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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 >
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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] 14 30 51 29 53 28 49 36 9 7 29 9 43 30 20 51 5 2 5 9 27 6 21 25 14< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [26] 20 29 22 42 51 56 39 31 47 1 10 56 7 54 13 39 20 44 10 37 45 26 42 53 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [51] 2 7 13 51 48 52 31 9 38 50 54 15 41 53 38 23 16 9 26 12 5 26 4 6 31< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [76] 7 40 27 55 57 22 52 27 36 26 16 10 48 23 36 49 47 6 6 56 22 51 48 44 24< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [101] 58 33 47 49 58 32 8 6 21 3 14 33 57 43 14 50 6 3 53 6 18 15 52 31 22< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [126] 7 47 6 42 39 45 1 49 23 53 13 18 35 8 57 12 11 17 3 55 16 12 54 55 14< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [151] 9 46 51 55 19 7 36 8 57 4 14 45 45 59 38 55 25 23 60 57 39 38 54 16 31< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [176] 3 16 39 50 37 40 14 53 60 6 34 32 14 3 30 52 24 23 1 59 52 11 41 7 26< / 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] FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [61] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [73] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [85] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [97] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [109] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [121] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [133] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [145] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [157] TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [169] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [181] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [193] TRUE TRUE FALSE FALSE TRUE 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: 6 × < / span > < / span >
< 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 > 2002-11-07 430011 82 F Clinical B_STPHY_CONS R NA R R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2002-10-18 E55128 57 F ICU B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2002-11-14 058917 76 F ICU B_STPHY_HMNS R NA S NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 2002-10-18 E55128 57 F ICU B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 2002-10-14 FCC668 54 F ICU B_ACNTB R NA NA NA < / span >
2023-01-24 10:29:55 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 36 more variables: AMC < sir> , AMP < sir> , TZP < sir> , CZO < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # FEP < sir> , CXM < sir> , FOX < sir> , CTX < sir> , CAZ < sir> , CRO < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # GEN < sir> , TOB < sir> , AMK < sir> , KAN < sir> , TMP < sir> , SXT < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # NIT < sir> , FOS < sir> , LNZ < sir> , CIP < sir> , MFX < sir> , VAN < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TEC < sir> , TCY < sir> , TGC < sir> , DOX < sir> , ERY < sir> , CLI < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # AZM < sir> , IPM < sir> , MEM < sir> , MTR < sir> , CHL < sir> , COL < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # 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 >
2023-01-23 15:07:54 +01:00
< 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 >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < 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 >
< span class = "r-in" > < span > size < span class = "op" > =< / span > < span class = "fl" > 200< / span > ,< / span > < / span >
< 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 >
2022-08-21 16:59:35 +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" > 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 >
2022-08-28 22:45:38 +02:00
< 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 > < / 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: 200 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: condition [3]< / 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 >
2023-01-24 16:39:56 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 277241 2005-08-31 A FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > A86006 2009-08-09 C FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 16DC39 2015-11-19 A FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > F68330 2009-04-09 A FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > A79917 2016-05-21 B FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > A80D37 2009-01-19 A FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 335263 2015-04-30 B FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 257844 2011-05-22 B FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > B8F499 2004-08-22 B FALSE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > F35553 2004-02-28 A FALSE < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 190 more rows< / 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 >
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 >
< 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< / 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 >
< 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: 200 × < / span > < / span >
2023-01-24 16:39:56 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: ward, patient [183]< / span > < / span >
< 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;" > < dbl> < / 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 > ICU 2005-08-31 277241 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Clinical 2009-08-09 A86006 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > ICU 2015-11-19 16DC39 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Clinical 2009-04-09 F68330 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > Clinical 2016-05-21 A79917 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > Clinical 2009-01-19 A80D37 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > Clinical 2015-04-30 335263 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > Clinical 2011-05-22 257844 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > Clinical 2004-08-22 B8F499 1 TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > ICU 2004-02-28 F35553 2 TRUE < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 190 more rows< / 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 >
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 >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical 114 15 53 73< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > ICU 62 12 38 46< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Outpatient 7 6 7 7< / span >
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< 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 >
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< 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 >
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< 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 >
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< 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 >
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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" > 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 >
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< 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 >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Including isolates from ICU.< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] FALSE< / span >
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< 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 >
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< 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 >
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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" > 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 >
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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 > 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 >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 200 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # Groups: patient, mo, ward [189]< / 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 > 277241 B_STPHY_AURS ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > A86006 B_STPHY_CONS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 16DC39 B_STPHY_HMLY ICU TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > F68330 B_STRPT_PNMN Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > A79917 B_ENTRC_FACM Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > A80D37 B_ESCHR_COLI Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 335263 B_ENTRBC_CLOC Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 257844 B_STPHY_CONS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > B8F499 B_STPHY_CONS Clinical TRUE < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > F35553 B_STPHY_AURS ICU TRUE < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with 190 more rows< / span > < / span >
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< 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" >
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< 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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