(v3.0.1.9059) Fix WISCA in vignette

2026-06-24 10:56:23 +02:00 · 2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
--- a/man/ab_from_text.Rd
+++ b/man/ab_from_text.Rd
@@ -4,9 +4,15 @@
 \alias{ab_from_text}
 \title{Retrieve Antimicrobial Drug Names and Doses from Clinical Text}
 \usage{
-ab_from_text(text, type = c("drug", "dose", "administration"),
-  collapse = NULL, translate_ab = FALSE, thorough_search = NULL,
-  info = interactive(), ...)
+ab_from_text(
+  text,
+  type = c("drug", "dose", "administration"),
+  collapse = NULL,
+  translate_ab = FALSE,
+  thorough_search = NULL,
+  info = interactive(),
+  ...
+)
 }
 \arguments{
 \item{text}{Text to analyse.}
--- a/man/ab_property.Rd
+++ b/man/ab_property.Rd
@@ -47,8 +47,13 @@ ab_url(x, open = FALSE, ...)

 ab_property(x, property = "name", language = get_AMR_locale(), ...)

-set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
-  snake_case = NULL)
+set_ab_names(
+  data,
+  ...,
+  property = "name",
+  language = get_AMR_locale(),
+  snake_case = NULL
+)
 }
 \arguments{
 \item{x}{Any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}.}
--- a/man/age_groups.Rd
+++ b/man/age_groups.Rd
@@ -4,8 +4,7 @@
 \alias{age_groups}
 \title{Split Ages into Age Groups}
 \usage{
-age_groups(x, split_at = c(0, 12, 25, 55, 75), names = NULL,
-  na.rm = FALSE)
+age_groups(x, split_at = c(0, 12, 25, 55, 75), names = NULL, na.rm = FALSE)
 }
 \arguments{
 \item{x}{Age, e.g. calculated with \code{\link[=age]{age()}}.}
--- a/man/amr-tidymodels.Rd
+++ b/man/amr-tidymodels.Rd
@@ -24,11 +24,25 @@ all_disk()

 all_disk_predictors()

-step_mic_log2(recipe, ..., role = NA, trained = FALSE, columns = NULL,
-  skip = FALSE, id = recipes::rand_id("mic_log2"))
+step_mic_log2(
+  recipe,
+  ...,
+  role = NA,
+  trained = FALSE,
+  columns = NULL,
+  skip = FALSE,
+  id = recipes::rand_id("mic_log2")
+)

-step_sir_numeric(recipe, ..., role = NA, trained = FALSE, columns = NULL,
-  skip = FALSE, id = recipes::rand_id("sir_numeric"))
+step_sir_numeric(
+  recipe,
+  ...,
+  role = NA,
+  trained = FALSE,
+  columns = NULL,
+  skip = FALSE,
+  id = recipes::rand_id("sir_numeric")
+)
 }
 \arguments{
 \item{recipe}{A recipe object. The step will be added to the sequence of
--- a/man/antibiogram.Rd
+++ b/man/antibiogram.Rd
@@ -10,37 +10,78 @@
 \alias{knit_print.antibiogram}
 \title{Generate Traditional, Combination, Syndromic, or WISCA Antibiograms}
 \usage{
-antibiogram(x, antimicrobials = where(is.sir), mo_transform = "shortname",
-  ab_transform = "name", syndromic_group = NULL, add_total_n = FALSE,
-  only_all_tested = FALSE, digits = ifelse(wisca, 1, 0),
-  formatting_type = getOption("AMR_antibiogram_formatting_type",
-  ifelse(wisca, 14, 18)), col_mo = NULL, language = get_AMR_locale(),
-  minimum = 30, combine_SI = TRUE, sep = " + ", sort_columns = TRUE,
-  wisca = FALSE, simulations = 1000, conf_interval = 0.95,
-  interval_side = "two-tailed", info = interactive(), parallel = FALSE,
-  ...)
-
-wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
-  syndromic_group = NULL, only_all_tested = FALSE, digits = 1,
+wisca(
+  x,
+  antimicrobials = where(is.sir),
+  ab_transform = "name",
+  syndromic_group = NULL,
+  only_all_tested = FALSE,
+  digits = 1,
  formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
-  col_mo = NULL, language = get_AMR_locale(), combine_SI = TRUE,
-  sep = " + ", sort_columns = TRUE, simulations = 1000,
-  conf_interval = 0.95, interval_side = "two-tailed",
-  info = interactive(), parallel = FALSE, ...)
+  col_mo = NULL,
+  language = get_AMR_locale(),
+  combine_SI = TRUE,
+  sep = " + ",
+  sort_columns = TRUE,
+  simulations = 1000,
+  conf_interval = 0.95,
+  interval_side = "two-tailed",
+  info = interactive(),
+  parallel = FALSE,
+  ...
+)
+
+antibiogram(
+  x,
+  antimicrobials = where(is.sir),
+  mo_transform = "shortname",
+  ab_transform = "name",
+  syndromic_group = NULL,
+  add_total_n = FALSE,
+  only_all_tested = FALSE,
+  digits = ifelse(wisca, 1, 0),
+  formatting_type = getOption("AMR_antibiogram_formatting_type", ifelse(wisca, 14, 18)),
+  col_mo = NULL,
+  language = get_AMR_locale(),
+  minimum = 30,
+  combine_SI = TRUE,
+  sep = " + ",
+  sort_columns = TRUE,
+  wisca = FALSE,
+  simulations = 1000,
+  conf_interval = 0.95,
+  interval_side = "two-tailed",
+  info = interactive(),
+  parallel = FALSE,
+  ...
+)

