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

[Viechtbauer, Wolfgang (SP)]

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