Re: [R] How do I print predicted effect sizes in forest plot?
Thank you very much Wolfgang and Michael for your help and information. Now I know how to get the predicted values. For information, my "mean" is the effect size for the one-sample-case. Obviously I used misleading labels, but I calculated the same with CMA and getting the same results, so it should be okay. Best wishes, Alma On Friday, December 6, 2013 3:10 PM, Michael Dewey wrote: At 21:05 05/12/2013, Alma Wilflinger wrote: >Hi, > >I am struggling a bit with creating a forest plot containing the >predicted effect size. As seen in other studies these effect sizes >are shown per study usually as a light grey diamond - which is what >I want to achieve. > >The calls I use are: >iat_result = rma(yi=Mean, vi=Variance_rounded, ni=N, sei=Std_error, >slab=Study_Name, subset=(Country == "AUT"), data=cma_iat, method="HS") Alma You do not need to specify both vi and sei as one is sufficient and you do not need ni as well. I realise that is not the question you asked (which Wolfgang has already answered). >summary.rma(iat_result) > > >#not sure how to use it or if needed >#predict(iat_result) > >forest(iat_result) > > >At the end I am getting the forest plot as is without the predicted values. > >I am not sure if I need the predict function and how to use it? - >the predict function deliveres the same values as already computed >in the rma object. > > >I checked the manual for package metafor but was not able to find >out how to print the predicted values per study. > > >kind regards, Alma > [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html [[alternative HTML version deleted]] __ R-help@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.
[R] How do I print predicted effect sizes in forest plot?
Hi, I am struggling a bit with creating a forest plot containing the predicted effect size. As seen in other studies these effect sizes are shown per study usually as a light grey diamond - which is what I want to achieve. The calls I use are: iat_result = rma(yi=Mean, vi=Variance_rounded, ni=N, sei=Std_error, slab=Study_Name, subset=(Country == "AUT"), data=cma_iat, method="HS") summary.rma(iat_result) #not sure how to use it or if needed #predict(iat_result) forest(iat_result) At the end I am getting the forest plot as is without the predicted values. I am not sure if I need the predict function and how to use it? - the predict function deliveres the same values as already computed in the rma object. I checked the manual for package metafor but was not able to find out how to print the predicted values per study. kind regards, Alma [[alternative HTML version deleted]] __ R-help@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.
Re: [R] dummy encoding in metafor
Dear Wolfgang, Thank you very much for answering! 1) No, I am doing a Meta Analysis and take the ds from existing studies. To be exactly, I do use D (Means of D-Measure which is not exactly d, but very similar) 3) Yes CMA makes a new column with st. error and variance differ from 1. for example my mean is 0,6, and I take 1 for the st. dev and 154 is my N, the new values are 0,080582 for the st. error and 6,49E-03 for the variance So did I make a mistake by taking the parameters for R? vi is my mean yi is my variance. I took the uncalculated variance which is 1. is this wrong? do I have to take the variances from the new column from CMA? kind regards, alma From: Viechtbauer Wolfgang (STAT) t.co.uk>; "r-help@r-project.org" Sent: Monday, January 28, 2013 10:38 AM Subject: RE: [R] dummy encoding in metafor Dear Alma, either there is a whole lot of miscommunicaton here, or you (and your supervisor) are way in over your head. You say that you are working with Cohen's d values. And you mentioned CMA. So, let me ask you some questions: 1) Has CMA computed those d values for you? 2) If yes, what information did you supply to CMA for the computation of those d values? (means, standard deviations, and the sample sizes of the two groups?) 3) Did CMA then provide you with a column of values that are the corresponding sampling variances or standard errors? (those values should NOT all be equal to 1!) Best, Wolfgang > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Alma Wilflinger > Sent: Sunday, January 27, 2013 21:52 > To: Michael Dewey; r-help@r-project.org > Subject: Re: [R] dummy encoding in metafor > > Hi Michael! > > Yes, I do use Cohens d. As a matter of fact my thesis supervisor told me > to use 1 as the value for standard deviation for all of my studies. > Unfortunately I am not totally sure myself why to do this have you ever > used such an approach? > > kind regards, > Alma > > > From: Michael Dewey > > t.co.uk>; "r-help@r-project.org" > Sent: Thursday, January 24, 2013 6:57 PM > Subject: Re: [R] dummy encoding in metafor > > At 22:06 23/01/2013, Alma Wilflinger wrote: > > > Hi Michael, > > > > The supervisor for my Master's Thesis told me that my means are the > effect size and cause of this I have to take figure 1 for all standard > deviations. So I hope that was the right information. > > Alma > There is a fairly comprehensive list of all the things which might be an > effect size on > http://en.wikipedia.org/wiki/Effect_size > Is what you call Mean one of them? > > > > > > From: Michael Dewey > > wolfgang.viechtba...@maastrichtuniversity.nl>; Michael Dewey > ; "r-help@r-project.org" > > Sent: Wednesday, January 23, 2013 10:22 AM > > Subject: Re: [R] dummy encoding in metafor > > > > At 08:30 23/01/2013, Alma Wilflinger wrote: > > > Dear Wolfgang and Michael, > > > > [[elided Yahoo spam]] > > > > > > Concerning the Variance: I took the variance I used for CMA (which > is always 1), so I think it should be the right one. > > > > It seems unlikely to me that the variance from each study would be the > same although I suppose it could be possible. Are you sure you are > supplying the right values to CMA? > > > > > > > Thank you for noticing and mentioning though :) > > > > > > I really appreciate how helpful you both are. > > > > > > best, > > > Alma [[alternative HTML version deleted]] __ R-help@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.
