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

K Amoatwi @mo@tw|k20 @end|ng |rom gm@||@com
Tue Jun 23 17:58:28 CEST 2020


Thank Michael and Wolfgang, very much appreciated.

Kobby

On Tue, Jun 23, 2020 at 11:39 AM Michael Dewey <lists using 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.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
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help using 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
>

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