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commit 1227e2c60c
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reference/get_episode.md
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@@ -178,28 +178,28 @@ x
df <- example_isolates[sample(seq_len(2000), size = 100), ]
get_episode(df$date, episode_days = 60) # indices
#> [1] 17 19 32 7 48 16 36 11 41 30 43 42 3 37 6 42 16 46 12 6 38 15 31 23 44
#> [26] 35 42 21 10 21 18 22 9 29 40 8 22 14 31 47 18 26 28 18 25 20 11 49 8 27
#> [51] 50 23 46 3 27 6 31 1 33 10 23 31 11 20 46 13 4 24 4 27 8 48 16 2 20
#> [76] 35 31 19 33 34 16 14 33 17 46 24 15 17 7 9 39 14 50 5 12 2 45 35 8 28
#> [1] 43 9 7 14 28 40 49 29 19 27 10 44 18 22 42 12 8 36 13 3 46 5 4 35 38
#> [26] 16 22 23 16 10 42 13 2 45 18 19 39 32 22 36 40 45 39 40 11 23 25 39 26 23
#> [51] 25 12 17 23 30 30 34 16 21 37 40 26 11 7 4 16 43 22 47 37 39 31 25 41 1
#> [76] 45 39 23 32 45 20 22 15 14 13 43 9 38 29 6 48 24 21 23 44 19 31 1 3 33
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [13] TRUE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE
#> [25] TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE
#> [37] FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE
#> [49] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
#> [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
#> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE
#> [97] TRUE FALSE FALSE FALSE
#> [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
# filter on results from the third 60-day episode only, using base R
df[which(get_episode(df$date, 60) == 3), ]
#> # A tibble: 2 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R
#> 2 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S
#> 2 2002-10-18 E55128 57 F ICU B_STPHY_AURS R NA S R
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
@@ -233,19 +233,19 @@ if (require("dplyr")) {
arrange(patient, condition, date)
}
#> # A tibble: 100 × 4
#> # Groups: patient, condition [95]
#> # Groups: patient, condition [96]
#> patient date condition new_episode
#> <chr> <date> <chr> <lgl>
#> 1 011307 2011-09-20 B TRUE
#> 2 011307 2011-09-20 C TRUE
#> 3 021368 2016-03-25 A TRUE
#> 4 060287 2007-03-11 B TRUE
#> 5 078381 2014-07-17 A TRUE
#> 6 097186 2015-10-28 B TRUE
#> 7 0DBB93 2003-10-02 A TRUE
#> 8 0DBF93 2015-12-03 C TRUE
#> 9 114570 2003-04-22 A TRUE
#> 10 141061 2014-10-22 C TRUE
#> 1 022060 2004-05-04 A TRUE
#> 2 060287 2007-03-11 A TRUE
#> 3 0E2483 2007-04-06 C TRUE
#> 4 101305 2006-12-13 A TRUE
#> 5 141061 2014-10-22 A TRUE
#> 6 146F70 2009-08-14 A TRUE
#> 7 15D386 2004-08-01 B TRUE
#> 8 187841 2008-04-22 C TRUE
#> 9 195736 2008-08-29 C TRUE
#> 10 195736 2008-08-29 C FALSE
#> # ℹ 90 more rows
if (require("dplyr")) {
@@ -259,19 +259,19 @@ if (require("dplyr")) {
arrange(patient, ward, date)
}
#> # A tibble: 100 × 5
#> # Groups: ward, patient [93]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <int> <lgl>
#> 1 Clinical 2011-09-20 011307 1 TRUE
#> 2 Clinical 2011-09-20 011307 1 FALSE
#> 3 Outpatient 2016-03-25 021368 1 TRUE
#> 4 Clinical 2007-03-11 060287 1 TRUE
#> 5 ICU 2014-07-17 078381 1 TRUE
#> 6 Clinical 2015-10-28 097186 1 TRUE
#> 7 ICU 2003-10-02 0DBB93 1 TRUE
#> 8 ICU 2015-12-03 0DBF93 1 TRUE
#> 9 ICU 2003-04-22 114570 1 TRUE
#> 10 Clinical 2014-10-22 141061 1 TRUE
#> # Groups: ward, patient [91]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <int> <lgl>
#> 1 ICU 2004-05-04 022060 1 TRUE
#> 2 Clinical 2007-03-11 060287 1 TRUE
#> 3 Clinical 2007-04-06 0E2483 1 TRUE
#> 4 Clinical 2006-12-13 101305 1 TRUE
#> 5 Clinical 2014-10-22 141061 1 TRUE
#> 6 Clinical 2009-08-14 146F70 1 TRUE
#> 7 ICU 2004-08-01 15D386 1 TRUE
#> 8 Clinical 2008-04-22 187841 1 TRUE
#> 9 Clinical 2008-08-29 195736 1 TRUE
#> 10 Clinical 2008-08-29 195736 1 FALSE
#> # ℹ 90 more rows
if (require("dplyr")) {
@@ -287,9 +287,9 @@ 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 51 12 33 43
#> 2 ICU 31 11 26 30
#> 3 Outpatient 11 8 11 11
#> 1 Clinical 58 14 38 44
#> 2 ICU 26 7 20 23
#> 3 Outpatient 7 4 6 7
# grouping on patients and microorganisms leads to the same
# results as first_isolate() when using 'episode-based':
@@ -307,7 +307,7 @@ if (require("dplyr")) {
identical(x, y)
}
#> [1] TRUE
#> [1] FALSE
# but is_new_episode() has a lot more flexibility than first_isolate(),
# since you can now group on anything that seems relevant:
@@ -318,19 +318,19 @@ if (require("dplyr")) {
select(group_vars(.), flag_episode)
}
#> # A tibble: 100 × 4
#> # Groups: patient, mo, ward [95]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 690B42 B_ESCHR_COLI ICU TRUE
#> 2 550406 B_ESCHR_COLI Outpatient TRUE
#> 3 F86227 B_STPHY_CONS Clinical TRUE
#> 4 859863 B_STPHY_EPDR ICU TRUE
#> 5 987C84 B_ESCHR_COLI Clinical TRUE
#> 6 E19440 B_ESCHR_COLI ICU TRUE
#> 7 F42C5F B_MRGNL_MRGN Clinical TRUE
#> 8 F54261 B_STPHY_AURS Clinical TRUE
#> 9 5D1690 B_ESCHR_COLI Outpatient TRUE
#> 10 874171 B_STPHY_CONS Clinical TRUE
#> # 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
#> # ℹ 90 more rows
# }
```