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.viechtba...@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:amoatwi...@gmail.com]
Sent: Tuesday, 23 June, 2020 16:37
To: Viechtbauer, Wolfgang (SP)
Cc: r-help@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.viechtba...@maastrichtuniversity.nl> wrote:
Dear Kobby,
Please post the output of sessionInfo() and class(result.md).
Best,
Wolfgang
-----Original Message-----
From: K Amoatwi [mailto:amoatwi...@gmail.com]
Sent: Monday, 22 June, 2020 22:30
To: Viechtbauer, Wolfgang (SP)
Cc: r-help@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.viechtba...@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-boun...@r-project.org] On Behalf Of K
Amoatwi
Sent: Tuesday, 16 June, 2020 4:50
To: r-help@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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Michael
http://www.dewey.myzen.co.uk/home.html
______________________________________________
R-help@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.
