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$date, episode_days = 60) # indices
#> [1] 18 31 37 38 34 17 23 19 11 33 12 38 17 4 37 6 47 45 1 31 32 41 23 21 30
#> [26] 7 45 43 44 42 6 45 11 42 21 40 9 31 4 26 11 21 19 18 1 36 37 23 41 43
#> [51] 39 31 28 18 9 14 20 9 26 2 5 35 45 24 38 15 15 5 33 13 35 25 27 29 16
#> [76] 13 47 15 10 45 27 21 32 34 39 18 48 20 3 22 44 17 19 41 40 8 28 7 46 3
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE
#> [13] FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE
#> [25] TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE
#> [37] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> [49] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE
#> [61] TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE
#> [73] TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
#> [85] FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE
#> [97] 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: 2 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2003-01-25 088256 73 F ICU B_STPHY_CONS R NA R R
#> 2 2003-03-18 889500 61 M Clinical B_STPHY_CONS 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>,
#> # 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 [95]
#> ward date patient new_index new_logical
#> <chr> <date> <chr> <dbl> <lgl>
#> 1 Clinical 2007-08-22 005088 1 TRUE
#> 2 Clinical 2009-07-24 006827 1 TRUE
#> 3 Clinical 2012-11-24 023456 1 TRUE
#> 4 Clinical 2013-10-30 066601 1 TRUE
#> 5 ICU 2014-06-28 078381 1 TRUE
#> 6 ICU 2002-06-04 082413 1 TRUE
#> 7 ICU 2014-02-08 082622 1 TRUE
#> 8 ICU 2003-01-25 088256 1 TRUE
#> 9 Clinical 2008-07-22 0E2483 1 TRUE
#> 10 ICU 2007-08-10 0E2483 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 54 13 34 44
#> 2 ICU 34 9 24 28
#> 3 Outpatient 7 5 7 7
# 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] TRUE
# 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 [97]
#> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl>
#> 1 A66134 B_STPHY_AURS Outpatient TRUE
#> 2 824233 B_STPHY_AURS Clinical TRUE
#> 3 078381 B_STPHY_EPDR ICU TRUE
#> 4 483195 B_STPHY_HMNS Clinical TRUE
#> 5 B33776 B_ACNTB Clinical TRUE
#> 6 851259 B_STRPT_PNMN Clinical TRUE
#> 7 6F0804 B_STRPT_PNMN Clinical TRUE
#> 8 122506 B_STPHY_AURS Clinical TRUE
#> 9 904485 B_STRPT ICU TRUE
#> 10 695956 B_STRPT_PNMN Outpatient TRUE
#> # … with 90 more rows
# }