctrl, > names = name, data = cochrane) > ------------------------------------ > OR (lower 95% upper) > Auckland 0.58 0.38 0.89 > Block 0.16 0.02 1.45 > Doran 0.25 0.07 0.81 > Gamsu 0.70 0.34 1.45 > Morrison 0.35 0.09 1.41 > Papageorgiou 0.14 0.02 1.16 > Tauesch 1.02 0.37 2.77 > ------------------------------------ > Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and > p-value ?) > Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 )You might easily recompute them : use the confidence interval to guesstimate the standard deviation of OR, its value and the damn Z and p you long for... Remember that it's log(OR) that is (asymptotically) normally distributed. The weights are proportional to inverse of variance and sum to 1. You might peek at the source code for enlightment... Alternatively, you may grow lazy an use the "meta" package, whose function metabin() will give you all that. The recent "metafor" package seems also quite interesting. Another (smarter(?)) alternative is to ask yourself *why* you need Z and p. Z is just a computing device allowing you to use a known density. And the real meaning of p and its usefulness has been discussed, disputed and fought over at exceedingly large lengths in the past 80 years. Of course, if you have an instructor to please ... HTH, Emmanuel Charpentier
The object "a" has log.estimates and selog.estimates: > str(a) List of 10 $ logOR : num [1:7] -0.548 -1.804 -1.404 -0.357 -1.055 ... $ selogOR : num [1:7] 0.22 1.11 0.611 0.372 0.715 ... $ logMH : num -0.632 $ selogMH : num 0.16 snipped remainder of output. You can also look at the the code of meta.MH: meta.MH On Jun 27, 2009, at 1:02 AM, sdzhangping wrote:> Dear R users: > > In the example of meta-analysis (cochrane, package rmeta), I can not > found the p-value of Test for overall effect, and some other indices > (Z, I, weight and et al). How can I get the these indices listed? >> library(rmeta) >> data(cochrane) >> cochrane > name ev.trt n.trt ev.ctrl n.ctrl > 1 Auckland 36 532 60 538 > 2 Block 1 69 5 61 > 3 Doran 4 81 11 63 > 4 Gamsu 14 131 20 137 > 5 Morrison 3 67 7 59 > 6 Papageorgiou 1 71 7 75 > 7 Tauesch 8 56 10 71 >> a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane) >> summary(a) > Fixed effects ( Mantel-Haenszel ) meta-analysis > Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = > ev.ctrl, > names = name, data = cochrane) > ------------------------------------ > OR (lower 95% upper) > Auckland 0.58 0.38 0.89 > Block 0.16 0.02 1.45 > Doran 0.25 0.07 0.81 > Gamsu 0.70 0.34 1.45 > Morrison 0.35 0.09 1.41 > Papageorgiou 0.14 0.02 1.16 > Tauesch 1.02 0.37 2.77 > ------------------------------------ > Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p- > value ?) > Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) >David Winsemius, MD Heritage Laboratories West Hartford, CT
At 06:02 27/06/2009, sdzhangping wrote:>Dear R users: > >In the example of meta-analysis (cochrane, package rmeta), I can not >found the p-value of Test for overall effect, and some other indices >(Z, I, weight and et al). How can I get the these indices listed? > > library(rmeta) > > data(cochrane) > > cochrane > name ev.trt n.trt ev.ctrl n.ctrl >1 Auckland 36 532 60 538 >2 Block 1 69 5 61 >3 Doran 4 81 11 63 >4 Gamsu 14 131 20 137 >5 Morrison 3 67 7 59 >6 Papageorgiou 1 71 7 75 >7 Tauesch 8 56 10 71 > > a=meta.MH(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane)If at this point you do str(a) you will find what a contains which may or may not help you answer your question. Similarly str(summary(a)) may also be revealing. Of course R lets you do anything you want but if the author did not print out a test and a p-value you might like to ask yourself whether that suggests anything (as someone has already pointed out in another reply).> > summary(a) >Fixed effects ( Mantel-Haenszel ) meta-analysis >Call: meta.MH(ntrt = n.trt, nctrl = n.ctrl, ptrt = ev.trt, pctrl = ev.ctrl, > names = name, data = cochrane) >------------------------------------ > OR (lower 95% upper) >Auckland 0.58 0.38 0.89 >Block 0.16 0.02 1.45 >Doran 0.25 0.07 0.81 >Gamsu 0.70 0.34 1.45 >Morrison 0.35 0.09 1.41 >Papageorgiou 0.14 0.02 1.16 >Tauesch 1.02 0.37 2.77 >------------------------------------ >Mantel-Haenszel OR =0.53 95% CI ( 0.39,0.73 ) (where is Z and p-value ?) >Test for heterogeneity: X^2( 6 ) = 6.9 ( p-value 0.3303 ) > > > >Thanks >Yours Ping Zhang > > > [[alternative HTML version deleted]]Michael Dewey http://www.aghmed.fsnet.co.uk
On Sat, 27 Jun 2009, Emmanuel Charpentier wrote:> Le samedi 27 juin 2009 ? 13:02 +0800, sdzhangping a ?crit : >> Dear R users: >> >> In the example of meta-analysis (cochrane, package rmeta), I can not >> found the p-value of Test for overall effect, and some other indices >> (Z, I, weight and et al). How can I get the these indices listed? > >Another (smarter(?)) alternative is to ask yourself *why* you need Z and >p. Z is just a computing device allowing you to use a known density. And >the real meaning of p and its usefulness has been discussed, disputed >and fought over at exceedingly large lengths in the past 80 years.The $MHtest component of the object (for Mantel-Haenszel) or $test component otherwise, has the test statistic and p-value. -thomas ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle