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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Determine Clinical or Epidemic Episodes< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/get_episode.R" class = "external-link" > < code > R/get_episode.R< / code > < / a > < / small >
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< div class = "d-none name" > < code > get_episode.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > These functions determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The < code > get_episode()< / code > function returns the index number of the episode per group, while the < code > is_new_episode()< / code > function returns < code > TRUE< / code > for every new < code > get_episode()< / code > index. Both absolute and relative episode determination are supported.< / p >
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< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , episode_days < span class = "op" > =< / span > < span class = "cn" > NULL< / span > , case_free_days < span class = "op" > =< / span > < span class = "cn" > NULL< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
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< span > < / span >
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< span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , episode_days < span class = "op" > =< / span > < span class = "cn" > NULL< / span > , case_free_days < span class = "op" > =< / span > < span class = "cn" > NULL< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
< dd > < p > vector of dates (class < code > Date< / code > or < code > POSIXt< / code > ), will be sorted internally to determine episodes< / p > < / dd >
< dt > episode_days< / dt >
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< dd > < p > episode length in days to specify the time period after which a new episode begins, can also be less than a day or < code > Inf< / code > , see < em > Details< / em > < / p > < / dd >
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< dt > case_free_days< / dt >
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< dd > < p > (inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or < code > Inf< / code > , see < em > Details< / em > < / p > < / dd >
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< dt > ...< / dt >
< dd > < p > ignored, only in place to allow future extensions< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
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< ul > < li > < p > < code > get_episode()< / code > : an < a href = "https://rdrr.io/r/base/integer.html" class = "external-link" > integer< / a > vector< / p > < / li >
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< li > < p > < code > is_new_episode()< / code > : a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > vector< / p > < / li >
< / ul > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< p > Episodes can be determined in two ways: absolute and relative.< / p > < ol > < li > < p > Absolute< / p >
< p > This method uses < code > episode_days< / code > to define an episode length in days, after which a new episode will start. A common use case in AMR data analysis is microbial epidemiology: episodes of < em > S. aureus< / em > bacteraemia in ICU patients for example. The episode length could then be 30 days, so that new < em > S. aureus< / em > isolates after an ICU episode of 30 days will be considered a different (or new) episode.< / p >
< p > Thus, this method counts < strong > since the start of the previous episode< / strong > .< / p > < / li >
< li > < p > Relative< / p >
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< p > This method uses < code > case_free_days< / code > to quantify the duration of case-free days (the inter-epidemic interval), after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.< / p >
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< p > Thus, this methods counts < strong > since the last case in the previous episode< / strong > .< / p > < / li >
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< / ol > < p > In a table:< / p > < table class = "table table" > < tr > < td > Date< / td > < td > Using < code > episode_days = 7< / code > < / td > < td > Using < code > case_free_days = 7< / code > < / td > < / tr > < tr > < td > 2023-01-01< / td > < td > 1< / td > < td > 1< / td > < / tr > < tr > < td > 2023-01-02< / td > < td > 1< / td > < td > 1< / td > < / tr > < tr > < td > 2023-01-05< / td > < td > 1< / td > < td > 1< / td > < / tr > < tr > < td > 2023-01-08< / td > < td > 2**< / td > < td > 1< / td > < / tr > < tr > < td > 2023-02-21< / td > < td > 3< / td > < td > 2***< / td > < / tr > < tr > < td > 2023-02-22< / td > < td > 3< / td > < td > 2< / td > < / tr > < tr > < td > 2023-02-23< / td > < td > 3< / td > < td > 2< / td > < / tr > < tr > < td > 2023-02-24< / td > < td > 3< / td > < td > 2< / td > < / tr > < tr > < td > 2023-03-01< / td > < td > 4< / td > < td > 2< / td > < / tr > < / table > < p > ** This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). < br >
*** This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).< / p >
< p > Either < code > episode_days< / code > or < code > case_free_days< / code > must be provided in the function.< / p > < div class = "section" >
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< h3 id = "difference-between-get-episode-and-is-new-episode-" > Difference between < code > get_episode()< / code > and < code > is_new_episode()< / code > < a class = "anchor" aria-label = "anchor" href = "#difference-between-get-episode-and-is-new-episode-" > < / a > < / h3 >
< p > The < code > get_episode()< / code > function returns the index number of the episode, so all cases/patients/isolates in the first episode will have the number 1, all cases/patients/isolates in the second episode will have the number 2, etc.< / p >
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< p > The < code > is_new_episode()< / code > function on the other hand, returns < code > TRUE< / code > for every new < code > get_episode()< / code > index.< / p >
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< p > To specify, when setting < code > episode_days = 365< / code > (using method 1 as explained above), this is how the two functions differ:< / p > < table class = "table table" > < tr > < td > patient< / td > < td > date< / td > < td > < code > get_episode()< / code > < / td > < td > < code > is_new_episode()< / code > < / td > < / tr > < tr > < td > A< / td > < td > 2019-01-01< / td > < td > 1< / td > < td > TRUE< / td > < / tr > < tr > < td > A< / td > < td > 2019-03-01< / td > < td > 1< / td > < td > FALSE< / td > < / tr > < tr > < td > A< / td > < td > 2021-01-01< / td > < td > 2< / td > < td > TRUE< / td > < / tr > < tr > < td > B< / td > < td > 2008-01-01< / td > < td > 1< / td > < td > TRUE< / td > < / tr > < tr > < td > B< / td > < td > 2008-01-01< / td > < td > 1< / td > < td > FALSE< / td > < / tr > < tr > < td > C< / td > < td > 2020-01-01< / td > < td > 1< / td > < td > TRUE< / td > < / tr > < / table > < / div >
< div class = "section" >
< h3 id = "other" > Other< a class = "anchor" aria-label = "anchor" href = "#other" > < / a > < / h3 >
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< p > The < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > function is a wrapper around the < code > is_new_episode()< / code > function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.< / p >
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< p > The < code > dplyr< / code > package is not required for these functions to work, but these episode functions do support < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > variable grouping< / a > and work conveniently inside < code > dplyr< / code > verbs such as < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter()< / a > < / code > , < code > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate()< / a > < / code > and < code > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise()< / a > < / code > .< / p >
