@ -78,7 +78,7 @@
< / 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 = "Released version" > 0.6.1.9040 < / span >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 0.6.1.9042 < / span >
< / span >
< / div >
@ -287,6 +287,17 @@ Please create an issue in one of our repositories if you want additions in this
< ul >
< li > speed improvement for microbial IDs< / li >
< li > fixed level names in markdown< / li >
< li >
< p > support for boxplots:< / p >
< div class = "sourceCode" id = "cb2" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb2-1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb2-2" title = "2" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb2-3" title = "3" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2-4" title = "4" > < span class = "co" > # grouped boxplots:< / span > < / a >
< a class = "sourceLine" id = "cb2-5" title = "5" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb2-6" title = "6" > < span class = "st" > < / span > < span class = "kw" > group_by< / span > (hospital_id) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb2-7" title = "7" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb2-8" title = "8" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > ()< / a > < / code > < / pre > < / div >
< / li >
< / ul >
< / li >
< li > Removed all hardcoded EUCAST rules and replaced them with a new reference file: < code > ./inst/eucast/eucast.tsv< / code >
@ -367,32 +378,32 @@ This data is updated annually - check the included version with the new function
< / li >
< li >
< p > New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:< / p >
< div class = "sourceCode" id = "cb2 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb2 -1" title = "1" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_aminoglycosides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -2" title = "2" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_carbapenems< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -3" title = "3" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -4" title = "4" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_1st_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -5" title = "5" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_2nd_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -6" title = "6" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_3rd_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -7" title = "7" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_4th_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -8" title = "8" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_fluoroquinolones< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -9" title = "9" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -10" title = "10" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_macrolides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb2 -11" title = "11" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_tetracyclines< / a > < / span > ()< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb3 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb3 -1" title = "1" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_aminoglycosides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -2" title = "2" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_carbapenems< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -3" title = "3" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -4" title = "4" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_1st_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -5" title = "5" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_2nd_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -6" title = "6" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_3rd_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -7" title = "7" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_4th_cephalosporins< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -8" title = "8" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_fluoroquinolones< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -9" title = "9" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -10" title = "10" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_macrolides< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb3 -11" title = "11" > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_tetracyclines< / a > < / span > ()< / a > < / code > < / pre > < / div >
< p > The < code > antibiotics< / code > data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the < code > antibiotics< / code > data set. For example:< / p >
< div class = "sourceCode" id = "cb3 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb3 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > (< span class = "dt" > result =< / span > < span class = "st" > "R"< / span > )< / a >
< a class = "sourceLine" id = "cb3 -2" title = "2" > < span class = "co" > # Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R< / span > < / a >
< a class = "sourceLine" id = "cb3 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > (< span class = "dt" > result =< / span > < span class = "st" > "R"< / span > , < span class = "dt" > scope =< / span > < span class = "st" > "all"< / span > )< / a >
< a class = "sourceLine" id = "cb3 -4" title = "4" > < span class = "co" > # Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb4 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb4 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > (< span class = "dt" > result =< / span > < span class = "st" > "R"< / span > )< / a >
< a class = "sourceLine" id = "cb4 -2" title = "2" > < span class = "co" > # Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R< / span > < / a >
