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$date, episode_days = 60) # indices
#> [1] 53 62 32 61 13 24 5 35 42 38 15 9 6 4 24 17 13 61 29 35 46 18 27 5 29
#> [26] 15 43 28 19 12 13 32 59 8 32 6 20 2 5 23 21 32 43 45 32 56 37 48 38 29
#> [51] 13 18 53 7 48 52 24 7 36 52 60 6 32 29 31 5 21 12 58 15 44 31 25 8 41
#> [76] 29 8 44 32 56 11 44 9 32 39 31 13 60 30 33 17 49 10 47 8 19 19 11 7 46
#> [101] 31 15 47 3 25 30 61 36 1 22 55 23 20 60 60 44 63 36 46 58 58 26 51 12 41
#> [126] 13 11 7 2 63 12 23 18 45 26 51 46 54 32 21 11 1 59 9 53 59 62 59 47 8
#> [151] 54 10 15 56 39 36 50 38 40 57 42 22 31 34 14 49 34 4 26 29 63 59 62 31 8
#> [176] 4 63 33 28 40 40 3 32 4 58 13 11 16 5 58 29 1 46 38 61 59 7 51 34 27
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE
#> [13] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
#> [25] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [37] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE
#> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE
#> [61] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE
#> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE
#> [85] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE
#> [97] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
#> [109] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE
#> [121] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
#> [133] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [145] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE
#> [157] TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE
#> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [181] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
#> [193] FALSE FALSE FALSE FALSE TRUE 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: 2 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <rsi> <rsi> <rsi> <rsi>
#> 1 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA
#> 2 2002-06-18 012595 30 M ICU B_CRYNB I NA NA NA
#> # … 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 F76601 2015-09-20 A FALSE
#> 2 D20588 2017-08-17 A FALSE
#> 3 48BB05 2010-03-15 B TRUE
#> 4 871020 2017-07-20 B FALSE
#> 5 554965 2005-08-29 B FALSE
#> 6 451990 2008-03-22 B FALSE
#> 7 E44854 2003-03-22 C FALSE
#> 8 D91230 2010-12-06 A TRUE
#> 9 743093 2012-09-14 C FALSE
#> 10 BC9909 2011-07-08 A FALSE
#> # … 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 [182]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <dbl> <lgl>
#> 1 ICU 2015-09-20 F76601 1 TRUE
#> 2 ICU 2017-08-17 D20588 1 TRUE
#> 3 Clinical 2010-03-15 48BB05 1 TRUE
#> 4 Clinical 2017-07-20 871020 1 TRUE
#> 5 Clinical 2005-08-29 554965 1 TRUE
#> 6 Clinical 2008-03-22 451990 1 TRUE
#> 7 ICU 2003-03-22 E44854 1 TRUE
#> 8 Clinical 2010-12-06 D91230 1 TRUE
#> 9 Outpatient 2012-09-14 743093 1 TRUE
#> 10 Clinical 2011-07-08 BC9909 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 112 15 51 70
#> 2 ICU 61 13 37 43
#> 3 Outpatient 9 6 9 9
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 [188]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 F76601 B_ESCHR_COLI ICU TRUE
#> 2 D20588 B_STPHY_HMNS ICU TRUE
#> 3 48BB05 B_STPHY_CONS Clinical TRUE
#> 4 871020 B_STPHY_EPDR Clinical TRUE
#> 5 554965 B_STPHY_AURS Clinical TRUE
#> 6 451990 B_ESCHR_COLI Clinical TRUE
#> 7 E44854 B_STRPT_PNMN ICU TRUE
#> 8 D91230 B_STPHY_EPDR Clinical TRUE
#> 9 743093 B_ENTRBC_CLOC Outpatient TRUE
#> 10 BC9909 B_ENTRBC_CLOC Clinical TRUE
#> # … with 190 more rows
# }