 retrieve_wisca_parameters(wisca_model, ...)

 \method{plot}{antibiogram}(x, ...)

-\method{autoplot}{antibiogram}(object, geom = c("pointrange", "point", "col",
-  "bar", "errorbar"), ci = TRUE, sort = TRUE, flip = NULL,
-  caption = NULL, ...)
+\method{autoplot}{antibiogram}(
+  object,
+  geom = c("pointrange", "point", "col", "bar", "errorbar"),
+  ci = TRUE,
+  sort = TRUE,
+  flip = NULL,
+  caption = NULL,
+  ...
+)

-wisca_plot(wisca_model, wisca_plot_type = c("susceptibility_incidence",
-  "posterior_coverage"), ...)
+wisca_plot(
+  wisca_model,
+  wisca_plot_type = c("susceptibility_incidence", "posterior_coverage"),
+  ...
+)

-\method{knit_print}{antibiogram}(x, italicise = TRUE,
-  na = getOption("knitr.kable.NA", default = ""), ...)
+\method{knit_print}{antibiogram}(
+  x,
+  italicise = TRUE,
+  na = getOption("knitr.kable.NA", default = ""),
+  ...
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see \code{\link[=as.sir]{as.sir()}}).}
@@ -66,14 +107,10 @@ wisca_plot(wisca_model, wisca_plot_type = c("susceptibility_incidence",
 }
 }}

-\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"domain"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"morphology"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, or \code{"snomed"}. Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.}
-
 \item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): \code{"ab"}, \code{"cid"}, \code{"name"}, \code{"group"}, \code{"atc"}, \code{"atc_group1"}, \code{"atc_group2"}, \code{"abbreviations"}, \code{"synonyms"}, \code{"oral_ddd"}, \code{"oral_units"}, \code{"iv_ddd"}, \code{"iv_units"}, or \code{"loinc"}. Can also be \code{NULL} to not transform the input.}

 \item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}

-\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
-
 \item{only_all_tested}{(for combination antibiograms): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see \emph{Details}.}

 \item{digits}{Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise.}
@@ -84,18 +121,12 @@ wisca_plot(wisca_model, wisca_plot_type = c("susceptibility_incidence",

 \item{language}{Language to translate text, which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}

-\item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
-
 \item{combine_SI}{A \link{logical} to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is \code{TRUE}).}

 \item{sep}{A separating character for antimicrobial columns in combination antibiograms.}

 \item{sort_columns}{A \link{logical} to indicate whether the antimicrobial columns must be sorted on name.}

-\item{wisca}{A \link{logical} to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is \code{FALSE}). This will use a Bayesian decision model to estimate regimen coverage probabilities using \href{https://en.wikipedia.org/wiki/Monte_Carlo_method}{Monte Carlo simulations}. Per \doi{10.1093/jac/dkv397}, susceptibility priors are \eqn{\beta(0.5, 0.5)} (Jeffreys) and intrinsically resistant pairs (based on \link{intrinsic_resistant}) use \eqn{\beta(1, 9999)}.
-
-Set \code{simulations}, \code{conf_interval}, and \code{interval_side} to adjust.}
-
 \item{simulations}{(for WISCA) a numerical value to set the number of Monte Carlo simulations.}