< a class = "sourceLine" id = "cb4 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/filter_ab_class.html" > filter_glycopeptides< / a > < / span > (< span class = "dt" > result =< / span > < span class = "st" > "R"< / span > , < span class = "dt" > scope =< / span > < span class = "st" > "all"< / span > )< / a >
< a class = "sourceLine" id = "cb4 -4" title = "4" > < span class = "co" > # Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R< / span > < / a > < / code > < / pre > < / div >
< / li >
< li >
< p > All < code > ab_*< / code > functions are deprecated and replaced by < code > atc_*< / code > functions:< / p >
< div class = "sourceCode" id = "cb4 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb4 -1" title = "1" > ab_property -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_property< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb4 -2" title = "2" > ab_name -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_name< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb4 -3" title = "3" > ab_official -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_official< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb4 -4" title = "4" > ab_trivial_nl -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_trivial_nl< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb4 -5" title = "5" > ab_certe -> < span class = "st" > < / span > < span class = "kw" > atc_certe< / span > ()< / a >
< a class = "sourceLine" id = "cb4 -6" title = "6" > ab_umcg -> < span class = "st" > < / span > < span class = "kw" > atc_umcg< / span > ()< / a >
< a class = "sourceLine" id = "cb4 -7" title = "7" > ab_tradenames -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_tradenames< / a > < / span > ()< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb5 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb5 -1" title = "1" > ab_property -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_property< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb5 -2" title = "2" > ab_name -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_name< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb5 -3" title = "3" > ab_official -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_official< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb5 -4" title = "4" > ab_trivial_nl -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_trivial_nl< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb5 -5" title = "5" > ab_certe -> < span class = "st" > < / span > < span class = "kw" > atc_certe< / span > ()< / a >
< a class = "sourceLine" id = "cb5 -6" title = "6" > ab_umcg -> < span class = "st" > < / span > < span class = "kw" > atc_umcg< / span > ()< / a >
< a class = "sourceLine" id = "cb5 -7" title = "7" > ab_tradenames -> < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > atc_tradenames< / a > < / span > ()< / a > < / code > < / pre > < / div >
These functions use < code > < a href = "../reference/as.atc.html" > as.atc()< / a > < / code > internally. The old < code > atc_property< / code > has been renamed < code > < a href = "../reference/atc_online.html" > atc_online_property()< / a > < / code > . This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class < code > atc< / code > or must be coerable to this class. Properties of these classes should start with the same class name, analogous to < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > and e.g. < code > mo_genus< / code > .< / li >
< li > New functions < code > < a href = "../reference/mo_source.html" > set_mo_source()< / a > < / code > and < code > < a href = "../reference/mo_source.html" > get_mo_source()< / a > < / code > to use your own predefined MO codes as input for < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > and consequently all < code > mo_*< / code > functions< / li >
< li > Support for the upcoming < a href = "https://dplyr.tidyverse.org" > < code > dplyr< / code > < / a > version 0.8.0< / li >
@ -404,20 +415,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
< li > New function < code > < a href = "../reference/age_groups.html" > age_groups()< / a > < / code > to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.< / li >
< li >
< p > New function < code > < a href = "../reference/resistance_predict.html" > ggplot_rsi_predict()< / a > < / code > as well as the base R < code > < a href = "https://www.rdocumentation.org/packages/graphics/topics/plot" > plot()< / a > < / code > function can now be used for resistance prediction calculated with < code > < a href = "../reference/resistance_predict.html" > resistance_predict()< / a > < / code > :< / p >
< div class = "sourceCode" id = "cb5 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb5 -1" title = "1" > x < -< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/resistance_predict.html" > resistance_predict< / a > < / span > (septic_patients, < span class = "dt" > col_ab =< / span > < span class = "st" > "amox"< / span > )< / a >
< a class = "sourceLine" id = "cb5 -2" title = "2" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/plot" > plot< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb5 -3" title = "3" > < span class = "kw" > < a href = "../reference/resistance_predict.html" > ggplot_rsi_predict< / a > < / span > (x)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb6 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6 -1" title = "1" > x < -< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/resistance_predict.html" > resistance_predict< / a > < / span > (septic_patients, < span class = "dt" > col_ab =< / span > < span class = "st" > "amox"< / span > )< / a >
