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 TRUE for every new get_episode() index, and is thus equal to !duplicated(get_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 episode 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 = 100), ]
get_episode(df$date, episode_days = 60) # indices
#> [1] 8 20 30 31 41 14 26 24 14 7 41 41 5 19 44 29 34 15 40 42 43 16 45 8 6
#> [26] 10 37 42 32 9 36 18 19 42 28 19 29 20 46 27 1 2 42 39 11 4 12 36 13 18
#> [51] 17 6 31 8 1 38 46 8 25 17 27 31 3 27 10 18 29 29 24 16 44 17 33 10 25
#> [76] 36 2 23 7 44 42 12 46 45 44 34 2 17 38 21 22 35 22 25 32 39 43 30 35 11
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE
#> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE
#> [25] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE
#> [37] FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE
#> [49] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
#> [61] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [73] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> [85] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE 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), ]
#> # 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 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA
#> # … 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>,
#> # NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>,
#> # TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>,
#> # AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>,
#> # MUP <sir>, RIF <sir>
# 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)
}
#> Error in mutate(., condition = sample(x = c("A", "B", "C"), size = 200, replace = TRUE)): ℹ In argument: `condition = sample(x = c("A", "B", "C"), size = 200,
#> replace = TRUE)`.
#> Caused by error:
#> ! `condition` must be size 100 or 1, not 200.
if (require("dplyr")) {
df %>%
group_by(ward, patient) %>%
transmute(date,
patient,
new_index = get_episode(date, 60),
new_logical = is_new_episode(date, 60)
) %>%
arrange(patient, ward, date)
}
#> # A tibble: 100 × 5
#> # Groups: ward, patient [94]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <dbl> <lgl>
#> 1 ICU 2004-05-04 022060 1 TRUE
#> 2 Clinical 2006-07-21 059414 1 TRUE
#> 3 Clinical 2002-05-14 077552 1 TRUE
#> 4 Clinical 2003-10-01 0DBB93 1 TRUE
#> 5 ICU 2009-05-08 0DBB93 1 TRUE
#> 6 ICU 2007-06-21 0E2483 1 TRUE
#> 7 Clinical 2012-09-03 107DD1 1 TRUE
#> 8 Clinical 2010-11-01 119392 1 TRUE
#> 9 Clinical 2007-08-10 122506 1 TRUE
#> 10 Clinical 2009-08-14 146F70 1 TRUE
#> # … with 90 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 65 13 38 50
#> 2 ICU 25 10 18 25
#> 3 Outpatient 4 3 4 4
# grouping on patients and microorganisms leads to the same
# results as first_isolate() when using 'episode-based':
if (require("dplyr")) {
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)
}
#> [1] FALSE
# but is_new_episode() has a lot more flexibility than first_isolate(),
# since you can now group on anything that seems relevant:
if (require("dplyr")) {
df %>%
group_by(patient, mo, ward) %>%
mutate(flag_episode = is_new_episode(date, 365)) %>%
select(group_vars(.), flag_episode)
}
#> # A tibble: 100 × 4
#> # Groups: patient, mo, ward [95]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 955371 B_STPHY_AURS ICU TRUE
#> 2 0E2483 B_ESCHR_COLI ICU TRUE
#> 3 119392 B_STPHY_CONS Clinical TRUE
#> 4 A26106 B_ESCHR_COLI Clinical TRUE
#> 5 557266 B_STPHY_HMLY Clinical TRUE
#> 6 5DF436 B_STPHY_AURS ICU TRUE
#> 7 501361 B_ESCHR_COLI Clinical TRUE
#> 8 195736 B_STPHY_AURS Outpatient TRUE
#> 9 904485 B_STRPT_ANGN ICU TRUE
#> 10 842593 B_STPHY_CONS ICU TRUE
#> # … with 90 more rows
# }