Re: [R] dummy encoding in metafor
Hi Michael! Yes, I do use Cohens d. As a matter of fact my thesis supervisor told me to use 1 as the value for standard deviation for all of my studies. Unfortunately I am not totally sure myself why to do this have you ever used such an approach? kind regards, Alma From: Michael Dewey t.co.uk>; "r-help@r-project.org" Sent: Thursday, January 24, 2013 6:57 PM Subject: Re: [R] dummy encoding in metafor At 22:06 23/01/2013, Alma Wilflinger wrote: > Hi Michael, > > The supervisor for my Master's Thesis told me that my means are the effect > size and cause of this I have to take figure 1 for all standard deviations. > So I hope that was the right information. Alma There is a fairly comprehensive list of all the things which might be an effect size on http://en.wikipedia.org/wiki/Effect_size Is what you call Mean one of them? > > From: Michael Dewey wolfgang.viechtba...@maastrichtuniversity.nl>; Michael Dewey ; "r-help@r-project.org" > Sent: Wednesday, January 23, 2013 10:22 AM > Subject: Re: [R] dummy encoding in metafor > > At 08:30 23/01/2013, Alma Wilflinger wrote: > > Dear Wolfgang and Michael, > > [[elided Yahoo spam]] > > > > Concerning the Variance: I took the variance I used for CMA (which is > > always 1), so I think it should be the right one. > > It seems unlikely to me that the variance from each study would be the same > although I suppose it could be possible. Are you sure you are supplying the > right values to CMA? > > > > Thank you for noticing and mentioning though :) > > > > I really appreciate how helpful you both are. > > > > best, > > Alma > > > > > > > > From: Viechtbauer Wolfgang (STAT) > > <<mailto:wolfgang.viechtba...@maastrichtuniversity.nl>wolfgang.viechtba...@maastrichtuniversity.nl> > > To: Michael Dewey <<mailto:i...@aghmed.fsnet.co.uk>i...@aghmed.fsnet.co "<mailto:r-help@r-project.org>r-help@r-project.org" <<mailto:r-help@r-project.org>r-help@r-project.org> > > Sent: Monday, January 21, 2013 11:10 AM > > Subject: RE: [R] dummy encoding in metafor > > > > As Michael already mentioned, the error: > > > > Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve > > > > indeed indicates that your design matrix is not of full rank (i.e., there > > are linear dependencies among your predictors). With this many factors in > > the same model, this is not surprising if k is "only" 94 (which is actually > > quite large for a meta-analysis). One options is to leave out some of the > > predictors. You can also try collapsing some of the levels of the factors. > > Of course, you lose some "details" that way, but apparently you don't have > > enough data in the first place to carry out such a detailed analysis. > > > > One other thing I noticed. You wrote: > > > > rma(yi=Mean, vi=Variance, ni=N.1, ...) > > > > I suspect that your variable "Variance" is actually the variance of the raw > > scores. However, the vi argument is used to pass the sampling variances of > > the yi values to the function -- not the variance of raw scores. The > > (estimated) sampling variance of a mean is s^2 / n, so if I am not > > mistaken, you really want to use: > > > > rma(yi=Mean, vi=Variance/N.1, ...) > > > > Best, > > Wolfgang > > > > -- > > Wolfgang Viechtbauer, Ph.D., Statistician > > Department of Psychiatry and Psychology > > School for Mental Health and Neuroscience > > Faculty of Health, Medicine, and Life Sciences > > Maastricht University, P.O. Box 616 (VIJV1) > > 6200 MD Maastricht, The Netherlands > > +31 (43) 388-4170 | http://www.wvbauer.com > > > > > -Original Message- > > > From: > > > <mailto:r-help-boun...@r-project.org><mailto:r-help-boun...@r-project.org>r-help-boun...@r-project.org > > > [mailto:r-help-boun...@r-project.org] > > > On Behalf Of Michael Dewey > > > Sent: Monday, January 21, 2013 10:40 > > > To: Alma Wilflinger; Michael Dewey; > > > <mailto:r-help@r-project.org><mailto:r-help@r-project.org>r-help@r-project.org > > > Subject: Re: [R] dummy encoding in metafor > > > > > > At 14:48 20/01/2013, Alma Wilflinger wrote: > > > >Hi, > > > > > > > >thank you very much for your kind answer. > > > > > > > > >If you look a bit further down the manual page you will see > > > > >### using a model
Re: [R] dummy encoding in metafor
