Error message in meta-analysis package Metafor-weights =""

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Error message in meta-analysis package Metafor-weights =""

K Amoatwi
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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Re: Error message in meta-analysis package Metafor-weights =""

Viechtbauer, Wolfgang (SP)
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:[hidden email]] On Behalf Of K Amoatwi
>Sent: Tuesday, 16 June, 2020 4:50
>To: [hidden email]
>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

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error message in meta-analysis package Metafor-weights =""

K Amoatwi
Thank you, very much appreciated.

On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) <
[hidden email]> 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:[hidden email]] On Behalf Of K Amoatwi
> >Sent: Tuesday, 16 June, 2020 4:50
> >To: [hidden email]
> >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]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: Error message in meta-analysis package Metafor-weights =""

K Amoatwi
In reply to this post by Viechtbauer, Wolfgang (SP)
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) <
[hidden email]> 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:[hidden email]] On Behalf Of K Amoatwi
> >Sent: Tuesday, 16 June, 2020 4:50
> >To: [hidden email]
> >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]]

______________________________________________
[hidden email] 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.
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Re: Error message in meta-analysis package Metafor-weights =""

Viechtbauer, Wolfgang (SP)
Dear Kobby,

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

Best,
Wolfgang

>-----Original Message-----
>From: K Amoatwi [mailto:[hidden email]]
>Sent: Monday, 22 June, 2020 22:30
>To: Viechtbauer, Wolfgang (SP)
>Cc: [hidden email]
>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)
><[hidden email]> 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:[hidden email]] On Behalf Of K Amoatwi
>>Sent: Tuesday, 16 June, 2020 4:50
>>To: [hidden email]
>>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
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error message in meta-analysis package Metafor-weights =""

K 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) <
[hidden email]> wrote:

> Dear Kobby,
>
> Please post the output of sessionInfo() and class(result.md).
>
> Best,
> Wolfgang
>
> >-----Original Message-----
> >From: K Amoatwi [mailto:[hidden email]]
> >Sent: Monday, 22 June, 2020 22:30
> >To: Viechtbauer, Wolfgang (SP)
> >Cc: [hidden email]
> >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)
> ><[hidden email]> 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:[hidden email]] On Behalf Of K
> Amoatwi
> >>Sent: Tuesday, 16 June, 2020 4:50
> >>To: [hidden email]
> >>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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Re: 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:[hidden email]]
>Sent: Tuesday, 23 June, 2020 16:37
>To: Viechtbauer, Wolfgang (SP)
>Cc: [hidden email]
>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)
><[hidden email]> wrote:
>Dear Kobby,
>
>Please post the output of sessionInfo() and class(result.md).
>
>Best,
>Wolfgang
>
>>-----Original Message-----
>>From: K Amoatwi [mailto:[hidden email]]
>>Sent: Monday, 22 June, 2020 22:30
>>To: Viechtbauer, Wolfgang (SP)
>>Cc: [hidden email]
>>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)
>><[hidden email]> 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:[hidden email]] On Behalf Of K Amoatwi
>>>Sent: Tuesday, 16 June, 2020 4:50
>>>To: [hidden email]
>>>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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Re: Error message in meta-analysis package Metafor-weights =""

K Amoatwi
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) <
[hidden email]> 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:[hidden email]]
> >Sent: Tuesday, 23 June, 2020 16:37
> >To: Viechtbauer, Wolfgang (SP)
> >Cc: [hidden email]
> >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)
> ><[hidden email]> wrote:
> >Dear Kobby,
> >
> >Please post the output of sessionInfo() and class(result.md).
> >
> >Best,
> >Wolfgang
> >
> >>-----Original Message-----
> >>From: K Amoatwi [mailto:[hidden email]]
> >>Sent: Monday, 22 June, 2020 22:30
> >>To: Viechtbauer, Wolfgang (SP)
> >>Cc: [hidden email]
> >>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)
> >><[hidden email]> 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:[hidden email]] On Behalf Of K
> Amoatwi
> >>>Sent: Tuesday, 16 June, 2020 4:50
> >>>To: [hidden email]
> >>>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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Re: Error message in meta-analysis package Metafor-weights =""

Michael Dewey-3
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) <
> [hidden email]> 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:[hidden email]]
>>> Sent: Tuesday, 23 June, 2020 16:37
>>> To: Viechtbauer, Wolfgang (SP)
>>> Cc: [hidden email]
>>> 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)
>>> <[hidden email]> wrote:
>>> Dear Kobby,
>>>
>>> Please post the output of sessionInfo() and class(result.md).
>>>
>>> Best,
>>> Wolfgang
>>>
>>>> -----Original Message-----
>>>> From: K Amoatwi [mailto:[hidden email]]
>>>> Sent: Monday, 22 June, 2020 22:30
>>>> To: Viechtbauer, Wolfgang (SP)
>>>> Cc: [hidden email]
>>>> 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)
>>>> <[hidden email]> 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:[hidden email]] On Behalf Of K
>> Amoatwi
>>>>> Sent: Tuesday, 16 June, 2020 4:50
>>>>> To: [hidden email]
>>>>> 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]]
>
> ______________________________________________
> [hidden email] 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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Re: Error message in meta-analysis package Metafor-weights =""

K Amoatwi
Thank Michael and Wolfgang, very much appreciated.

Kobby

On Tue, Jun 23, 2020 at 11:39 AM Michael Dewey <[hidden email]>
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) <
> > [hidden email]> 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:[hidden email]]
> >>> Sent: Tuesday, 23 June, 2020 16:37
> >>> To: Viechtbauer, Wolfgang (SP)
> >>> Cc: [hidden email]
> >>> 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)
> >>> <[hidden email]> wrote:
> >>> Dear Kobby,
> >>>
> >>> Please post the output of sessionInfo() and class(result.md).
> >>>
> >>> Best,
> >>> Wolfgang
> >>>
> >>>> -----Original Message-----
> >>>> From: K Amoatwi [mailto:[hidden email]]
> >>>> Sent: Monday, 22 June, 2020 22:30
> >>>> To: Viechtbauer, Wolfgang (SP)
> >>>> Cc: [hidden email]
> >>>> 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)
> >>>> <[hidden email]> 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:[hidden email]] On Behalf Of K
> >> Amoatwi
> >>>>> Sent: Tuesday, 16 June, 2020 4:50
> >>>>> To: [hidden email]
> >>>>> 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]]
> >
> > ______________________________________________
> > [hidden email] 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
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.