# `example_isolates` is a data set available in the AMR package.
+ # difference between absolute and relative determination of episodes:
+x <- data.frame(dates = as.Date(c(
+ "2021-01-01",
+ "2021-01-02",
+ "2021-01-05",
+ "2021-01-08",
+ "2021-02-21",
+ "2021-02-22",
+ "2021-02-23",
+ "2021-02-24",
+ "2021-03-01",
+ "2021-03-01"
+)))
+x$absolute <- get_episode(x$dates, episode_days = 7)
+x$relative <- get_episode(x$dates, case_free_days = 7)
+x
+#> dates absolute relative
+#> 1 2021-01-01 1 1
+#> 2 2021-01-02 1 1
+#> 3 2021-01-05 1 1
+#> 4 2021-01-08 2 1
+#> 5 2021-02-21 3 2
+#> 6 2021-02-22 3 2
+#> 7 2021-02-23 3 2
+#> 8 2021-02-24 3 2
+#> 9 2021-03-01 4 2
+#> 10 2021-03-01 4 2
+
+
+# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates
df <- example_isolates[sample(seq_len(2000), size = 100), ]
get_episode(df$date, episode_days = 60) # indices
-#> [1] 9 22 13 21 3 23 7 38 25 45 23 26 10 3 30 40 14 18 36 16 33 13 34 30 11
-#> [26] 49 48 33 34 29 27 4 14 48 47 2 37 18 11 49 5 38 8 41 11 41 36 19 43 31
-#> [51] 25 24 28 11 5 12 44 19 20 4 42 27 2 44 27 29 3 13 15 35 20 39 18 1 15
-#> [76] 2 47 6 15 14 32 17 29 44 22 36 27 9 15 9 11 31 17 21 17 22 46 12 18 40
+#> [1] 51 2 6 10 25 14 44 49 31 26 32 13 41 22 44 7 38 44 22 50 14 24 28 35 41
+#> [26] 42 15 40 3 20 37 40 50 26 19 48 46 9 8 1 29 47 23 47 47 2 24 6 14 15
+#> [51] 6 45 34 22 1 2 9 43 4 16 38 42 17 30 35 8 26 5 12 40 9 7 15 35 17
+#> [76] 32 38 17 16 18 36 11 25 51 22 20 28 1 39 21 20 23 27 33 48 43 7 36 14 19
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
-#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE
-#> [13] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE
-#> [25] TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE
-#> [37] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE
-#> [49] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE
-#> [61] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE
-#> [73] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE
-#> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
-#> [97] TRUE FALSE FALSE FALSE
+#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
+#> [13] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE
+#> [25] FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE
+#> [37] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
+#> [49] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE
+#> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE
+#> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE
+#> [85] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE 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), ]
-#> # A tibble: 3 × 46
-#> date patient age gender ward mo PEN OXA FLC AMX
-#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
-#> 1 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA
-#> 2 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R
-#> 3 2002-08-14 785317 51 F ICU B_ESCHR_COLI R NA NA NA
+#> # A tibble: 1 × 46
+#> date patient age gender ward mo PEN OXA FLC AMX
+#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
+#> 1 2002-10-22 718963 82 M ICU B_STPHY_EPDR R NA R R
#> # … with 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>,
@@ -249,19 +299,19 @@
arrange(patient, condition, date)
}
#> # A tibble: 100 × 4