< a class = "sourceLine" id = "cb6 -2" title = "2" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/plot" > plot< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb6 -3" title = "3" > < span class = "kw" > < a href = "../reference/resistance_predict.html" > ggplot_rsi_predict< / a > < / span > (x)< / a > < / code > < / pre > < / div >
< / li >
< li >
< p > Functions < code > < a href = "../reference/first_isolate.html" > filter_first_isolate()< / a > < / code > and < code > < a href = "../reference/first_isolate.html" > filter_first_weighted_isolate()< / a > < / code > to shorten and fasten filtering on data sets with antimicrobial results, e.g.:< / p >
< div class = "sourceCode" id = "cb6 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > (...)< / a >
< a class = "sourceLine" id = "cb6 -2" title = "2" > < span class = "co" > # or< / span > < / a >
< a class = "sourceLine" id = "cb6 -3" title = "3" > < span class = "kw" > < a href = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > (septic_patients, ...)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb7 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb7 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > (...)< / a >
< a class = "sourceLine" id = "cb7 -2" title = "2" > < span class = "co" > # or< / span > < / a >
< a class = "sourceLine" id = "cb7 -3" title = "3" > < span class = "kw" > < a href = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > (septic_patients, ...)< / a > < / code > < / pre > < / div >
< p > is equal to:< / p >
< div class = "sourceCode" id = "cb7 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb7 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb7 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > mutate< / span > (< span class = "dt" > only_firsts =< / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > first_isolate< / a > < / span > (septic_patients, ...)) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb7 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/stats/topics/filter" > filter< / a > < / span > (only_firsts < span class = "op" > ==< / span > < span class = "st" > < / span > < span class = "ot" > TRUE< / span > ) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb7 -4" title = "4" > < span class = "st" > < / span > < span class = "kw" > select< / span > (< span class = "op" > -< / span > only_firsts)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb8 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb8 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb8 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > mutate< / span > (< span class = "dt" > only_firsts =< / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > first_isolate< / a > < / span > (septic_patients, ...)) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb8 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/stats/topics/filter" > filter< / a > < / span > (only_firsts < span class = "op" > ==< / span > < span class = "st" > < / span > < span class = "ot" > TRUE< / span > ) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb8 -4" title = "4" > < span class = "st" > < / span > < span class = "kw" > select< / span > (< span class = "op" > -< / span > only_firsts)< / a > < / code > < / pre > < / div >
< / li >
< li > New function < code > < a href = "../reference/availability.html" > availability()< / a > < / code > to check the number of available (non-empty) results in a < code > data.frame< / code >
< / li >
@ -446,33 +457,33 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
< ul >
< li >
< p > Now handles incorrect spelling, like < code > i< / code > instead of < code > y< / code > and < code > f< / code > instead of < code > ph< / code > :< / p >
< div class = "sourceCode" id = "cb8 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb8 -1" title = "1" > < span class = "co" > # mo_fullname() uses as.mo() internally< / span > < / a >
< a class = "sourceLine" id = "cb8 -2" title = "2" > < / a >
< a class = "sourceLine" id = "cb8 -3" title = "3" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "Sthafilokockus aaureuz"< / span > )< / a >
< a class = "sourceLine" id = "cb8 -4" title = "4" > < span class = "co" > #> [1] "Staphylococcus aureus"< / span > < / a >
< a class = "sourceLine" id = "cb8 -5" title = "5" > < / a >
< a class = "sourceLine" id = "cb8 -6" title = "6" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. klossi"< / span > )< / a >
< a class = "sourceLine" id = "cb8 -7" title = "7" > < span class = "co" > #> [1] "Staphylococcus kloosii"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb9 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb9 -1" title = "1" > < span class = "co" > # mo_fullname() uses as.mo() internally< / span > < / a >
< a class = "sourceLine" id = "cb9 -2" title = "2" > < / a >
< a class = "sourceLine" id = "cb9 -3" title = "3" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "Sthafilokockus aaureuz"< / span > )< / a >
< a class = "sourceLine" id = "cb9 -4" title = "4" > < span class = "co" > #> [1] "Staphylococcus aureus"< / span > < / a >
< a class = "sourceLine" id = "cb9 -5" title = "5" > < / a >
< a class = "sourceLine" id = "cb9 -6" title = "6" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. klossi"< / span > )< / a >
< a class = "sourceLine" id = "cb9 -7" title = "7" > < span class = "co" > #> [1] "Staphylococcus kloosii"< / span > < / a > < / code > < / pre > < / div >
< / li >
< li >
< p > Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default < code > allow_uncertain = TRUE< / code > is equal to uncertainty level 2. Run < code > < a href = "../reference/as.mo.html" > ?as.mo< / a > < / code > for more info about these levels.< / p >
< div class = "sourceCode" id = "cb9 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb9 -1" title = "1" > < span class = "co" > # equal:< / span > < / a >
