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Fix data cleaning bug: days threshold

pull/95/head
Meng Li 2020-08-06 17:26:37 -04:00
parent 2859a53202
commit 18d220d6c0
1 changed files with 6 additions and 5 deletions
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11
src/models/clean_features_for_model.R
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@ -3,22 +3,23 @@ library(tidyr)
library(dplyr)
filter_participant_without_enough_days <- function(clean_features, days_before_threshold, days_after_threshold){
clean_features$day_type <- ifelse(clean_features$day_idx < 0, -1, ifelse(clean_features$day_idx > 0, 1, 0))
if("pid" %in% colnames(clean_features)){
clean_features <- clean_features %>%
group_by(pid) %>%
add_count(pid, day_idx) # this adds a new column "n"
add_count(pid, day_type) # this adds a new column "n"
} else {
clean_features <- clean_features %>% add_count(day_idx)
clean_features <- clean_features %>% add_count(day_type < 0)
}
# Only keep participants with enough days before surgery and after discharge
clean_features <- clean_features %>%
mutate(count_before = ifelse(day_idx < 0, n, NA), # before surgery
count_after = ifelse(day_idx > 0, n, NA)) %>% # after discharge
mutate(count_before = ifelse(day_type == -1, n, NA), # before surgery
count_after = ifelse(day_type == 1, n, NA)) %>% # after discharge
fill(count_before, .direction = "downup") %>%
fill(count_after, .direction = "downup") %>%
filter(count_before >= days_before_threshold & count_after >= days_after_threshold) %>%
select(-n, -count_before, -count_after) %>%
select(-n, -count_before, -count_after, -day_type) %>%
ungroup()
return(clean_features)