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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Download Data Sets for Own Use
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Set User- Or Team-specific Package Settings
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Conduct Principal Component Analysis for AMR
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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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AMR & dplyr/tidyverse
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AMR & base R
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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > AMR Plots with < code > ggplot2< / code > < / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/ggplot_sir.R" class = "external-link" > < code > R/ggplot_sir.R< / code > < / a > < / small >
< div class = "d-none name" > < code > ggplot_sir.Rd< / code > < / div >
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< / div >
< div class = "ref-description section level2" >
< p > Use these functions to create bar plots for AMR data analysis. All functions rely on < a href = "https://ggplot2.tidyverse.org/reference/ggplot.html" class = "external-link" > ggplot2< / a > functions.< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > ggplot_sir< / span > < span class = "op" > (< / span > < / span >
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< span > < span class = "va" > data< / span > ,< / span >
< span > position < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > x < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span >
< span > fill < span class = "op" > =< / span > < span class = "st" > "interpretation"< / span > ,< / span >
< span > facet < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > breaks < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/seq.html" class = "external-link" > seq< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 0< / span > , < span class = "fl" > 1< / span > , < span class = "fl" > 0.1< / span > < span class = "op" > )< / span > ,< / span >
< span > limits < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > translate_ab < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > combine_SI < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > minimum < span class = "op" > =< / span > < span class = "fl" > 30< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > nrow < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > colours < 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 > S < span class = "op" > =< / span > < span class = "st" > "#3CAEA3"< / span > , SI < span class = "op" > =< / span > < span class = "st" > "#3CAEA3"< / span > , I < span class = "op" > =< / span > < span class = "st" > "#F6D55C"< / span > , IR < span class = "op" > =< / span > < span class = "st" > "#ED553B"< / span > , R < span class = "op" > =< / span > < / span >
< span > < span class = "st" > "#ED553B"< / span > < span class = "op" > )< / span > ,< / span >
< span > datalabels < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > datalabels.size < span class = "op" > =< / span > < span class = "fl" > 2.5< / span > ,< / span >
< span > datalabels.colour < span class = "op" > =< / span > < span class = "st" > "grey15"< / span > ,< / span >
< span > title < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > subtitle < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > caption < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > x.title < span class = "op" > =< / span > < span class = "st" > "Antimicrobial"< / span > ,< / span >
< span > y.title < span class = "op" > =< / span > < span class = "st" > "Proportion"< / span > ,< / span >
< span > < span class = "va" > ...< / span > < / span >
< span > < span class = "op" > )< / span > < / span >
< span > < / span >
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< span > < span class = "fu" > geom_sir< / span > < span class = "op" > (< / span > < / span >
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< span > position < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< 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" > "antibiotic"< / span > , < span class = "st" > "interpretation"< / span > < span class = "op" > )< / span > ,< / span >
< span > fill < span class = "op" > =< / span > < span class = "st" > "interpretation"< / span > ,< / span >
< span > translate_ab < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > minimum < span class = "op" > =< / span > < span class = "fl" > 30< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > combine_SI < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > < span class = "va" > ...< / span > < / span >
< span > < span class = "op" > )< / span > < / span >
< span > < / span >
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< span > < span class = "fu" > facet_sir< / span > < span class = "op" > (< / span > facet < 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" > "interpretation"< / span > , < span class = "st" > "antibiotic"< / span > < span class = "op" > )< / span > , nrow < span class = "op" > =< / span > < span class = "cn" > NULL< / span > < span class = "op" > )< / span > < / span >
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< span > < / span >
< span > < span class = "fu" > scale_y_percent< / span > < span class = "op" > (< / span > breaks < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/seq.html" class = "external-link" > seq< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 0< / span > , < span class = "fl" > 1< / span > , < span class = "fl" > 0.1< / span > < span class = "op" > )< / span > , limits < span class = "op" > =< / span > < span class = "cn" > NULL< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
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< span > < span class = "fu" > scale_sir_colours< / span > < span class = "op" > (< / span > < span class = "va" > ...< / span > , aesthetics < span class = "op" > =< / span > < span class = "st" > "fill"< / span > < span class = "op" > )< / span > < / span >
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< span > < / span >
