Take rows with a specific number of repeated values - r

Question

In R, I have a large dataframe where the first two columns are the primary ID (object) and a secondary ID (element of the object).
I want to create a subset of this dataframe, with the condition that the primary and secondary ID had to be repeated in former dataframe for 20 times. I have also to repeat this process for other dataframes with the same structure.
Right now, I'm first counting how many times each couple of values (primary and secondary IDs) repeats itself in a new dataframe and then using a for loop to create the new dataframe, but the process is extremely slow and inefficient: the loop writes 20 rows/second starting from a dataframe that has from 500.000 to 1 million of rows.
for (i in 1:13){
x <- fread(dataframe_list[i]) #list which contains the dataframes that have to be analyzed
x1 <- ddply(x,.(Primary_ID,Secondary_ID), nrow) #creating a dataframe which shows how many times a couple of values repeats itself
x2 <- subset(x1, x1$V1 == 20) #selecting all couples that are repeated for 20 times
for (n in 1:length(x2$Primary_ID)){
x3 <- subset(x, (x$Primary_ID == x2$Primary_ID[n]) & (x$Secondary_ID == x2$Secondary_ID[n]))
outfiles <- paste0("B:/Results/Code_3_", Band[i], ".csv")
fwrite(x3, file=outfiles, append = TRUE, sep = ",")
}
}
How to take, for example, all the rows from the former dataframe that have as values for the primary and secondary ID the ones obtained in the x2 dataframe at once instead of writing one set of 20 rows at a time? Maybe in SQL is easier but I have to deal with R for now.
Edit:
Sure. Let's say I'm starting from a dataframe like this (with other rows with repeating IDs, I'll just stop to 5 rows to be short):
Primary ID Secondary ID Variable
1 1 1 0.5729
2 1 2 0.6289
3 1 3 0.3123
4 2 1 0.4569
5 2 2 0.7319
Then with my code I count in a new dataframe the repeated rows (for a threshold value of 4 instead of 20, so I can give you a short example):
Primary ID Secondary ID Count
1 1 1 1
2 1 2 3
3 1 3 4
4 2 1 2
5 2 2 4
The wanted output should be a dataframe like this:
Primary ID Secondary ID Variable
1 1 3 0.5920
2 1 3 0.6289
3 1 3 0.3123
4 1 3 0.4569
5 2 2 0.7319
6 2 2 0.5729
7 2 2 0.6289
8 2 2 0.3123

Answer 1

If anyone is interested, I managed to find a way. After counting with the code above how many times the couple of values is repeated, the output that I wanted can be obtained in this simple way:
#Select all the couples that are repeated 20 times
x2 <- subset(x1, x1$V1 == 20)
#Create a dataframe which contains the repeated primary and secondary IDs from x2
x3 <- as.data.frame(cbind(x2$Primary_ID, x2$Secondary_ID)
#Wanted output
dataframe <- inner_join(x, x3)
#Joining, by c("Primary_ID", "Secondary_ID")