For loops to make leave-one-out analysis with netmeta - r

Question

I'm doing a network metanalysis of 29 studies using the netmeta package with R and I now have to do the leave-one-out analysis. I was thus wondering whether there is a way to use for loops to gain the results of a such method in order not to do it by manually excluding one trial at a time.
I came up with this:
for (i in 1:29){
NMA_DB_L<-NMA_DB[-i,]
yi_All_cause<-summary(escalc(ai= NMA_DB_L$All_Cause_d_C, bi=NMA_DB_L$PTS_All_Cause_d_C - NMA_DB_L$All_Cause_d_C,
ci= NMA_DB_L$All_Cause_d_I, di= NMA_DB_L$PTS_All_Cause_d_I - NMA_DB_L$All_Cause_d_I,
measure = "RR"))[,"yi"]
sei_All_cause<-summary(escalc(ai= NMA_DB_L$All_Cause_d_C, bi=NMA_DB_L$PTS_All_Cause_d_C - NMA_DB_L$All_Cause_d_C,
ci= NMA_DB_L$All_Cause_d_I, di= NMA_DB_L$PTS_All_Cause_d_I - NMA_DB_L$All_Cause_d_I,
measure = "RR"))[,"sei"]
netmeta(TE=yi_All_cause, seTE = sei_All_cause, treat1 = NMA_DB_L$Arm_1, treat2 = NMA_DB_L$INT, sm="RR",
studlab = NMA_DB_L$Study, reference.group = "Standard_DAPT")
}
and it seems to work properly, but I cannot find a way to save the results of each analysis without one of the trials.
Does anyone have an idea of how to do so?

Answer 1

Consider also lapply (to avoid bookkeeping of initializing a list and assign in for loop by index). Also, use a defined method and avoid rerunning summary + escalc just to retrieve attributes. Run it once and extract attributes as needed.
# DEFINED METHOD TO RUN CALCULATIONS
# AVOID DRY (I.E., DON'T REPEAT YOURSELF)
run_trials <- function(i) {
NMA_DB_L <- NMA_DB[-i,]
results <- summary(escalc(
ai = NMA_DB_L$All_Cause_d_C,
bi = NMA_DB_L$PTS_All_Cause_d_C - NMA_DB_L$All_Cause_d_C,
ci = NMA_DB_L$All_Cause_d_I,
di = NMA_DB_L$PTS_All_Cause_d_I - NMA_DB_L$All_Cause_d_I,
measure = "RR"
))
yi_All_cause <- results[,"yi"]
sei_All_cause <- results[,"sei"]
netmeta(
TE = yi_All_cause,
seTE = sei_All_cause,
treat1 = NMA_DB_L$Arm_1,
treat2 = NMA_DB_L$INT, sm="RR",
studlab = NMA_DB_L$Study,
reference.group = "Standard_DAPT"
)
}
# BUILD LIST OF RESULTS
netmeta_results <- lapply(1:29, run_trials)

Answer 2

Why not save the outputs of netmeta function into a list?
# Create list of length 29
net_results <- vector('list', 29)
for (i in 1:29) {
NMA_DB_L<-NMA_DB[-i,]
...
net <- netmeta(TE=yi_All_cause, seTE = sei_All_cause,
treat1 = NMA_DB_L$Arm_1, treat2 = NMA_DB_L$INT, sm="RR",
studlab = NMA_DB_L$Study, reference.group = "Standard_DAPT")
net_results[[i]] <- net
}
You can then access results of the specific run with net_results[[1]] etc.
R lists can in general contain any type of element which makes it a suitable structure for this type of problems.