 \item{conf_interval}{A numerical value to set confidence interval (default is \code{0.95}).}
@@ -108,6 +139,16 @@ Set \code{simulations}, \code{conf_interval}, and \code{interval_side} to adjust

 \item{...}{Currently unused.}

+\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"domain"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"morphology"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, or \code{"snomed"}. Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.}
+
+\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
+
+\item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
+
+\item{wisca}{A \link{logical} to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is \code{FALSE}). This will use a Bayesian decision model to estimate regimen coverage probabilities using \href{https://en.wikipedia.org/wiki/Monte_Carlo_method}{Monte Carlo simulations}. Per \doi{10.1093/jac/dkv397}, susceptibility priors are \eqn{\beta(0.5, 0.5)} (Jeffreys) and intrinsically resistant pairs (based on \link{intrinsic_resistant}) use \eqn{\beta(1, 9999)}.
+
+Set \code{simulations}, \code{conf_interval}, and \code{interval_side} to adjust.}
+
 \item{wisca_model}{The outcome of \code{\link[=wisca]{wisca()}} or \code{\link[=antibiogram]{antibiogram(..., wisca = TRUE)}}.}

 \item{object}{An \code{\link[=antibiogram]{antibiogram()}} object.}
--- a/man/antimicrobial_selectors.Rd
+++ b/man/antimicrobial_selectors.Rd
@@ -45,8 +45,12 @@
 \alias{not_intrinsic_resistant}
 \title{Antimicrobial Selectors}
 \usage{
-aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+aminoglycosides(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 aminopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)

@@ -54,41 +58,68 @@ antifungals(only_sir_columns = FALSE, return_all = TRUE, ...)

 antimycobacterials(only_sir_columns = FALSE, return_all = TRUE, ...)

-betalactams(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+betalactams(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

-betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
-  ...)
+betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE, ...)

-carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+carbapenems(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

-cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+cephalosporins(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)

 cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)

-cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+cephalosporins_3rd(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)

 cephalosporins_5th(only_sir_columns = FALSE, return_all = TRUE, ...)

-fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+fluoroquinolones(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)

 ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)

-isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+isoxazolylpenicillins(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

-lincosamides(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+lincosamides(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 lipoglycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)

@@ -108,11 +139,19 @@ phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)

 phosphonics(only_sir_columns = FALSE, return_all = TRUE, ...)

-polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+polymyxins(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

-quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+quinolones(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)

@@ -122,25 +161,43 @@ streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)

 sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)

-tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+tetracyclines(
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)

 ureidopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)

-amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+amr_class(
+  amr_class,
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

-amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
-  return_all = TRUE, ...)
+amr_selector(
+  filter,
+  only_sir_columns = FALSE,
+  only_treatable = TRUE,
+  return_all = TRUE,
+  ...
+)

 administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)

 administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)

-not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
-  version_expected_phenotypes = 1.2, ...)
+not_intrinsic_resistant(
+  only_sir_columns = FALSE,
+  col_mo = NULL,
+  version_expected_phenotypes = 1.2,
+  ...
+)
 }
 \arguments{
 \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE}.}
--- a/man/as.ab.Rd
+++ b/man/as.ab.Rd
@@ -9,8 +9,13 @@
 \alias{NA_ab_}
 \title{Transform Input to an Antibiotic ID}
 \usage{
-as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
-  info = interactive(), ...)
+as.ab(
+  x,
+  flag_multiple_results = TRUE,
+  language = get_AMR_locale(),
+  info = interactive(),
+  ...
+)

 is.ab(x)

--- a/man/as.mic.Rd
+++ b/man/as.mic.Rd
@@ -12,15 +12,19 @@
 \alias{droplevels.mic}
 \title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
 \usage{
-as.mic(x, na.rm = FALSE, keep_operators = "all",
-  round_to_next_log2 = FALSE)
+as.mic(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2 = FALSE)

 is.mic(x)

 NA_mic_

-rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE,
-  round_to_next_log2 = FALSE)
+rescale_mic(
+  x,
+  mic_range,
+  keep_operators = "edges",
+  as.mic = TRUE,
+  round_to_next_log2 = FALSE
+)

 mic_p50(x, na.rm = FALSE, ...)