Hi Michael, The supervisorfor my Master'sThesis told me that my means are the effect size and cause of this I have to take figure 1 for all standard deviations. So I hope that was the right information. From: Michael Dewey lfgang.viechtba...@maastrichtuniversity.nl>; Michael Dewey ; "r-help@r-project.org" Sent: Wednesday, January 23, 2013 10:22 AM Subject: Re: [R] dummy encoding in metafor At 08:30 23/01/2013, Alma Wilflinger wrote: > Dear Wolfgang and Michael, > [[elided Yahoo spam]] > > Concerning the Variance: I took the variance I used for CMA (which is always > 1), so I think it should be the right one. It seems unlikely to me that the variance from each study would be the same although I suppose it could be possible. Are you sure you are supplying the right values to CMA? > Thank you for noticing and mentioning though :) > > I really appreciate how helpful you both are. > > best, > Alma > > > > From: Viechtbauer Wolfgang (STAT) > > To: Michael Dewey ; Alma Wilflinger > ; "r-help@r-project.org" > Sent: Monday, January 21, 2013 11:10 AM > Subject: RE: [R] dummy encoding in metafor > > As Michael already mentioned, the error: > > Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve > > indeed indicates that your design matrix is not of full rank (i.e., there are > linear dependencies among your predictors). With this many factors in the > same model, this is not surprising if k is "only" 94 (which is actually quite > large for a meta-analysis). One options is to leave out some of the > predictors. You can also try collapsing some of the levels of the factors. Of > course, you lose some "details" that way, but apparently you don't have > enough data in the first place to carry out such a detailed analysis. > > One other thing I noticed. You wrote: > > rma(yi=Mean, vi=Variance, ni=N.1, ...) > > I suspect that your variable "Variance" is actually the variance of the raw > scores. However, the vi argument is used to pass the sampling variances of > the yi values to the function -- not the variance of raw scores. The > (estimated) sampling variance of a mean is s^2 / n, so if I am not mistaken, > you really want to use: > > rma(yi=Mean, vi=Variance/N.1, ...) > > Best, > Wolfgang > > -- > Wolfgang Viechtbauer, Ph.D., Statistician > Department of Psychiatry and Psychology > School for Mental Health and Neuroscience > Faculty of Health, Medicine, and Life Sciences > Maastricht University, P.O. Box 616 (VIJV1) > 6200 MD Maastricht, The Netherlands > +31 (43) 388-4170 | http://www.wvbauer.com > > > -Original Message- > > From: <mailto:r-help-boun...@r-project.org>r-help-boun...@r-project.org > > [mailto:r-help-boun...@r-project.org] > > On Behalf Of Michael Dewey > > Sent: Monday, January 21, 2013 10:40 > > To: Alma Wilflinger; Michael Dewey; > > <mailto:r-help@r-project.org>r-help@r-project.org > > Subject: Re: [R] dummy encoding in metafor > > > > At 14:48 20/01/2013, Alma Wilflinger wrote: > > >Hi, > > > > > >thank you very much for your kind answer. > > > > > > >If you look a bit further down the manual page you will see > > > >### using a model formula to specify the same model > > > >rma(yi, vi, mods=~factor(alloc)+year+ablat, data=dat, method="REML", > > > >btt=c(2,3)) > > > > > > >which is much easier. > > > > > >I have seen the possibility of using a model formula for dummy > > >encoding and you are right it is much easier than doing it by hand. > > >Thing is that if I include some moderator variables into the > > >parameters I get the error: > > > > > >Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve > > > > I suspect that you have a linear dependence between your moderator > > variables. Depending on how many levels there are for country, > > sample, and so on you do have a lot of predictors (you presumably > > know that a factor counts as levels-1 for this purpose?) > > > > > > >For example this call works: > > >result = rma(yi=Mean, vi=Variance, ni=N.1, mods=~factor(Country) + > > >relevel(factor(Sample), ref="Students") + Gender + Age + > > >factor(Category) + relevel(factor(Block), ref="c")+ > > >relevel(factor(order), ref="x"), data=csvDataCmaAll, method="REML") > > > > > >If I add the trials which is of type INT: > > >result = rma(y
Re: [R] dummy encoding in metafor