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< span > < span class = "fu" > theme_sir< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span >
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< span > < / span >
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< span > < span class = "fu" > labels_sir_count< / span > < span class = "op" > (< / span > < / span >
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< span > position < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > x < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span >
< span > translate_ab < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > minimum < span class = "op" > =< / span > < span class = "fl" > 30< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > combine_SI < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > datalabels.size < span class = "op" > =< / span > < span class = "fl" > 3< / span > ,< / span >
< span > datalabels.colour < span class = "op" > =< / span > < span class = "st" > "grey15"< / span > < / span >
< 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 > data< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > with column(s) of class < code > < a href = "as.sir.html" > sir< / a > < / code > (see < code > < a href = "as.sir.html" > as.sir()< / a > < / code > )< / p > < / dd >
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< dt > position< / dt >
< dd > < p > position adjustment of bars, either < code > "fill"< / code > , < code > "stack"< / code > or < code > "dodge"< / code > < / p > < / dd >
< dt > x< / dt >
< dd > < p > variable to show on x axis, either < code > "antibiotic"< / code > (default) or < code > "interpretation"< / code > or a grouping variable< / p > < / dd >
< dt > fill< / dt >
< dd > < p > variable to categorise using the plots legend, either < code > "antibiotic"< / code > (default) or < code > "interpretation"< / code > or a grouping variable< / p > < / dd >
< dt > facet< / dt >
< dd > < p > variable to split plots by, either < code > "interpretation"< / code > (default) or < code > "antibiotic"< / code > or a grouping variable< / p > < / dd >
< dt > breaks< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/numeric.html" class = "external-link" > numeric< / a > vector of positions< / p > < / dd >
< dt > limits< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/numeric.html" class = "external-link" > numeric< / a > vector of length two providing limits of the scale, use < code > NA< / code > to refer to the existing minimum or maximum< / p > < / dd >
< dt > translate_ab< / dt >
< dd > < p > a column name of the < a href = "antibiotics.html" > antibiotics< / a > data set to translate the antibiotic abbreviations to, using < code > < a href = "ab_property.html" > ab_property()< / a > < / code > < / p > < / dd >
< dt > combine_SI< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is < code > TRUE< / code > < / p > < / dd >
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< dt > minimum< / dt >
< dd > < p > the minimum allowed number of available (tested) isolates. Any isolate count lower than < code > minimum< / code > will return < code > NA< / code > with a warning. The default number of < code > 30< / code > isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see < em > Source< / em > .< / p > < / dd >
< dt > language< / dt >
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< dd > < p > language of the returned text - the default is the current system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > ) and can also be set with the < a href = "AMR-options.html" > package option< / a > < code > < a href = "AMR-options.html" > AMR_locale< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / dd >
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< dt > nrow< / dt >
< dd > < p > (when using < code > facet< / code > ) number of rows< / p > < / dd >
< dt > colours< / dt >
< dd > < p > a named vactor with colour to be used for filling. The default colours are colour-blind friendly.< / p > < / dd >
< dt > datalabels< / dt >
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< dd > < p > show datalabels using < code > labels_sir_count()< / code > < / p > < / dd >
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< dt > datalabels.size< / dt >
< dd > < p > size of the datalabels< / p > < / dd >
< dt > datalabels.colour< / dt >
< dd > < p > colour of the datalabels< / p > < / dd >
< dt > title< / dt >
< dd > < p > text to show as title of the plot< / p > < / dd >
< dt > subtitle< / dt >
< dd > < p > text to show as subtitle of the plot< / p > < / dd >
< dt > caption< / dt >
< dd > < p > text to show as caption of the plot< / p > < / dd >
< dt > x.title< / dt >
< dd > < p > text to show as x axis description< / p > < / dd >
< dt > y.title< / dt >
< dd > < p > text to show as y axis description< / p > < / dd >
< dt > ...< / dt >
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< dd > < p > other arguments passed on to < code > geom_sir()< / code > or, in case of < code > scale_sir_colours()< / code > , named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See < em > Examples< / em > .< / p > < / dd >
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< dt > aesthetics< / dt >
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< dd > < p > aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"< / p > < / dd >
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< / dl > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > At default, the names of antibiotics will be shown on the plots using < code > < a href = "ab_property.html" > ab_name()< / a > < / code > . This can be set with the < code > translate_ab< / code > argument. See < code > < a href = "count.html" > count_df()< / a > < / code > .< / p > < div class = "section" >
< h3 id = "the-functions" > The Functions< a class = "anchor" aria-label = "anchor" href = "#the-functions" > < / a > < / h3 >
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< p > < code > geom_sir()< / code > will take any variable from the data that has an < code > < a href = "as.sir.html" > sir< / a > < / code > class (created with < code > < a href = "as.sir.html" > as.sir()< / a > < / code > ) using < code > < a href = "proportion.html" > sir_df()< / a > < / code > and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.< / p >