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< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
< div class = "dont-index" > < p > < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > < / p > < / div >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # difference between absolute and relative determination of episodes:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > dates < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/as.Date.html" class = "external-link" > as.Date< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-01-01"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-01-02"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-01-05"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-01-08"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-02-21"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-02-22"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-02-23"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-02-24"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-03-01"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "2021-03-01"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > $< / span > < span class = "va" > absolute< / span > < span class = "op" > < -< / span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > $< / span > < span class = "va" > dates< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 7< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > $< / span > < span class = "va" > relative< / span > < span class = "op" > < -< / span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > $< / span > < span class = "va" > dates< / span > , case_free_days < span class = "op" > =< / span > < span class = "fl" > 7< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > dates absolute relative< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 2021-01-01 1 1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 2021-01-02 1 1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 2021-01-05 1 1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 2021-01-08 2 1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 2021-02-21 3 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 2021-02-22 3 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 2021-02-23 3 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 2021-02-24 3 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 2021-03-01 4 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 2021-03-01 4 2< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # `example_isolates` is a data set available in the AMR package.< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # See ?example_isolates< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" class = "external-link" > sample< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/seq.html" class = "external-link" > seq_len< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 2000< / span > < span class = "op" > )< / span > , size < span class = "op" > =< / span > < span class = "fl" > 100< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span > < / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > $< / span > < span class = "va" > date< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 60< / span > < span class = "op" > )< / span > < span class = "co" > # indices< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 39 42 29 45 31 14 41 39 26 40 18 36 15 39 18 45 32 27 10 2 13 24 43 12 8< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [26] 5 3 12 31 9 16 4 1 26 32 27 21 45 42 17 16 21 8 4 30 1 17 25 34 5< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [51] 10 1 18 44 33 4 6 12 43 2 43 45 37 33 18 38 45 36 46 4 35 40 12 7 11< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [76] 23 10 35 20 4 5 29 27 41 12 30 45 18 47 22 28 39 19 27 16 4 21 40 33 39< / span >
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< span class = "r-in" > < span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > $< / span > < span class = "va" > date< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 60< / span > < span class = "op" > )< / span > < span class = "co" > # TRUE/FALSE< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [61] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [73] FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [85] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [97] FALSE FALSE FALSE FALSE< / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # filter on results from the third 60-day episode only, using base R< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/which.html" class = "external-link" > which< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > $< / span > < span class = "va" > date< / span > , < span class = "fl" > 60< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "fl" > 3< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 1 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > date patient age gender ward mo PEN OXA FLC AMX < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2002-12-13 285137 78 F ICU B_ESCHR_COLI R NA NA NA < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < sir> , AMP < sir> , TZP < sir> , CZO < sir> , FEP < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # CXM < sir> , FOX < sir> , CTX < sir> , CAZ < sir> , CRO < sir> , GEN < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TOB < sir> , AMK < sir> , KAN < sir> , TMP < sir> , SXT < sir> , NIT < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # FOS < sir> , LNZ < sir> , CIP < sir> , MFX < sir> , VAN < sir> , TEC < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TCY < sir> , TGC < sir> , DOX < sir> , ERY < sir> , CLI < sir> , AZM < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # IPM < sir> , MEM < sir> , MTR < sir> , CHL < sir> , COL < sir> , MUP < sir> , RIF < sir> < / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # the functions also work for less than a day, e.g. to include one per hour:< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/Sys.time.html" class = "external-link" > Sys.time< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/Sys.time.html" class = "external-link" > Sys.time< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < span class = "fl" > 60< / span > < span class = "op" > *< / span > < span class = "fl" > 60< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > episode_days < span class = "op" > =< / span > < span class = "fl" > 1< / span > < span class = "op" > /< / span > < span class = "fl" > 24< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 1 2< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # is_new_episode() can also be used in dplyr verbs to determine patient< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # episodes based on any (combination of) grouping variables:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > condition < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" class = "external-link" > sample< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > x < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "A"< / span > , < span class = "st" > "B"< / span > , < span class = "st" > "C"< / span > < span class = "op" > )< / span > ,< / span > < / span >
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< span class = "r-in" > < span > size < span class = "op" > =< / span > < span class = "fl" > 100< / span > ,< / span > < / span >