Dear Wolfgang and Michael, thank you very much for your help! Concerning the Variance: I took the variance I used for CMA (which is always 1), so I think it should be the right one. Thank you for noticing and mentioning though :) I really appreciate how helpful you both are. best, Alma From: Viechtbauer Wolfgang (STAT) To: Michael Dewey ; Alma Wilflinger ; "r-help@r-project.org" Sent: Monday, January 21, 2013 11:10 AM Subject: RE: [R] dummy encoding in metafor As Michael already mentioned, the error: Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve indeed indicates that your design matrix is not of full rank (i.e., there are linear dependencies among your predictors). With this many factors in the same model, this is not surprising if k is "only" 94 (which is actually quite large for a meta-analysis). One options is to leave out some of the predictors. You can also try collapsing some of the levels of the factors. Of course, you lose some "details" that way, but apparently you don't have enough data in the first place to carry out such a detailed analysis. One other thing I noticed. You wrote: rma(yi=Mean, vi=Variance, ni=N.1, ...) I suspect that your variable "Variance" is actually the variance of the raw scores. However, the vi argument is used to pass the sampling variances of the yi values to the function -- not the variance of raw scores. The (estimated) sampling variance of a mean is s^2 / n, so if I am not mistaken, you really want to use: rma(yi=Mean, vi=Variance/N.1, ...) Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Michael Dewey > Sent: Monday, January 21, 2013 10:40 > To: Alma Wilflinger; Michael Dewey; r-help@r-project.org > Subject: Re: [R] dummy encoding in metafor > > At 14:48 20/01/2013, Alma Wilflinger wrote: > >Hi, > > > >thank you very much for your kind answer. > > > > >If you look a bit further down the manual page you will see > > >### using a model formula to specify the same model > > >rma(yi, vi, mods=~factor(alloc)+year+ablat, data=dat, method="REML", > > >btt=c(2,3)) > > > > >which is much easier. > > > >I have seen the possibility of using a model formula for dummy > >encoding and you are right it is much easier than doing it by hand. > >Thing is that if I include some moderator variables into the > >parameters I get the error: > > > >Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve > > I suspect that you have a linear dependence between your moderator > variables. Depending on how many levels there are for country, > sample, and so on you do have a lot of predictors (you presumably > know that a factor counts as levels-1 for this purpose?) > > > >For example this call works: > >result = rma(yi=Mean, vi=Variance, ni=N.1, mods=~factor(Country) + > >relevel(factor(Sample), ref="Students") + Gender + Age + > >factor(Category) + relevel(factor(Block), ref="c")+ > >relevel(factor(order), ref="x"), data=csvDataCmaAll, method="REML") > > > >If I add the trials which is of type INT: > >result = rma(yi=Mean, vi=Variance, ni=N.1, mods=~factor(Country) + > >relevel(factor(Sample), ref="Students") + Gender + Age + > >factor(Category) + relevel(factor(Block), ref="c")+ > >relevel(factor(order), ref="x") + trials, data=csvDataCmaAll, > method="REML") > > > >I get the error and I was not able to find a definite reason for > >this error or how to solve it I wanted to try it by doing it manually. > >I think I have found out that it somehow relates to the > > > > >If you code them yourself R does not know. You know. > > > >Regarding this I think my question was not clear enough. If R does > >the dummy encoding automatically via a model formula it leaves out > >one of the factors and uses it as a baseline automatically. If I do > >it by hand R is still able to execute the function but the baseline > >is missing because I do not define it via a parameter. > > You perhaps would benefit from rereading some of the introductory > material about formulas. Also look for anything about the model > matrix (also called the design matrix) > &
Re: [R] dummy encoding in metafor
Hi, thank you very much for your kind answer. >If you look a bit further down the manual page you will see >### using a model formula to specify the same model >rma(yi, vi, mods=~factor(alloc)+year+ablat, data=dat, method="REML", >btt=c(2,3)) >which is much easier. I have seen the possibility of using a model formula for dummy encoding and you are right it is much easier than doing it by hand. Thing is that if I include some moderator variables into the parameters I get the error: Error in qr.solve(wX, diag(k)) : singular matrix 'a' in solve For example this call works: result = rma(yi=Mean, vi=Variance, ni=N.1, mods=~factor(Country) + relevel(factor(Sample), ref="Students") + Gender + Age + factor(Category) + relevel(factor(Block), ref="c")+ relevel(factor(order), ref="x"), data=csvDataCmaAll, method="REML") If I add the trials which is of type INT: result = rma(yi=Mean, vi=Variance, ni=N.1, mods=~factor(Country) + relevel(factor(Sample), ref="Students") + Gender + Age + factor(Category) + relevel(factor(Block), ref="c")+ relevel(factor(order), ref="x") + trials, data=csvDataCmaAll, method="REML") I get the error and I was not able to find a definite reason for