Thank Michael and Wolfgang, very much appreciated. Kobby
On Tue, Jun 23, 2020 at 11:39 AM Michael Dewey <li...@dewey.myzen.co.uk> wrote: > The two packages both define a function forest. When you load the second > package R will have told you that it was masking the definition of > forest from the first package. If you had loaded them in the other order > it would have masked the other one. > > In fact it masked seven functions in total in this case as the message > told you. > > Michael > > On 23/06/2020 16:29, K Amoatwi wrote: > > Dear Wolfgang, > > Yes! The "metafor::forest(result.md)" works > > > > Thank you very much. > > > > Any reason why "forest(result.md)" was not working? > > > > Kobby > > > > On Tue, Jun 23, 2020 at 11:18 AM Viechtbauer, Wolfgang (SP) < > > wolfgang.viechtba...@maastrichtuniversity.nl> wrote: > > > >> You have loaded the 'meta' package after 'metafor' and then forest() > will > >> try to use the corresponding function from the meta package and not > >> metafor. With: > >> > >> metafor::forest(result.md) > >> > >> it should work. > >> > >> Best, > >> Wolfgang > >> > >>> -----Original Message----- > >>> From: K Amoatwi [mailto:amoatwi...@gmail.com] > >>> Sent: Tuesday, 23 June, 2020 16:37 > >>> To: Viechtbauer, Wolfgang (SP) > >>> Cc: r-help@r-project.org > >>> Subject: Re: [R] Error message in meta-analysis package Metafor-weights > >> ="" > >>> > >>> Dear Wolfgang, > >>> I have posted the requested information you asked for. > >>> > >>>> sessionInfo() > >>> R version 4.0.1 (2020-06-06) > >>> Platform: x86_64-w64-mingw32/x64 (64-bit) > >>> Running under: Windows 10 x64 (build 18362) > >>> > >>> Matrix products: default > >>> > >>> locale: > >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >>> States.1252 > >>> [3] LC_MONETARY=English_United States.1252 > >>> LC_NUMERIC=C > >>> [5] LC_TIME=English_United States.1252 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] meta_4.12-0 reshape2_1.4.4 metafor_2.4-0 Matrix_1.2-18 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] Rcpp_1.0.4.6 lattice_0.20-41 MASS_7.3- > >>> 51.6 grid_4.0.1 > >>> [5] plyr_1.8.6 nlme_3.1- > >>> 148 magrittr_1.5 stringi_1.4.6 > >>> [9] minqa_1.2.4 nloptr_1.2.2.1 boot_1.3- > >>> 25 splines_4.0.1 > >>> [13] statmod_1.4.34 lme4_1.1- > >>> 23 tools_4.0.1 stringr_1.4.0 > >>> [17] CompQuadForm_1.4.3 compiler_4.0.1 > >>>> > >>> > >>>> class(result.md) > >>> [1] "rma.uni" "rma" > >>>> > >>> > >>> Thank you > >>> Kobby > >>> > >>> On Tue, Jun 23, 2020 at 3:24 AM Viechtbauer, Wolfgang (SP) > >>> <wolfgang.viechtba...@maastrichtuniversity.nl> wrote: > >>> Dear Kobby, > >>> > >>> Please post the output of sessionInfo() and class(result.md). > >>> > >>> Best, > >>> Wolfgang > >>> > >>>> -----Original Message----- > >>>> From: K Amoatwi [mailto:amoatwi...@gmail.com] > >>>> Sent: Monday, 22 June, 2020 22:30 > >>>> To: Viechtbauer, Wolfgang (SP) > >>>> Cc: r-help@r-project.org > >>>> Subject: Re: [R] Error message in meta-analysis package > Metafor-weights > >> ="" > >>>> > >>>> Hi Wolfgang and All, > >>>> I am still practising my meta-analysis with the "Metafor" package, I > >> tried > >>>> to run the code for "Forest plot" and got error message as shown > below: > >>>> forest(result.md) > >>>>> forest(result.md) > >>>> Error in UseMethod("forest") : > >>>> no applicable method for 'forest' applied to an object of class > >>>> "c('rma.uni', 'rma')" > >>>> > >>>> Thank you in advance for your support > >>>> > >>>> regards > >>>> Kobby > >>>> > >>>> On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) > >>>> <wolfgang.viechtba...