< a class = "sourceLine" id = "cb9 -2" title = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "ot" > TRUE< / span > )< / a >
< a class = "sourceLine" id = "cb9 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "dv" > 2< / span > )< / a >
< a class = "sourceLine" id = "cb9 -4" title = "4" > < / a >
< a class = "sourceLine" id = "cb9 -5" title = "5" > < span class = "co" > # also equal:< / span > < / a >
< a class = "sourceLine" id = "cb9 -6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "ot" > FALSE< / span > )< / a >
< a class = "sourceLine" id = "cb9 -7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "dv" > 0< / span > )< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb10 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb10 -1" title = "1" > < span class = "co" > # equal:< / span > < / a >
< a class = "sourceLine" id = "cb10 -2" title = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "ot" > TRUE< / span > )< / a >
< a class = "sourceLine" id = "cb10 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "dv" > 2< / span > )< / a >
< a class = "sourceLine" id = "cb10 -4" title = "4" > < / a >
< a class = "sourceLine" id = "cb10 -5" title = "5" > < span class = "co" > # also equal:< / span > < / a >
< a class = "sourceLine" id = "cb10 -6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "ot" > FALSE< / span > )< / a >
< a class = "sourceLine" id = "cb10 -7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (..., < span class = "dt" > allow_uncertain =< / span > < span class = "dv" > 0< / span > )< / a > < / code > < / pre > < / div >
Using < code > < a href = "../reference/as.mo.html" > as.mo(..., allow_uncertain = 3)< / a > < / code > could lead to very unreliable results.< / li >
< li > Implemented the latest publication of Becker < em > et al.< / em > (2019), for categorising coagulase-negative < em > Staphylococci< / em >
< / li >
< li > All microbial IDs that found are now saved to a local file < code > ~/.Rhistory_mo< / code > . Use the new function < code > clean_mo_history()< / code > to delete this file, which resets the algorithms.< / li >
< li >
< p > Incoercible results will now be considered ‘ ’ < code > UNKNOWN< / code > . On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:< / p >
< div class = "sourceCode" id = "cb10 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb10 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (< span class = "st" > "qwerty"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > )< / a >
< a class = "sourceLine" id = "cb10 -2" title = "2" > < span class = "co" > # Warning: < / span > < / a >
< a class = "sourceLine" id = "cb10 -3" title = "3" > < span class = "co" > # one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.< / span > < / a >
< a class = "sourceLine" id = "cb10 -4" title = "4" > < span class = "co" > #> [1] "(género desconocido)"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb11 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb11 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (< span class = "st" > "qwerty"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > )< / a >
< a class = "sourceLine" id = "cb11 -2" title = "2" > < span class = "co" > # Warning: < / span > < / a >
< a class = "sourceLine" id = "cb11 -3" title = "3" > < span class = "co" > # one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.< / span > < / a >
< a class = "sourceLine" id = "cb11 -4" title = "4" > < span class = "co" > #> [1] "(género desconocido)"< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > Fix for vector containing only empty values< / li >
< li > Finds better results when input is in other languages< / li >
@ -518,19 +529,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< ul >
< li >
< p > Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:< / p >
< div class = "sourceCode" id = "cb11 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb11 -1" title = "1" > < span class = "co" > # Determine genus of microorganisms (mo) in `septic_patients` data set:< / span > < / a >
< a class = "sourceLine" id = "cb11 -2" title = "2" > < span class = "co" > # OLD WAY< / span > < / a >
< a class = "sourceLine" id = "cb11 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb11 -4" title = "4" > < span class = "st" > < / span > < span class = "kw" > mutate< / span > (< span class = "dt" > genus =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo)) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb11 -5" title = "5" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (genus)< / a >
< a class = "sourceLine" id = "cb11 -6" title = "6" > < span class = "co" > # NEW WAY< / span > < / a >
< a class = "sourceLine" id = "cb11 -7" title = "7" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb11 -8" title = "8" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo))< / a >
< a class = "sourceLine" id = "cb11 -9" title = "9" > < / a >
< a class = "sourceLine" id = "cb11 -10" title = "10" > < span class = "co" > # Even supports grouping variables:< / span > < / a >
< a class = "sourceLine" id = "cb11 -11" title = "11" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb11 -12" title = "12" > < span class = "st" > < / span > < span class = "kw" > group_by< / span > (gender) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb11 -13" title = "13" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo))< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb12 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb12 -1" title = "1" > < span class = "co" > # Determine genus of microorganisms (mo) in `septic_patients` data set:< / span > < / a >