this error or how to solve it I wanted to try it by doing it manually. I think I have found out that it somehow relates to the >If you code them yourself R does not know. You know. Regarding this I think my question was not clear enough. If R does the dummy encoding automatically via a model formula it leaves out one of the factors and uses it as a baseline automatically. If I do it by hand R is still able to execute the function but the baseline is missing because I do not define it via a parameter. I simply want to know how R is handling this and what I have to do by hand to get the correct results. Sorry, this may be a beginners question, but as stated I am new to this field. >You say you have seven moderator variables. Unless you have a shed >load of studies you will not be able to look at them simultaneously. >Apologies if you already knew that. No I have not known that. In total I have about 94 studies and want to test different sets of moderators. Do you think this is sufficient or do you suggest another approach? I started in CMA (comprehensive meta analysis) but one of the benefits of R is that I am able to test multiple moderators at once - at least as I was told. kind regards, Alma From: Michael Dewey r-project.org> Sent: Sunday, January 20, 2013 12:52 PM Subject: Re: [R] dummy encoding in metafor At 17:14 19/01/2013, Alma Wilflinger wrote: >Hi, > >I am quite new to R and in need of some advice. I am trying to >conduct a meta regression over a some studies with about 7 mod >variables which I have to dummy encode. Alma, although you can generate your own dummy variables by hand you do not have to as R will do it for you. See below for more comments. >I have found the following piece of code in the manual for the >metafor library: > >### manual dummy coding of the allocation factor >alloc.random <- ifelse(dat$alloc == "random", 1, 0) >alloc.alternate <- ifelse(dat$alloc == "alternate", 1, 0) >alloc.systematic <- ifelse(dat$alloc == "systematic", 1, 0) If you look a bit further down the manual page you will see ### using a model formula to specify the same model rma(yi, vi, mods=~factor(alloc)+year+ablat, data=dat, method="REML", btt=c(2,3)) which is much easier. >### test the allocation factor (in the presence of the other moderators) >### note: "alternate" is the reference level of the allocation factor >### note: the intercept is the first coefficient, so btt=c(2,3) >rma(yi, vi, mods=cbind(alloc.random, alloc.systematic, year, ablat), >data=dat, method="REML", btt=c(2,3)) > >What I do not understand is the following: >How does R know which columns in my data.frame are related to the >dummy encoded variables? If you code them yourself R does not know. You know. >It is clear that in the call of cbind I just do not use the >reference variable as a parameter but I do not get it how R knows >that alloc.random and alloc.systematic refer to the column alloc in >the data frame. > >Thank you very much in advance for your help, > You say you have seven moderator variables. Unless you have a shed load of studies you will not be able to look at them simultaneously. Apologies if you already knew that. >kind regards, >Alma > [[alternative HTML version deleted]] Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] dummy encoding in metafor
Hi, I am quite new to R and in need of some advice. I am trying to conduct a meta regression over a some studies with about 7 mod variables which I have to dummy encode. I have found the following piece of code in the manual for the metafor library: ### manual dummy coding of the allocation factor alloc.random <- ifelse(dat$alloc == "random", 1, 0) alloc.alternate <- ifelse(dat$alloc == "alternate", 1, 0) alloc.systematic <- ifelse(dat$alloc == "systematic", 1, 0) ### test the allocation factor (in the presence of the other moderators) ### note: "alternate" is the reference level of the allocation factor ### note: the intercept is the first coefficient, so btt=c(2,3) rma(yi, vi, mods=cbind(alloc.random, alloc.systematic, year, ablat), data=dat, method="REML", btt=c(2,3)) What I do not understand is the following: How does R know which columns in my data.frame are related to the dummy encoded variables? It is clear that in the call of cbind I just do not use the reference variable as a parameter but I do not get it how R knows that alloc.random and alloc.systematic refer to the column alloc in the data frame. Thank you very much in advance for your help, kind regards, Alma [[alternative HTML version deleted]] __ R-help@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.
