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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Determine (Clinical) 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 >
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< 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, based on the argument < code > episode_days< / code > . 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, and is thus equal to < code > !duplicated(get_episode(...))< / code > .< / 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 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > get_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > episode_days< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > is_new_episode< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > episode_days< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / 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 >
< dd > < p > required episode length in days, can also be less than a day or < code > Inf< / code > , see < em > Details< / em > < / p > < / dd >
< 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 > The functions < code > get_episode()< / code > and < code > is_new_episode()< / code > differ in this way when setting < code > episode_days< / code > to 365:< / p > < table class = "table table" > < tr > < td > person_id< / 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 > < p > 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 < code > episode_days< / code > 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 < code > episode_days< / code > 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.< / p >
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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 >
< 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 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # `example_isolates` is a data set available in the AMR package.< / span > < / span > < / span >
< 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] 5 27 24 19 46 12 45 39 38 2 2 31 20 24 36 49 47 22 49 34 23 49 51 9 11< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [26] 22 1 17 13 5 43 45 27 6 19 7 10 23 45 32 12 9 4 34 26 30 21 48 47 36< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [51] 41 44 1 23 14 21 11 29 9 28 8 50 48 42 32 36 15 38 6 2 32 25 44 18 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [76] 16 42 35 9 29 36 17 43 33 12 10 40 43 29 16 11 4 19 37 23 41 21 46 8 51< / 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 TRUE TRUE TRUE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [61] TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [73] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [85] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE< / span >
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< 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 >
2023-02-12 15:18:14 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > date patient age gender ward mo PEN OXA FLC AMX AMC < / 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 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 > 2002-06-18 012595 30 M ICU B_CRYNB I NA NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 35 more variables: 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 >
2022-08-21 16:59:35 +02:00
< 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 >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > get_episode< / 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 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 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 class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< 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 >
2022-08-28 22:45:38 +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 > 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 >
2023-02-12 15:18:14 +01:00
< span class = "r-in" > < span > size < span class = "op" > =< / span > < span class = "fl" > 100< / span > ,< / span > < / span >
2022-08-28 22:45:38 +02:00
< 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 >
2023-02-12 15:18:14 +01:00
< 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" > 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 >
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 > 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 >
2023-02-12 15:18:14 +01:00
< 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 >
< 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 >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-02-12 15:18:14 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 100 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: patient, condition [97]< / span > < / span >
< 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 >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 005088 2007-08-22 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 012595 2002-06-18 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 023456 2009-11-02 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 071099 2005-01-11 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 077552 2002-05-14 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 080086 2010-08-08 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 0E2483 2007-08-10 A TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 0E2483 2007-11-10 A FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 0E2483 2007-04-06 C TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 114570 2003-04-22 B TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 90 more rows< / 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 >
2023-02-10 16:26:36 +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 >
< 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 >
2023-02-12 15:18:14 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: ward, patient [95]< / span > < / span >
2023-01-24 16:39:56 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > ward date patient new_index new_logical< / span >
2023-02-12 15:18:14 +01:00
< 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 >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical 2007-08-22 005088 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > ICU 2002-06-18 012595 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Clinical 2009-11-02 023456 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Clinical 2005-01-11 071099 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > Clinical 2002-05-14 077552 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > Clinical 2010-08-08 080086 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > Clinical 2007-04-06 0E2483 2 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > Clinical 2007-11-10 0E2483 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > ICU 2007-08-10 0E2483 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > ICU 2003-04-22 114570 1 TRUE < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 90 more rows< / span > < / span >
< 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 >
2023-02-12 15:18:14 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical 58 14 41 49< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > ICU 31 11 25 27< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Outpatient 6 5 6 6< / 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 >
2023-02-12 11:30:57 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] FALSE< / 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 >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < 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 >
2023-02-12 15:18:14 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: patient, mo, ward [97]< / 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 > 762305 B_BCTRD_FRGL Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 889500 B_STPHY_CONS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 777449 B_STPHY_CONS ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 59C7F2 B_STRPT_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 432724 B_STPHY_CONS ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 690605 B_STRPT_DYSG ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > E04500 B_STPHY_HMNS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 255339 B_ESCHR_COLI Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 905108 B_STRPT_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 130252 B_ENTRC_FCLS ICU TRUE < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 90 more rows< / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< / code > < / pre > < / div >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
2022-12-11 11:50:34 +01:00
< p > < / p > < p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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2022-12-11 11:50:34 +01:00
< p > < / p > < p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
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