It's not really a factor problem you are having, its a shiny problem.
Assuming you have a reasonable sort of data.frame in merge_cli_mi such as
merge_cli_mi <- tribble( ~Gender,~SomeOtherVariable,
"female",99,
"male",-88
)
merge_cli_mi$Gender<-factor(merge_cli_mi$Gender,levels = c("female","male"),labels = c(1,2))
merge_cli_mi
therefore you would have a dataframe with the Gender variable as a factor with labels 1 and 2.
Problem in your code as provided is you only pass the Gender vector rather than the whole merge_cli_mi object to numeric_con, and you have two layers of renderTabler...
Try this
numeric_con<-reactive({
merge_cli_mi$Gender<-factor(merge_cli_mi$Gender,levels = c("female","male"),labels = c(1,2))
merge_cli_mi
})
output$num1<-renderTable({
numeric_con()
})