< a class = "sourceLine" id = "cb12 -2" title = "2" > < span class = "co" > # OLD WAY< / span > < / a >
< a class = "sourceLine" id = "cb12 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb12 -4" title = "4" > < span class = "st" > < / span > < span class = "kw" > mutate< / span > (< span class = "dt" > genus =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo)) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb12 -5" title = "5" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (genus)< / a >
< a class = "sourceLine" id = "cb12 -6" title = "6" > < span class = "co" > # NEW WAY< / span > < / a >
< a class = "sourceLine" id = "cb12 -7" title = "7" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb12 -8" title = "8" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo))< / a >
< a class = "sourceLine" id = "cb12 -9" title = "9" > < / a >
< a class = "sourceLine" id = "cb12 -10" title = "10" > < span class = "co" > # Even supports grouping variables:< / span > < / a >
< a class = "sourceLine" id = "cb12 -11" title = "11" > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb12 -12" title = "12" > < span class = "st" > < / span > < span class = "kw" > group_by< / span > (gender) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb12 -13" title = "13" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (mo))< / a > < / code > < / pre > < / div >
< / li >
< li > Header info is now available as a list, with the < code > header< / code > function< / li >
< li > The parameter < code > header< / code > is now set to < code > TRUE< / code > at default, even for markdown< / li >
@ -605,10 +616,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< li > Fewer than 3 characters as input for < code > as.mo< / code > will return NA< / li >
< li >
< p > Function < code > as.mo< / code > (and all < code > mo_*< / code > wrappers) now supports genus abbreviations with “species” attached< / p >
< div class = "sourceCode" id = "cb12 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb12 -1" title = "1" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. species"< / span > ) < span class = "co" > # B_ESCHR< / span > < / a >
< a class = "sourceLine" id = "cb12 -2" title = "2" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "E. spp."< / span > ) < span class = "co" > # "Escherichia species"< / span > < / a >
< a class = "sourceLine" id = "cb12 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. spp"< / span > ) < span class = "co" > # B_STPHY< / span > < / a >
< a class = "sourceLine" id = "cb12 -4" title = "4" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. species"< / span > ) < span class = "co" > # "Staphylococcus species"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb13 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb13 -1" title = "1" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. species"< / span > ) < span class = "co" > # B_ESCHR< / span > < / a >
< a class = "sourceLine" id = "cb13 -2" title = "2" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "E. spp."< / span > ) < span class = "co" > # "Escherichia species"< / span > < / a >
< a class = "sourceLine" id = "cb13 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. spp"< / span > ) < span class = "co" > # B_STPHY< / span > < / a >
< a class = "sourceLine" id = "cb13 -4" title = "4" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. species"< / span > ) < span class = "co" > # "Staphylococcus species"< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > Added parameter < code > combine_IR< / code > (TRUE/FALSE) to functions < code > portion_df< / code > and < code > count_df< / code > , to indicate that all values of I and R must be merged into one, so the output only consists of S vs. < / li >
< li > Fix for < code > portion_*(..., as_percent = TRUE)< / code > when minimal number of isolates would not be met< / li >
@ -621,15 +632,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< ul >
< li >
< p > Support for grouping variables, test with:< / p >
< div class = "sourceCode" id = "cb13 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb13 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb13 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > group_by< / span > (hospital_id) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb13 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (gender)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb14 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb14 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb14 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > group_by< / span > (hospital_id) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb14 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (gender)< / a > < / code > < / pre > < / div >
< / li >
< li >
< p > Support for (un)selecting columns:< / p >
< div class = "sourceCode" id = "cb14 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb14 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb14 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb14 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > select< / span > (< span class = "op" > -< / span > count, < span class = "op" > -< / span > cum_count) < span class = "co" > # only get item, percent, cum_percent< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb15 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb15 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb15 -2" title = "2" > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / a >
< a class = "sourceLine" id = "cb15 -3" title = "3" > < span class = "st" > < / span > < span class = "kw" > select< / span > (< span class = "op" > -< / span > count, < span class = "op" > -< / span > cum_count) < span class = "co" > # only get item, percent, cum_percent< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > Check for < code > < a href = "https://www.rdocumentation.org/packages/hms/topics/hms" > hms::is.hms< / a > < / code >
