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2026-02-08 22:40:23 +00:00
parent 0551ea51cb
commit 8b71d0eb99
255 changed files with 23625 additions and 810 deletions
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46
reference/get_episode.md
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@@ -178,20 +178,20 @@ x
df <- example_isolates[sample(seq_len(2000), size = 100), ]
get_episode(df$date, episode_days = 60) # indices
#> [1] 43 9 7 14 28 40 49 29 19 27 10 44 18 22 42 12 8 36 13 3 46 5 4 35 38
#> [26] 16 22 23 16 10 42 13 2 45 18 19 39 32 22 36 40 45 39 40 11 23 25 39 26 23
#> [51] 25 12 17 23 30 30 34 16 21 37 40 26 11 7 4 16 43 22 47 37 39 31 25 41 1
#> [76] 45 39 23 32 45 20 22 15 14 13 43 9 38 29 6 48 24 21 23 44 19 31 1 3 33
#> [1] 29 42 9 7 14 28 39 48 29 19 27 10 43 18 22 41 12 8 35 13 3 45 5 4 34
#> [26] 37 16 22 23 16 10 41 13 2 44 18 19 38 32 22 35 39 44 38 39 11 23 25 38 26
#> [51] 23 25 12 17 23 30 30 33 16 21 36 39 26 11 7 4 16 42 22 46 36 38 31 25 40
#> [76] 1 44 38 23 32 44 20 22 15 14 13 42 9 37 29 6 47 24 21 23 43 19 31 1 3
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE
#> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [25] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
#> [37] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE
#> [49] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE
#> [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE
#> [73] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE
#> [85] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
#> [97] FALSE FALSE FALSE TRUE
#> [25] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
#> [37] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
#> [49] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE
#> [61] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> [73] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
#> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE
#> [97] FALSE FALSE FALSE FALSE
# filter on results from the third 60-day episode only, using base R
df[which(get_episode(df$date, 60) == 3), ]
@@ -287,7 +287,7 @@ if (require("dplyr")) {
#> # A tibble: 3 × 5
#> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30
#> <chr> <int> <int> <int> <int>
#> 1 Clinical 58 14 38 44
#> 1 Clinical 58 13 37 44
#> 2 ICU 26 7 20 23
#> 3 Outpatient 7 4 6 7
@@ -321,16 +321,16 @@ if (require("dplyr")) {
#> # Groups: patient, mo, ward [96]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 917895 B_STPHY_CPTS ICU TRUE
#> 2 022060 B_ENTRBC_CLOC ICU TRUE
#> 3 C36883 B_ESCHR_COLI Clinical TRUE
#> 4 5DF436 B_STPHY_AURS ICU TRUE
#> 5 971739 B_STPHY_CONS Clinical TRUE
#> 6 488175 B_ESCHR_COLI Clinical TRUE
#> 7 5DB1C8 B_STPHY_CPTS Clinical TRUE
#> 8 BC9909 B_ENTRBC_CLOC Clinical TRUE
#> 9 5B78D5 B_STPHY_AURS Clinical TRUE
#> 10 284FFF B_STPHY_EPDR Clinical TRUE
#> 1 473F39 B_ESCHR_COLI Clinical TRUE
#> 2 917895 B_STPHY_CPTS ICU TRUE
#> 3 022060 B_ENTRBC_CLOC ICU TRUE
#> 4 C36883 B_ESCHR_COLI Clinical TRUE
#> 5 5DF436 B_STPHY_AURS ICU TRUE
#> 6 971739 B_STPHY_CONS Clinical TRUE
#> 7 488175 B_ESCHR_COLI Clinical TRUE
#> 8 5DB1C8 B_STPHY_CPTS Clinical TRUE
#> 9 BC9909 B_ENTRBC_CLOC Clinical TRUE
#> 10 5B78D5 B_STPHY_AURS Clinical TRUE
#> # ℹ 90 more rows
# }
```