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< span class = "r-in" > < span > replace < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > condition< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > new_episode < span class = "op" > =< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fl" > 365< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > date< / span > , < span class = "va" > condition< / span > , < span class = "va" > new_episode< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/arrange.html" class = "external-link" > arrange< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > condition< / span > , < span class = "va" > date< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 100 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: patient, condition [97]< / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > patient date condition new_episode< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 036063 2010-01-28 A TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 077922 2009-08-18 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 080086 2010-08-08 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 0DBF93 2015-10-12 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 105248 2005-06-16 A TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 114570 2003-04-08 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 119392 2010-11-01 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 161740 2005-06-21 A TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 174209 2011-10-03 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 210105 2009-06-13 C TRUE < / span >
2023-04-14 11:23:10 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ward< / span > , < span class = "va" > patient< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/transmute.html" class = "external-link" > transmute< / a > < / span > < span class = "op" > (< / span > < span class = "va" > date< / span > ,< / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "va" > patient< / span > ,< / span > < / span >
< span class = "r-in" > < span > new_index < span class = "op" > =< / span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fl" > 60< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > new_logical < span class = "op" > =< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fl" > 60< / span > < span class = "op" > )< / span > < / span > < / span >
2023-02-12 17:20:08 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/arrange.html" class = "external-link" > arrange< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > ward< / span > , < span class = "va" > date< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 100 × < / span > < / span >
2024-06-16 21:00:31 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: ward, patient [96]< / span > < / span >
2024-02-13 13:53:34 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ward date patient new_index new_logical< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span >
2024-06-16 21:00:31 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical 2010-01-28 036063 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Clinical 2009-08-18 077922 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Clinical 2010-08-08 080086 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Clinical 2015-10-12 0DBF93 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > Clinical 2005-06-16 105248 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > ICU 2003-04-08 114570 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > Clinical 2010-11-01 119392 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > Clinical 2005-06-21 161740 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > Outpatient 2011-10-03 174209 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > Clinical 2009-06-13 210105 1 TRUE < / span >
2023-04-14 11:23:10 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ward< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > n_patients < span class = "op" > =< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" class = "external-link" > n_distinct< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > n_episodes_365 < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sum.html" class = "external-link" > sum< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 365< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > n_episodes_60 < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sum.html" class = "external-link" > sum< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 60< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > n_episodes_30 < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sum.html" class = "external-link" > sum< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , episode_days < span class = "op" > =< / span > < span class = "fl" > 30< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 3 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ward n_patients n_episodes_365 n_episodes_60 n_episodes_30< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span >
2024-06-16 21:00:31 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical 64 13 37 47< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > ICU 23 9 17 20< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Outpatient 9 7 7 9< / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # grouping on patients and microorganisms leads to the same< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # results as first_isolate() when using 'episode-based':< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "first_isolate.html" > filter_first_isolate< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > include_unknown < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span > < / span >
< span class = "r-in" > < span > method < span class = "op" > =< / span > < span class = "st" > "episode-based"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > y< / span > < span class = "op" > < -< / span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > mo< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fl" > 365< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > ungroup< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/identical.html" class = "external-link" > identical< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > y< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2024-06-16 21:00:31 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TRUE< / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < span class = "co" > # but is_new_episode() has a lot more flexibility than first_isolate(),< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # since you can now group on anything that seems relevant:< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > patient< / span > , < span class = "va" > mo< / span > , < span class = "va" > ward< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > flag_episode < span class = "op" > =< / span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fl" > 365< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_data.html" class = "external-link" > group_vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > .< / span > < span class = "op" > )< / span > , < span class = "va" > flag_episode< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 100 × < / span > < / span >
2024-06-16 21:00:31 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: patient, mo, ward [96]< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > patient mo ward flag_episode< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > A76045 B_ENTRC_FACM ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 964129 B_SERRT_MRCS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 686445 B_STPHY_CONS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > D39422 B_KLBSL_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 298662 B_ESCHR_COLI Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 5B78D5 B_STPHY_AURS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > E52625 B_STRPT_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 645121 B_SERRT_MRCS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 807228 B_STRPT_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > D41749 B_ESCHR_COLI ICU TRUE < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
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