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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Determine (New) Episodes for Patients< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/episode.R" class = "external-link" > < code > R/episode.R< / code > < / a > < / small >
< div class = "d-none name" > < code > get_episode.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
< 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 values < code > TRUE< / code > /< code > FALSE< / code > to indicate whether an item in a vector is the start of a new episode.< / p >
< / 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 >
< ul > < li > < p > < code > get_episode()< / code > : a < a href = "https://rdrr.io/r/base/double.html" class = "external-link" > double< / a > vector< / p > < / li >
< 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 >
< 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 >
< 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 >
< p > The < code > dplyr< / code > package is not required for these functions to work, but these 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 >
< / 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 >
< 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" > 200< / 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" > 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] 37 22 35 49 56 34 5 24 8 19 29 58 1 25 23 2 63 43 7 18 52 35 30 50 39< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [26] 51 60 35 37 36 7 26 55 12 28 31 29 21 12 26 39 11 5 43 15 45 32 11 51 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [51] 12 1 59 39 10 26 46 1 57 46 44 61 17 59 17 53 39 4 27 48 51 10 16 52 8< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [76] 45 16 56 39 34 34 36 30 15 28 53 3 12 29 32 7 10 20 38 12 61 16 1 59 29< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [101] 34 2 39 35 14 49 41 28 48 58 54 6 7 38 46 50 54 25 34 49 54 3 18 5 36< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [126] 42 63 24 13 42 26 19 8 36 54 56 18 11 13 14 58 43 13 9 54 32 52 50 49 47< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [151] 22 4 40 49 27 22 55 43 38 1 33 47 9 30 5 11 60 37 62 24 18 50 9 5 29< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [176] 63 50 32 51 5 3 44 4 43 63 62 33 54 9 7 4 54 48 40 19 37 53 12 49 24< / 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 FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [61] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [73] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [97] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [109] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [121] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [133] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [145] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [157] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [181] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [193] TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE< / 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: 3 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo < / 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;" > < fct> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / 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 >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2002-07-16 D FALSE FALSE TRUE 78 M 241328 B_STPHY_CONS< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 40 more variables: PEN < rsi> , OXA < rsi> , FLC < rsi> , AMX < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # AMC < rsi> , AMP < rsi> , TZP < rsi> , CZO < rsi> , FEP < rsi> , CXM < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # FOX < rsi> , CTX < rsi> , CAZ < rsi> , CRO < rsi> , GEN < rsi> , TOB < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # AMK < rsi> , KAN < rsi> , TMP < rsi> , SXT < rsi> , NIT < rsi> , FOS < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # LNZ < rsi> , CIP < rsi> , MFX < rsi> , VAN < rsi> , TEC < rsi> , TCY < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TGC < rsi> , DOX < rsi> , ERY < rsi> , CLI < rsi> , AZM < rsi> , IPM < rsi> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # MEM < rsi> , MTR < rsi> , CHL < rsi> , COL < rsi> , MUP < rsi> , RIF < rsi> , and …< / span > < / span >
< 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 >
< 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 >
< 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 >
< 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 > 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 >
< span class = "r-in" > < span > size < span class = "op" > =< / span > < span class = "fl" > 2000< / span > ,< / span > < / span >
< span class = "r-in" > < span > replace < span class = "op" > =< / span > < span class = "cn" > TRUE< / 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" > group_by< / a > < / span > < span class = "op" > (< / 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 >
< 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 >
< 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_id< / span > , < span class = "va" > date< / span > , < span class = "va" > condition< / span > , < span class = "va" > new_episode< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < 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 >
< 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" > hospital_id< / span > , < span class = "va" > patient_id< / 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/mutate.html" class = "external-link" > transmute< / a > < / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > patient_id< / 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 class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < 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 >
< 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" > hospital_id< / 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 > 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_id< / 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 class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< 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 = "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 > 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 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_id< / 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 > < / span >
< 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 >
< 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 >
< 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_id< / span > , < span class = "va" > mo< / span > , < span class = "va" > hospital_id< / span > , < span class = "va" > ward_icu< / 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/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 >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > < span class = "error" > Error in mutate(., condition = sample(x = c("A", "B", "C"), size = 2000, replace = TRUE)):< / span > Problem while computing `condition = sample(x = c("A", "B", "C"), size =< / span >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > 2000, replace = TRUE)`.< / span >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > < span style = "color: #BB0000;" > ✖< / span > `condition` must be size 200 or 1, not 2000.< / span >
< 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 >
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< p > < / p > < p > < code > AMR< / code > (for R). Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > in collaboration with non-profit organisations< br > < a target = "_blank" href = "https://www.certe.nl" class = "external-link" > Certe Medical Diagnostics and Advice Foundation< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > .< / p >
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