@maastrichtuniversity.nl> wrote: > >>>> Dear Amoatwi, > >>>> > >>>> This way of using the escalc() function has been deprecated. It might > be > >>>> added back once there is actually any benefit from having this > >>>> functionality, but for years it just meant that I had to maintain two > >>>> different ways of doing the exact same thing without any additional > >>>> benefits. > >>>> > >>>> Best, > >>>> Wolfgang > >>>> > >>>> -- > >>>> Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry > and > >>>> Neuropsychology | 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 [mailto:r-help-boun...@r-project.org] On Behalf Of K > >> Amoatwi > >>>>> Sent: Tuesday, 16 June, 2020 4:50 > >>>>> To: r-help@r-project.org > >>>>> Subject: [R] Error message in meta-analysis package Metafor-weights > ="" > >>>>> > >>>>> Dear All, > >>>>> I am using the example from one of the tutorial about "Metafor" > package > >>> and > >>>>> "escalc" function, to learn how this package can be applied to do > >>>>> meta-analysi; the code and the data is directly from the tutorials > but > >>>>> "weights=freq" option in the escalc function is given me error > message > >>>>> This is the code below: > >>>>> > >>>>> library(metafor) # Load package > >>>>> #####DATASET 1: BCG Vaccine Trials > >>>>> data(dat.bcg) # BCG meta-analytic dataset > >>>>> > >>>>> ##Formula based Specification > >>>>> ##That is, what if I have multiple rows per study, corresponding to > >>>>> difference treatment groups? > >>>>> > >>>>> library(reshape2) # Load package for data reshaping > >>>>> > >>>>> bcg.long <- melt(dat.bcg[, c("trial", "tpos", "tneg", "cpos", > "cneg")], > >> id > >>>>> = "trial") > >>>>> bcg.long$pos <- ifelse(bcg.long$var == "tpos" | bcg.long$var == > "cpos", > >> 1, > >>>>> 0) > >>>>> bcg.long$group <- ifelse(bcg.long$var == "tpos" | bcg.long$var == > >> "tneg", > >>>>> 1, 0) > >>>>> > >>>>> ##sample of the data, the first 6 rows > >>>>> head(bcg.long) > >>>>> trial variable value pos group > >>>>> 1 1 tpos 4 1 1 > >>>>> 2 2 tpos 6 1 1 > >>>>> 3 3 tpos 3 1 1 > >>>>> 4 4 tpos 62 1 1 > >>>>> 5 5 tpos 33 1 1 > >>>>> 6 6 tpos 180 1 1 > >>>>> > >>>>> ##Now applying the " escalc " function > >>>>> > >>>>> escalc(factor(pos)~factor(group)| factor(trial),weights = value,data > = > >>>>> bcg.long, measure = "OR") > >>>>> > >>>>> ##Then I got this error message > >>>>> Error in escalc(factor(pos) ~ factor(group) | factor(trial), weights > = > >>>>> value, : > >>>>> object 'value' not found > >>>>> > >>>>> I used the same data with different example from another author and > got > >> a > >>>>> similar error message > >>>>> Second code with the same data but different coding > >>>>> Sample data > >>>>> > >>>>> with the first 6 rows of the rearranged data shown below. > (T=treatment, > >>>>> C=Control group, Out=outcome whether positive or negative, and then > >>>>> frequency) > >>>>> study grp out freq > >>>>> 1 1 T + 4 > >>>>> 2 1 T - 119 > >>>>> 3 1 C + 11 > >>>>> 4 1 C - 128 > >>>>> 5 2 T + 6 > >>>>> 6 2 T - 300 > >>>>> > >>>>>> escalc(out ~ grp | study, weights = freq, data = dat.fm, measure = > >> "OR") > >>>>> > >>>>> Error in escalc(out ~ grp | study, weights = freq, data = dat.fm, > >> measure > >>> = > >>>>> "OR") : > >>>>> object 'freq' not found > >>>>> > >>>>> I am not sure what I am doing wrong since both authors were able to > get > >>>>> their results while I am getting error messages. > >>>>> > >>>>> Any help will be very much appreciated > >>>>> > >>>>> Amoatwi > >> > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > > > > -- > Michael > http://www.dewey.myzen.co.uk/home.html > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.