These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode.
Arguments
- x
vector of dates (class
DateorPOSIXt), will be sorted internally to determine episodes- episode_days
required episode length in days, can also be less than a day or
Inf, see Details- ...
ignored, only in place to allow future extensions
Details
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least episode_days days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least episode_days days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
The first_isolate() function is a wrapper around the is_new_episode() function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.
The dplyr package is not required for these functions to work, but these functions do support variable grouping and work conveniently inside dplyr verbs such as filter(), mutate() and summarise().
Examples
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates
df <- example_isolates[sample(seq_len(2000), size = 200), ]
get_episode(df$date, episode_days = 60) # indices
#> [1] 56 21 10 22 60 49 59 8 10 10 65 26 58 62 39 39 50 7 41 9 63 25 46 11 56
#> [26] 66 44 3 13 54 23 25 3 50 5 41 48 33 28 51 54 1 14 37 6 27 62 11 52 7
#> [51] 21 61 44 19 54 47 57 12 28 62 48 60 12 59 64 19 16 5 46 66 46 13 67 6 65
#> [76] 11 7 8 26 39 66 51 1 8 3 49 49 32 14 27 28 67 34 39 11 58 53 22 5 23
#> [101] 38 44 16 31 45 5 14 56 28 16 31 58 14 13 49 44 46 42 2 58 49 2 61 5 42
#> [126] 17 67 19 38 55 4 53 66 1 19 60 23 27 30 62 38 8 36 13 46 58 45 47 25 52
#> [151] 20 35 14 46 57 3 17 57 40 32 38 19 67 57 24 61 13 10 11 5 24 40 42 61 28
#> [176] 37 39 54 34 20 30 14 18 29 15 48 41 19 29 63 44 62 27 26 12 43 61 17 30 63
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
#> [13] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE
#> [25] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
#> [37] FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE
#> [49] FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE
#> [61] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
#> [73] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
#> [85] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE
#> [97] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE
#> [109] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
#> [121] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE
#> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
#> [145] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE
#> [157] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
#> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE
#> [181] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
#> [193] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
# filter on results from the third 60-day episode only, using base R
df[which(get_episode(df$date, 60) == 3), ]
#> # A tibble: 4 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <rsi> <rsi> <rsi> <rsi>
#> 1 2002-12-13 285137 78 F ICU B_ESCHR_COLI R NA NA NA
#> 2 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA
#> 3 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA
#> 4 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S
#> # … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,
#> # FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,
#> # GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,
#> # NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>,
#> # TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>,
#> # AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>,
#> # MUP <rsi>, RIF <rsi>
# the functions also work for less than a day, e.g. to include one per hour:
get_episode(c(
Sys.time(),
Sys.time() + 60 * 60
),
episode_days = 1 / 24
)
#> [1] 1 2
# \donttest{
if (require("dplyr")) {
# is_new_episode() can also be used in dplyr verbs to determine patient
# episodes based on any (combination of) grouping variables:
df %>%
mutate(condition = sample(
x = c("A", "B", "C"),
size = 200,
replace = TRUE
)) %>%
group_by(condition) %>%
mutate(new_episode = is_new_episode(date, 365)) %>%
select(patient, date, condition, new_episode)
}
#> # A tibble: 200 × 4
#> # Groups: condition [3]
#> patient date condition new_episode
#> <chr> <date> <chr> <lgl>
#> 1 523893 2015-04-13 C FALSE
#> 2 89F578 2007-03-17 A FALSE
#> 3 E9C268 2004-06-11 C TRUE
#> 4 EF6234 2007-04-30 B FALSE
#> 5 960787 2016-03-27 C FALSE
#> 6 835073 2013-09-27 A FALSE
#> 7 559068 2016-01-03 C FALSE
#> 8 D27318 2003-12-18 C FALSE
#> 9 984417 2004-06-09 B FALSE
#> 10 389884 2004-06-07 B TRUE
#> # … with 190 more rows
if (require("dplyr")) {
df %>%
group_by(ward, patient) %>%
transmute(date,
patient,
new_index = get_episode(date, 60),
new_logical = is_new_episode(date, 60)
)
}
#> # A tibble: 200 × 5
#> # Groups: ward, patient [186]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <dbl> <lgl>
#> 1 Clinical 2015-04-13 523893 1 TRUE
#> 2 Clinical 2007-03-17 89F578 1 TRUE
#> 3 ICU 2004-06-11 E9C268 1 TRUE
#> 4 Clinical 2007-04-30 EF6234 1 TRUE
#> 5 Clinical 2016-03-27 960787 1 TRUE
#> 6 Clinical 2013-09-27 835073 1 TRUE
#> 7 Clinical 2016-01-03 559068 1 TRUE
#> 8 ICU 2003-12-18 D27318 1 TRUE
#> 9 Clinical 2004-06-09 984417 1 TRUE
#> 10 Clinical 2004-06-07 389884 1 TRUE
#> # … with 190 more rows
if (require("dplyr")) {
df %>%
group_by(ward) %>%
summarise(
n_patients = n_distinct(patient),
n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),
n_episodes_60 = sum(is_new_episode(date, episode_days = 60)),
n_episodes_30 = sum(is_new_episode(date, episode_days = 30))
)
}
#> # A tibble: 3 × 5
#> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30
#> <chr> <int> <int> <int> <int>
#> 1 Clinical 123 15 59 79
#> 2 ICU 50 11 33 43
#> 3 Outpatient 13 6 10 12
if (require("dplyr")) {
# grouping on patients and microorganisms leads to the same
# results as first_isolate() when using 'episode-based':
x <- df %>%
filter_first_isolate(
include_unknown = TRUE,
method = "episode-based"
)
y <- df %>%
group_by(patient, mo) %>%
filter(is_new_episode(date, 365)) %>%
ungroup()
identical(x, y)
}
#> Including isolates from ICU.
#> [1] FALSE
if (require("dplyr")) {
# but is_new_episode() has a lot more flexibility than first_isolate(),
# since you can now group on anything that seems relevant:
df %>%
group_by(patient, mo, ward) %>%
mutate(flag_episode = is_new_episode(date, 365)) %>%
select(group_vars(.), flag_episode)
}
#> # A tibble: 200 × 4
#> # Groups: patient, mo, ward [195]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 523893 B_STPHY_AURS Clinical TRUE
#> 2 89F578 B_STPHY_CONS Clinical TRUE
#> 3 E9C268 B_STPHY_EPDR ICU TRUE
#> 4 EF6234 B_STRPT_PYGN Clinical TRUE
#> 5 960787 B_KLBSL_PNMN Clinical TRUE
#> 6 835073 B_STPHY_HMNS Clinical TRUE
#> 7 559068 B_STPHY_CPTS Clinical TRUE
#> 8 D27318 B_STPHY_AURS ICU TRUE
#> 9 984417 UNKNOWN Clinical TRUE
#> 10 389884 B_STPHY_EPDR Clinical TRUE
#> # … with 190 more rows
# }