[R] Error message in meta-analysis package Metafor-weights =""

Tue Jun 23 17:29:46 CEST 2020

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.viechtbauer using 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:amoatwik20 using gmail.com]
> >Sent: Tuesday, 23 June, 2020 16:37
> >To: Viechtbauer, Wolfgang (SP)
> >Cc: r-help using 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.viechtbauer using maastrichtuniversity.nl> wrote:
> >Dear Kobby,
> >
> >Please post the output of sessionInfo() and class(result.md).
> >
> >Best,
> >Wolfgang
> >
> >>-----Original Message-----
> >>From: K Amoatwi [mailto:amoatwik20 using gmail.com]
> >>Sent: Monday, 22 June, 2020 22:30
> >>To: Viechtbauer, Wolfgang (SP)
> >>Cc: r-help using 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.viechtbauer using 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-bounces using r-project.org] On Behalf Of K
> Amoatwi
> >>>Sent: Tuesday, 16 June, 2020 4:50
> >>>To: r-help using 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
>

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