R help - Jun 2020 - 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 at 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 at r-project.org] On Behalf Of K
Amoatwi
> >Sent: Tuesday, 16 June, 2020 4:50
> >To: r-help at 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]]

Dear Kobby,

Please post the output of sessionInfo() and class(result.md).

Best,
Wolfgang
>-----Original Message-----
>From: K Amoatwi [mailto:amoatwik20 at gmail.com]
>Sent: Monday, 22 June, 2020 22:30
>To: Viechtbauer, Wolfgang (SP)
>Cc: r-help at 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 at 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 at r-project.org] On Behalf Of K
Amoatwi
>>Sent: Tuesday, 16 June, 2020 4:50
>>To: r-help at 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

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