< p > < code > facet_sir()< / code > creates 2d plots (at default based on S/I/R) using < code > < a href = "https://ggplot2.tidyverse.org/reference/facet_wrap.html" class = "external-link" > ggplot2::facet_wrap()< / a > < / code > .< / p >
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< p > < code > scale_y_percent()< / code > transforms the y axis to a 0 to 100% range using < code > < a href = "https://ggplot2.tidyverse.org/reference/scale_continuous.html" class = "external-link" > ggplot2::scale_y_continuous()< / a > < / code > .< / p >
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< p > < code > scale_sir_colours()< / code > sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.< / p >
< p > < code > theme_sir()< / code > is a [ggplot2 theme][< code > < a href = "https://ggplot2.tidyverse.org/reference/theme.html" class = "external-link" > ggplot2::theme()< / a > < / code > with minimal distraction.< / p >
< p > < code > labels_sir_count()< / code > print datalabels on the bars with percentage and amount of isolates using < code > < a href = "https://ggplot2.tidyverse.org/reference/geom_text.html" class = "external-link" > ggplot2::geom_text()< / a > < / code > .< / p >
< p > < code > ggplot_sir()< / code > is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (< code > %> %< / code > ). See < em > Examples< / em > .< / p >
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< / 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" > # \donttest{< / span > < / span > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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" > # get antimicrobial results for drugs against a UTI:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/ggplot.html" class = "external-link" > ggplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / 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" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / 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 = "fu" > geom_sir< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-plt img" > < img src = "ggplot_sir-1.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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" > # prettify the plot using some additional functions:< / 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" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / 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" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/ggplot.html" class = "external-link" > ggplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > geom_sir< / 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 = "fu" > scale_y_percent< / 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 = "fu" > scale_sir_colours< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > labels_sir_count< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > theme_sir< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-plt img" > < img src = "ggplot_sir-2.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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" > # or better yet, simplify this using the wrapper function - a single command:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / 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" > ggplot_sir< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-plt img" > < img src = "ggplot_sir-3.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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" > # get only proportions and no counts:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / 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" > ggplot_sir< / span > < span class = "op" > (< / span > datalabels < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-plt img" > < img src = "ggplot_sir-4.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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" > # add other ggplot2 arguments as you like:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / 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" > ggplot_sir< / span > < span class = "op" > (< / span > < / span > < / span >
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< span class = "r-in" > < span > width < span class = "op" > =< / span > < span class = "fl" > 0.5< / span > ,< / span > < / span >
< span class = "r-in" > < span > colour < span class = "op" > =< / span > < span class = "st" > "black"< / span > ,< / span > < / span >
< span class = "r-in" > < span > size < span class = "op" > =< / span > < span class = "fl" > 1< / span > ,< / span > < / span >
< span class = "r-in" > < span > linetype < span class = "op" > =< / span > < span class = "fl" > 2< / span > ,< / span > < / span >
< span class = "r-in" > < span > alpha < span class = "op" > =< / span > < span class = "fl" > 0.25< / 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 >
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< span class = "r-plt img" > < img src = "ggplot_sir-5.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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 = "co" > # you can alter the colours with colour names:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > ggplot_sir< / span > < span class = "op" > (< / span > colours < 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 > SI < span class = "op" > =< / span > < span class = "st" > "yellow"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