< / li >
@ -709,18 +720,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< / li >
< / ul >
< p > They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:< / p >
< div class = "sourceCode" id = "cb15 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb15 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > )< / a >
< a class = "sourceLine" id = "cb15 -2" title = "2" > < span class = "co" > # [1] "Gram negative"< / span > < / a >
< a class = "sourceLine" id = "cb15 -3" title = "3" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "de"< / span > ) < span class = "co" > # German< / span > < / a >
< a class = "sourceLine" id = "cb15 -4" title = "4" > < span class = "co" > # [1] "Gramnegativ"< / span > < / a >
< a class = "sourceLine" id = "cb15 -5" title = "5" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # Spanish< / span > < / a >
< a class = "sourceLine" id = "cb15 -6" title = "6" > < span class = "co" > # [1] "Gram negativo"< / span > < / a >
< a class = "sourceLine" id = "cb15 -7" title = "7" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. group A"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "pt"< / span > ) < span class = "co" > # Portuguese< / span > < / a >
< a class = "sourceLine" id = "cb15 -8" title = "8" > < span class = "co" > # [1] "Streptococcus grupo A"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb16 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb16 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > )< / a >
< a class = "sourceLine" id = "cb16 -2" title = "2" > < span class = "co" > # [1] "Gram negative"< / span > < / a >
< a class = "sourceLine" id = "cb16 -3" title = "3" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "de"< / span > ) < span class = "co" > # German< / span > < / a >
< a class = "sourceLine" id = "cb16 -4" title = "4" > < span class = "co" > # [1] "Gramnegativ"< / span > < / a >
< a class = "sourceLine" id = "cb16 -5" title = "5" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # Spanish< / span > < / a >
< a class = "sourceLine" id = "cb16 -6" title = "6" > < span class = "co" > # [1] "Gram negativo"< / span > < / a >
< a class = "sourceLine" id = "cb16 -7" title = "7" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. group A"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "pt"< / span > ) < span class = "co" > # Portuguese< / span > < / a >
< a class = "sourceLine" id = "cb16 -8" title = "8" > < span class = "co" > # [1] "Streptococcus grupo A"< / span > < / a > < / code > < / pre > < / div >
< p > Furthermore, former taxonomic names will give a note about the current taxonomic name:< / p >
< div class = "sourceCode" id = "cb16 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb16 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "Esc blattae"< / span > )< / a >
< a class = "sourceLine" id = "cb16 -2" title = "2" > < span class = "co" > # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)< / span > < / a >
< a class = "sourceLine" id = "cb16 -3" title = "3" > < span class = "co" > # [1] "Gram negative"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb17 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb17 -1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > (< span class = "st" > "Esc blattae"< / span > )< / a >
< a class = "sourceLine" id = "cb17 -2" title = "2" > < span class = "co" > # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)< / span > < / a >
< a class = "sourceLine" id = "cb17 -3" title = "3" > < span class = "co" > # [1] "Gram negative"< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > Functions < code > count_R< / code > , < code > count_IR< / code > , < code > count_I< / code > , < code > count_SI< / code > and < code > count_S< / code > to selectively count resistant or susceptible isolates
< ul >
@ -731,18 +742,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< / li >
< li >
< p > Functions < code > as.mo< / code > and < code > is.mo< / code > as replacements for < code > as.bactid< / code > and < code > is.bactid< / code > (since the < code > microoganisms< / code > data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The < code > as.mo< / code > function determines microbial IDs using intelligent rules:< / p >
< div class = "sourceCode" id = "cb17 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb17 -1" title = "1" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. coli"< / span > )< / a >
< a class = "sourceLine" id = "cb17 -2" title = "2" > < span class = "co" > # [1] B_ESCHR_COL< / span > < / a >
< a class = "sourceLine" id = "cb17 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "MRSA"< / span > )< / a >
< a class = "sourceLine" id = "cb17 -4" title = "4" > < span class = "co" > # [1] B_STPHY_AUR< / span > < / a >
< a class = "sourceLine" id = "cb17 -5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S group A"< / span > )< / a >
< a class = "sourceLine" id = "cb17 -6" title = "6" > < span class = "co" > # [1] B_STRPTC_GRA< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb18 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb18 -1" title = "1" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. coli"< / span > )< / a >
< a class = "sourceLine" id = "cb18 -2" title = "2" > < span class = "co" > # [1] B_ESCHR_COL< / span > < / a >
< a class = "sourceLine" id = "cb18 -3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "MRSA"< / span > )< / a >
< a class = "sourceLine" id = "cb18 -4" title = "4" > < span class = "co" > # [1] B_STPHY_AUR< / span > < / a >
