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Update 0-data_prep.R

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Kyle Belanger 2023-01-06 07:40:03 -05:00
parent e4e76c08ac
commit f10ee3fcd7
1 changed files with 13 additions and 1 deletions
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14
ML/0-data_prep.R
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@ -10,6 +10,8 @@ box::use(
,DBI[dbConnect,dbDisconnect]
,here[here]
,dplyr
,dbplyr
,tidyr
)
# globals -----------------------------------------------------------------
@ -43,8 +45,18 @@ test_list <- c(
# load data ---------------------------------------------------------------
ds <- dplyr$tbl(db, "labevents") %>% dplyr$filter(itemid %in% test_list) %>% dplyr$collect()
ds <- dplyr$tbl(db, "labevents") %>%
dplyr$filter(itemid %in% test_list) %>%
dplyr$select(-charttime,-storetime) %>%
tidyr$pivot_wider(
id_cols = c(subject_id,specimen_id)
,names_from = itemid
,values_from = valuenum
) %>%
dplyr$filter(!is.na(`50993`)) %>%
dplyr$collect()
ds <- ds %>% dplyr$collect()
# close database ----------------------------------------------------------