[R] Error message in meta-analysis package Metafor-weights =""
K Amoatwi
@mo@tw|k20 @end|ng |rom gm@||@com
Tue Jun 16 04:49:30 CEST 2020
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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