@ -24,16 +24,20 @@
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@ -46,7 +50,7 @@
< meta property = "og:title" content = "Determine first (weighted) isolates — first_isolate" / >
< meta property = "og:description" content = "Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." / >
< meta property = "og:image" content = "/logo.svg" / >
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR /logo.svg" / >
@ -64,7 +68,7 @@
< / head >
< body >
< body data-spy = "scroll" data-target = "#toc" >
< div class = "container template-reference-topic" >
< header >
< div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
@ -78,7 +82,7 @@
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.0.1.9004 < / span >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.0.1.9009 < / span >
< / span >
< / div >
@ -223,7 +227,7 @@
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Determine first (weighted) isolates< / h1 >
< small class = "dont-index" > Source: < a href = 'https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R' > < code > R/first_isolate.R< / code > < / a > < / small >
< div class = "hidden name" > < code > first_isolate.Rd< / code > < / div >
< / div >
@ -404,19 +408,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
< span class = 'co' > # Filter on first isolates:< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > first_isolate< / span > < span class = 'kw' > =< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > .< / span > ,
< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'st' > "date"< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'st' > "patient_id"< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'st' > "mo"< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > first_isolate< / span > < span class = 'kw' > =< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > .< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'no' > first_isolate< / span > < span class = 'kw' > ==< / span > < span class = 'fl' > TRUE< / span > )
< span class = 'co' > # Which can be shortened to:< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > filter_first_isolate< / span > ()
< span class = 'co' > # or for first weighted isolates:< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > filter_first_weighted_isolate< / span > ()
< span class = 'co' > # Now let's see if first isolates matter:< / span >
< span class = 'no' > A< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'no' > hospital_id< / span > ) < span class = 'kw' > %> %< / span >
@ -430,8 +424,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
< span class = 'kw' > resistance< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'proportion.html' > resistance< / a > < / span > (< span class = 'no' > GEN< / span > )) < span class = 'co' > # gentamicin resistance< / span >
< span class = 'co' > # Have a look at A and B.< / span >
< span class = 'co' > # B is more reliable because every isolate is only counted once.< / span >
< span class = 'co' > # Gentamicin resitance in hospital D appears to be 3.1 % higher than< / span >
< span class = 'co' > # B is more reliable because every isolate is counted only once.< / span >
< span class = 'co' > # Gentamicin resitance in hospital D appears to be 3.7 % higher than< / span >
< span class = 'co' > # when you (erroneously) would have used all isolates for analysis.< / span >
@ -439,6 +433,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
< span class = 'kw' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
< span class = 'co' > # Short-hand versions:< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > filter_first_isolate< / span > ()
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > filter_first_weighted_isolate< / span > ()
< span class = 'co' > # set key antibiotics to a new variable< / span >
< span class = 'no' > x< / span > $< span class = 'no' > keyab< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / span > (< span class = 'no' > x< / span > )
@ -450,19 +452,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
}< / pre >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#key-antibiotics" > Key antibiotics< / a > < / li >
< li > < a href = "#stable-lifecycle" > Stable lifecycle< / a > < / li >
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
< nav id = "toc" data-toggle = "toc" class = "sticky-top" >
< h2 data-toc-skip > Contents< / h2 >
< / nav >
< / div >
< / div >
@ -473,7 +465,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.900 0.< / p >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5. 0.< / p >
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