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Update 0-data_prep.R

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Kyle Belanger 2023-01-23 08:02:04 -05:00
parent a172a82a71
commit 2ed99f1fee
1 changed files with 1 additions and 8 deletions
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9
ML/0-data_prep.R
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@ -72,13 +72,6 @@ patients <- dplyr$tbl(db, "patients") %>%
dplyr$select(-anchor_year, -anchor_year_group, -dod) %>%
dplyr$collect()
admissions <- dplyr$tbl(db, "admissions") %>%
dplyr$select(subject_id, race, hadm_id) %>%
dplyr$collect()
admissions <- admissions %>% dplyr$mutate(dplyr$across(race, factor))
# usable data set is using chart time as it appears
# LIS uses different id's for groups of tests
# BMP and CBC Results together
@ -98,7 +91,7 @@ ds1 <- ds_bmp %>%
dplyr$filter(!is.na(`50993`) & !is.na(`50995`)) %>%
dplyr$left_join(patients, by = c("subject_id" = "subject_id")) %>%
dplyr$mutate(dplyr$across(`51300`, ~dplyr$if_else(!is.na(.),`51300`,`51301`))) %>%
dplyr$select(-`51301`) %>%
dplyr$select(-`51301`, -hadm_id) %>%
# dplyr$filter(dplyr$if_all(.fns = ~!is.na(.)))
dplyr$filter(rowSums(is.na(.)) <= 3) #allows for 3 missing test