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

Michael Dewey ||@t@ @end|ng |rom dewey@myzen@co@uk
Tue Jun 23 17:39:45 CEST 2020


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]]
> 
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-- 
Michael
http://www.dewey.myzen.co.uk/home.html



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