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rdplyr

Filtering subjects based on having sample at specific time points

I have a dataframe with multiple samples collected from different individuals looking like

ID Subject Week
ID01 S01 Week_2
ID02 S01 Week_4
ID03 S01 Week_5
ID04 S02 Week_3
ID05 S03 Week_2
ID06 S03 Week_4
ID07 S04 Week_1
ID08 S04 Week_4
ID09 S04 Week_5

I want to filter out the subjects and samples without both Week_4 and Week_5 collection time points using dplyr to have

ID Subject Week
ID01 S01 Week_2
ID02 S01 Week_4
ID03 S01 Week_5
ID07 S04 Week_1
ID08 S04 Week_4
ID09 S04 Week_5

at the end.

Solution

  • You may do this with all in filter for each Subject :

    library(dplyr)
keep_week <- c("Week_4", "Week_5")

df %>% filter(all(keep_week %in% Week), .by = Subject)

#    ID Subject   Week
#1 ID01     S01 Week_2
#2 ID02     S01 Week_4
#3 ID03     S01 Week_5
#4 ID07     S04 Week_1
#5 ID08     S04 Week_4
#6 ID09     S04 Week_5