-#> # Groups: patient, condition [100]
+#> # Groups: patient, condition [98]
#> patient date condition new_episode
#> <chr> <date> <chr> <lgl>
-#> 1 059414 2006-07-21 C TRUE
-#> 2 066601 2013-10-30 C TRUE
-#> 3 080086 2010-08-08 A TRUE
-#> 4 0E2483 2007-05-29 B TRUE
-#> 5 116866 2011-11-07 A TRUE
-#> 6 130252 2002-04-08 C TRUE
-#> 7 1343BD 2016-04-02 C TRUE
-#> 8 1435C8 2004-03-03 B TRUE
-#> 9 180928 2008-06-14 C TRUE
-#> 10 189363 2004-06-22 B TRUE
+#> 1 004531 2013-12-02 A TRUE
+#> 2 023456 2009-11-02 B TRUE
+#> 3 023456 2009-11-02 B FALSE
+#> 4 04C169 2012-07-18 A TRUE
+#> 5 062027 2015-09-21 B TRUE
+#> 6 077922 2017-02-02 A TRUE
+#> 7 092034 2006-06-12 B TRUE
+#> 8 0C0688 2014-09-05 C TRUE
+#> 9 0E2483 2007-05-29 B TRUE
+#> 10 151041 2006-02-10 C TRUE
#> # … with 90 more rows
if (require("dplyr")) {
@@ -275,19 +325,19 @@
arrange(patient, ward, date)
}
#> # A tibble: 100 × 5
-#> # Groups: ward, patient [98]
+#> # Groups: ward, patient [97]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <int> <lgl>
-#> 1 Clinical 2006-07-21 059414 1 TRUE
-#> 2 Clinical 2013-10-30 066601 1 TRUE
-#> 3 Clinical 2010-08-08 080086 1 TRUE
-#> 4 Clinical 2007-05-29 0E2483 1 TRUE
-#> 5 Clinical 2011-11-07 116866 1 TRUE
-#> 6 ICU 2002-04-08 130252 1 TRUE
-#> 7 Clinical 2016-04-02 1343BD 1 TRUE
-#> 8 Clinical 2004-03-03 1435C8 1 TRUE
-#> 9 Clinical 2008-06-14 180928 1 TRUE
-#> 10 Clinical 2004-06-22 189363 1 TRUE
+#> 1 Clinical 2013-12-02 004531 1 TRUE
+#> 2 Clinical 2009-11-02 023456 1 TRUE
+#> 3 Clinical 2009-11-02 023456 1 FALSE
+#> 4 Clinical 2012-07-18 04C169 1 TRUE
+#> 5 ICU 2015-09-21 062027 1 TRUE
+#> 6 Clinical 2017-02-02 077922 1 TRUE
+#> 7 ICU 2006-06-12 092034 1 TRUE
+#> 8 Clinical 2014-09-05 0C0688 1 TRUE
+#> 9 Clinical 2007-05-29 0E2483 1 TRUE
+#> 10 Clinical 2006-02-10 151041 1 TRUE
#> # … with 90 more rows
if (require("dplyr")) {
@@ -303,9 +353,9 @@
#> # A tibble: 3 × 5
#> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30
#> <chr> <int> <int> <int> <int>
-#> 1 Clinical 65 13 38 49
-#> 2 ICU 29 12 21 25
-#> 3 Outpatient 4 3 4 4
+#> 1 Clinical 63 14 40 52
+#> 2 ICU 28 10 21 24
+#> 3 Outpatient 6 5 6 6
# grouping on patients and microorganisms leads to the same
# results as first_isolate() when using 'episode-based':
@@ -334,19 +384,19 @@
select(group_vars(.), flag_episode)
}
#> # A tibble: 100 × 4
-#> # Groups: patient, mo, ward [99]
+#> # Groups: patient, mo, ward [98]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
-#> 1 4047F6 B_ESCHR_COLI ICU TRUE
-#> 2 7F8445 B_STPHY_EPDR Clinical TRUE
-#> 3 A87231 B_STPHY_CONS Clinical TRUE
-#> 4 532360 B_PSDMN_AERG Clinical TRUE
-#> 5 426426 B_ESCHR_COLI ICU TRUE
-#> 6 942999 B_STRPT_PNMN Clinical TRUE
-#> 7 1435C8 B_ESCHR_COLI Clinical TRUE
-#> 8 997433 B_STPHY_HMNS Clinical TRUE
-#> 9 982666 B_STRPT_DYSG Clinical TRUE
-#> 10 3B8892 B_ESCHR_COLI ICU TRUE
+#> 1 5DB1C8 B_STPHY_HMNS Clinical TRUE
+#> 2 B30560 B_STPHY_CONS Clinical TRUE
+#> 3 728932 B_ESCHR_COLI Clinical TRUE
+#> 4 619705 B_KLBSL_PNMN ICU TRUE
+#> 5 AB0003 B_ESCHR_COLI Clinical TRUE
+#> 6 7D4209 B_STRPT_PNMN Clinical TRUE
+#> 7 D07D73 B_STRPT_PYGN ICU TRUE
+#> 8 BF4515 B_ESCHR_COLI Clinical TRUE
+#> 9 BC9909 B_ESCHR_COLI Clinical TRUE
+#> 10 982666 B_STRPT_DYSG Clinical TRUE
#> # … with 90 more rows
# }