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< span class = "r-plt img" > < img src = "ggplot_sir-6.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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 = "co" > # but you can also use the built-in colour-blind friendly colours for< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # your plots, where "S" is green, "I" is yellow and "R" is red:< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / 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" > "Value1"< / span > , < span class = "st" > "Value2"< / span > , < span class = "st" > "Value3"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > y < 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 = "fl" > 1< / span > , < span class = "fl" > 2< / span > , < span class = "fl" > 3< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > z < 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" > "Value4"< / span > , < span class = "st" > "Value5"< / span > , < span class = "st" > "Value6"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/ggplot.html" class = "external-link" > ggplot< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/geom_bar.html" class = "external-link" > geom_col< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/aes.html" class = "external-link" > aes< / a > < / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "va" > x< / span > , y < span class = "op" > =< / span > < span class = "va" > y< / span > , fill < span class = "op" > =< / span > < span class = "va" > z< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > scale_sir_colours< / span > < span class = "op" > (< / span > Value4 < span class = "op" > =< / span > < span class = "st" > "S"< / span > , Value5 < span class = "op" > =< / span > < span class = "st" > "I"< / span > , Value6 < span class = "op" > =< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-plt img" > < img src = "ggplot_sir-7.png" alt = "" width = "700" height = "433" > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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 = "co" > # resistance of ciprofloxacine per age group< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / 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 > first_isolate < span class = "op" > =< / span > < span class = "fu" > < a href = "first_isolate.html" > first_isolate< / a > < / span > < span class = "op" > (< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > first_isolate< / span > < span class = "op" > ==< / span > < span class = "cn" > TRUE< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "va" > mo< / span > < span class = "op" > ==< / span > < span class = "fu" > < a href = "as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Escherichia coli"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # age_groups() is also a function in this AMR package:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > age_group < span class = "op" > =< / span > < span class = "fu" > < a href = "age_groups.html" > age_groups< / a > < / span > < span class = "op" > (< / span > < span class = "va" > age< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > age_group< / span > , < span class = "va" > CIP< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > ggplot_sir< / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "st" > "age_group"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2024-03-03 23:05:59 +01:00
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > < span class = "warning" > Warning: < / span > Removed 6 rows containing missing values or values outside the scale range< / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > (`geom_col()`).< / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > < span class = "warning" > Warning: < / span > Removed 6 rows containing missing values or values outside the scale range< / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > (`geom_text()`).< / span >
2023-01-21 23:53:21 +01:00
< span class = "r-plt img" > < img src = "ggplot_sir-8.png" alt = "" width = "700" height = "433" > < / 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://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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 = "co" > # a shorter version which also adjusts data label colours:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > ggplot_sir< / span > < span class = "op" > (< / span > colours < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-plt img" > < img src = "ggplot_sir-9.png" alt = "" width = "700" height = "433" > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://ggplot2.tidyverse.org" class = "external-link" > "ggplot2"< / a > < / span > < span class = "op" > )< / 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 = "co" > # it also supports groups (don't forget to use the group var on `x` or `facet`):< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "mo_property.html" > mo_is_gram_negative< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ward< / span > < span class = "op" > !=< / span > < span class = "st" > "Outpatient"< / 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 = "co" > # select only UTI-specific drugs< / 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" > ward< / span > , < span class = "va" > AMX< / span > , < span class = "va" > NIT< / span > , < span class = "va" > FOS< / span > , < span class = "va" > TMP< / span > , < span class = "va" > CIP< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > 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 >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > ggplot_sir< / span > < span class = "op" > (< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > x < span class = "op" > =< / span > < span class = "st" > "ward"< / span > ,< / span > < / span >
< span class = "r-in" > < span > facet < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > nrow < span class = "op" > =< / span > < span class = "fl" > 1< / span > ,< / span > < / span >
< span class = "r-in" > < span > title < span class = "op" > =< / span > < span class = "st" > "AMR of Anti-UTI Drugs Per Ward"< / span > ,< / span > < / span >
< span class = "r-in" > < span > x.title < span class = "op" > =< / span > < span class = "st" > "Ward"< / span > ,< / span > < / span >
< span class = "r-in" > < span > datalabels < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-plt img" > < img src = "ggplot_sir-10.png" alt = "" width = "700" height = "433" > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< / code > < / pre > < / div >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
2022-12-11 11:50:34 +01:00
< p > < / p > < p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "pkgdown-footer-right" >
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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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