< a class = "sourceLine" id = "cb18 -5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S group A"< / span > )< / a >
< a class = "sourceLine" id = "cb18 -6" title = "6" > < span class = "co" > # [1] B_STRPTC_GRA< / span > < / a > < / code > < / pre > < / div >
< p > And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:< / p >
< div class = "sourceCode" id = "cb18 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb18 -1" title = "1" > thousands_of_E_colis < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/rep" > rep< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dv" > 25000< / span > )< / a >
< a class = "sourceLine" id = "cb18 -2" title = "2" > microbenchmark< span class = "op" > ::< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (thousands_of_E_colis), < span class = "dt" > unit =< / span > < span class = "st" > "s"< / span > )< / a >
< a class = "sourceLine" id = "cb18 -3" title = "3" > < span class = "co" > # Unit: seconds< / span > < / a >
< a class = "sourceLine" id = "cb18 -4" title = "4" > < span class = "co" > # min median max neval< / span > < / a >
< a class = "sourceLine" id = "cb18 -5" title = "5" > < span class = "co" > # 0.01817717 0.01843957 0.03878077 100< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb19 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb19 -1" title = "1" > thousands_of_E_colis < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/rep" > rep< / a > < / span > (< span class = "st" > "E. coli"< / span > , < span class = "dv" > 25000< / span > )< / a >
< a class = "sourceLine" id = "cb19 -2" title = "2" > microbenchmark< span class = "op" > ::< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (thousands_of_E_colis), < span class = "dt" > unit =< / span > < span class = "st" > "s"< / span > )< / a >
< a class = "sourceLine" id = "cb19 -3" title = "3" > < span class = "co" > # Unit: seconds< / span > < / a >
< a class = "sourceLine" id = "cb19 -4" title = "4" > < span class = "co" > # min median max neval< / span > < / a >
< a class = "sourceLine" id = "cb19 -5" title = "5" > < span class = "co" > # 0.01817717 0.01843957 0.03878077 100< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > Added parameter < code > reference_df< / code > for < code > as.mo< / code > , so users can supply their own microbial IDs, name or codes as a reference table< / li >
< li > Renamed all previous references to < code > bactid< / code > to < code > mo< / code > , like:
@ -770,12 +781,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< li > Added three antimicrobial agents to the < code > antibiotics< / code > data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)< / li >
< li >
< p > Added 163 trade names to the < code > antibiotics< / code > data set, it now contains 298 different trade names in total, e.g.:< / p >
< div class = "sourceCode" id = "cb19 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb19 -1" title = "1" > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > ab_official< / a > < / span > (< span class = "st" > "Bactroban"< / span > )< / a >
< a class = "sourceLine" id = "cb19 -2" title = "2" > < span class = "co" > # [1] "Mupirocin"< / span > < / a >
< a class = "sourceLine" id = "cb19 -3" title = "3" > < span class = "kw" > < a href = "../reference/ab_property.html" > ab_name< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "st" > "Bactroban"< / span > , < span class = "st" > "Amoxil"< / span > , < span class = "st" > "Zithromax"< / span > , < span class = "st" > "Floxapen"< / span > ))< / a >
< a class = "sourceLine" id = "cb19 -4" title = "4" > < span class = "co" > # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"< / span > < / a >
< a class = "sourceLine" id = "cb19 -5" title = "5" > < span class = "kw" > < a href = "../reference/ab_property.html" > ab_atc< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "st" > "Bactroban"< / span > , < span class = "st" > "Amoxil"< / span > , < span class = "st" > "Zithromax"< / span > , < span class = "st" > "Floxapen"< / span > ))< / a >
< a class = "sourceLine" id = "cb19 -6" title = "6" > < span class = "co" > # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"< / span > < / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb20 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb20 -1" title = "1" > < span class = "kw" > < a href = "../reference/AMR-deprecated.html" > ab_official< / a > < / span > (< span class = "st" > "Bactroban"< / span > )< / a >
< a class = "sourceLine" id = "cb20 -2" title = "2" > < span class = "co" > # [1] "Mupirocin"< / span > < / a >
< a class = "sourceLine" id = "cb20 -3" title = "3" > < span class = "kw" > < a href = "../reference/ab_property.html" > ab_name< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "st" > "Bactroban"< / span > , < span class = "st" > "Amoxil"< / span > , < span class = "st" > "Zithromax"< / span > , < span class = "st" > "Floxapen"< / span > ))< / a >
< a class = "sourceLine" id = "cb20 -4" title = "4" > < span class = "co" > # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"< / span > < / a >
< a class = "sourceLine" id = "cb20 -5" title = "5" > < span class = "kw" > < a href = "../reference/ab_property.html" > ab_atc< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "st" > "Bactroban"< / span > , < span class = "st" > "Amoxil"< / span > , < span class = "st" > "Zithromax"< / span > , < span class = "st" > "Floxapen"< / span > ))< / a >
< a class = "sourceLine" id = "cb20 -6" title = "6" > < span class = "co" > # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"< / span > < / a > < / code > < / pre > < / div >
< / li >
< li > For < code > first_isolate< / code > , rows will be ignored when there’ < / li >
< li > Function < code > ratio< / code > is now deprecated and will be removed in a future release, as it is not really the scope of this package< / li >
@ -786,13 +797,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< / li >
< li >
< p > Support for quasiquotation in the functions series < code > count_*< / code > and < code > portions_*< / code > , and < code > n_rsi< / code > . This allows to check for more than 2 vectors or columns.< / p >
< div class = "sourceCode" id = "cb20 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb20 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > select< / span > (amox, cipr) < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/count.html" > count_IR< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb20 -2" title = "2" > < span class = "co" > # which is the same as:< / span > < / a >
< a class = "sourceLine" id = "cb20 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/count.html" > count_IR< / a > < / span > (amox, cipr)< / a >
< a class = "sourceLine" id = "cb20 -4" title = "4" > < / a >
< a class = "sourceLine" id = "cb20 -5" title = "5" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl)< / a >
< a class = "sourceLine" id = "cb20 -6" title = "6" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl, gent)< / a >
< a class = "sourceLine" id = "cb20 -7" title = "7" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl, gent, pita)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb21 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb21 -1" title = "1" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > select< / span > (amox, cipr) < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/count.html" > count_IR< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb21 -2" title = "2" > < span class = "co" > # which is the same as:< / span > < / a >
< a class = "sourceLine" id = "cb21 -3" title = "3" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/count.html" > count_IR< / a > < / span > (amox, cipr)< / a >
< a class = "sourceLine" id = "cb21 -4" title = "4" > < / a >
< a class = "sourceLine" id = "cb21 -5" title = "5" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl)< / a >
< a class = "sourceLine" id = "cb21 -6" title = "6" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl, gent)< / a >
< a class = "sourceLine" id = "cb21 -7" title = "7" > septic_patients < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/portion.html" > portion_S< / a > < / span > (amcl, gent, pita)< / a > < / code > < / pre > < / div >
< / li >
< li > Edited < code > ggplot_rsi< / code > and < code > geom_rsi< / code > so they can cope with < code > count_df< / code > . The new < code > fun< / code > parameter has value < code > portion_df< / code > at default, but can be set to < code > count_df< / code > .< / li >
< li > Fix for < code > ggplot_rsi< / code > when the < code > ggplot2< / code > package was not loaded< / li >
@ -806,12 +817,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
< / li >
< li >
< p > Support for types (classes) list and matrix for < code > freq< / code > < / p >
< div class = "sourceCode" id = "cb21 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb21 -1" title = "1" > my_matrix =< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/with" > with< / a > < / span > (septic_patients, < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/matrix" > matrix< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (age, gender), < span class = "dt" > ncol =< / span > < span class = "dv" > 2< / span > ))< / a >
< a class = "sourceLine" id = "cb21 -2" title = "2" > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (my_matrix)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb22 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb22 -1" title = "1" > my_matrix =< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/with" > with< / a > < / span > (septic_patients, < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/matrix" > matrix< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (age, gender), < span class = "dt" > ncol =< / span > < span class = "dv" > 2< / span > ))< / a >
< a class = "sourceLine" id = "cb22 -2" title = "2" > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (my_matrix)< / a > < / code > < / pre > < / div >
< p > For lists, subsetting is possible:< / p >
< div class = "sourceCode" id = "cb22 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb22 -1" title = "1" > my_list =< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/list" > list< / a > < / span > (< span class = "dt" > age =< / span > septic_patients< span class = "op" > $< / span > age, < span class = "dt" > gender =< / span > septic_patients< span class = "op" > $< / span > gender)< / a >
< a class = "sourceLine" id = "cb22 -2" title = "2" > my_list < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age)< / a >
< a class = "sourceLine" id = "cb22 -3" title = "3" > my_list < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (gender)< / a > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb23 " > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb23 -1" title = "1" > my_list =< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/list" > list< / a > < / span > (< span class = "dt" > age =< / span > septic_patients< span class = "op" > $< / span > age, < span class = "dt" > gender =< / span > septic_patients< span class = "op" > $< / span > gender)< / a >
< a class = "sourceLine" id = "cb23 -2" title = "2" > my_list < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age)< / a >
< a class = "sourceLine" id = "cb23 -3" title = "3" > my_list < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (gender)< / a > < / code > < / pre > < / div >
< / li >
< / ul >
< / div >