--- a/man/as.mo.Rd
+++ b/man/as.mo.Rd
@@ -13,14 +13,20 @@
 \alias{NA_mo_}
 \title{Transform Arbitrary Input to Valid Microbial Taxonomy}
 \usage{
-as.mo(x, Becker = FALSE, Lancefield = FALSE,
+as.mo(
+  x,
+  Becker = FALSE,
+  Lancefield = FALSE,
  minimum_matching_score = NULL,
  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
  reference_df = get_mo_source(),
  ignore_pattern = getOption("AMR_ignore_pattern", NULL),
  cleaning_regex = getOption("AMR_cleaning_regex", mo_cleaning_regex()),
  only_fungi = getOption("AMR_only_fungi", FALSE),
-  language = get_AMR_locale(), info = interactive(), ...)
+  language = get_AMR_locale(),
+  info = interactive(),
+  ...
+)

 is.mo(x)

--- a/man/as.sir.Rd
+++ b/man/as.sir.Rd
@@ -22,48 +22,86 @@ is.sir(x)

 is_sir_eligible(x, threshold = 0.05)

-\method{as.sir}{default}(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
-  R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
-  WT = "^(WT|6)+$", NWT = "^(NWT|7)+$", NS = "^(NS|8)+$",
-  info = interactive(), ...)
+\method{as.sir}{default}(
+  x,
+  S = "^(S|U|1)+$",
+  I = "^(I|2)+$",
+  R = "^(R|3)+$",
+  NI = "^(N|NI|V|4)+$",
+  SDD = "^(SDD|D|H|5)+$",
+  WT = "^(WT|6)+$",
+  NWT = "^(NWT|7)+$",
+  NS = "^(NS|8)+$",
+  info = interactive(),
+  ...
+)

-\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
-  guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
+\method{as.sir}{mic}(
+  x,
+  mo = NULL,
+  ab = deparse(substitute(x)),
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  uti = NULL,
  capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
  add_intrinsic_resistance = FALSE,
  reference_data = AMR::clinical_breakpoints,
  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
-  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
+    FALSE),
+  include_screening = getOption("AMR_include_screening", FALSE),
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
-  language = get_AMR_locale(), verbose = FALSE, info = interactive(),
-  conserve_capped_values = NULL, ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  host = NULL,
+  language = get_AMR_locale(),
+  verbose = FALSE,
+  info = interactive(),
+  conserve_capped_values = NULL,
+  ...
+)

-\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
-  guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
+\method{as.sir}{disk}(
+  x,
+  mo = NULL,
+  ab = deparse(substitute(x)),
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  uti = NULL,
  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
  add_intrinsic_resistance = FALSE,
  reference_data = AMR::clinical_breakpoints,
  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
-  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
+    FALSE),
+  include_screening = getOption("AMR_include_screening", FALSE),
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
-  language = get_AMR_locale(), verbose = FALSE, info = interactive(),
-  ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  host = NULL,
+  language = get_AMR_locale(),
+  verbose = FALSE,
+  info = interactive(),
+  ...
+)

-\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
-  guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
+\method{as.sir}{data.frame}(
+  x,
+  ...,
+  col_mo = NULL,
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  uti = NULL,
  capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
  as_wt_nwt = identical(breakpoint_type, "ECOFF"),
  add_intrinsic_resistance = FALSE,
  reference_data = AMR::clinical_breakpoints,
  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
-  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
+    FALSE),
+  include_screening = getOption("AMR_include_screening", FALSE),
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
-  language = get_AMR_locale(), verbose = FALSE, info = interactive(),
-  parallel = FALSE, conserve_capped_values = NULL)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  host = NULL,
+  language = get_AMR_locale(),
+  verbose = FALSE,
+  info = interactive(),
+  parallel = FALSE,
+  conserve_capped_values = NULL
+)

 sir_interpretation_history(clean = FALSE)
 }
--- a/man/atc_online.Rd
+++ b/man/atc_online.Rd
@@ -10,9 +10,13 @@
 \url{https://atcddd.fhi.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
 }
 \usage{
-atc_online_property(atc_code, property, administration = "O",
+atc_online_property(
+  atc_code,
+  property,
+  administration = "O",
  url = "https://atcddd.fhi.no/atc_ddd_index/?code=\%s&showdescription=no",
-  url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=\%s&showdescription=no")
+  url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=\%s&showdescription=no"
+)

 atc_online_groups(atc_code, ...)

--- a/man/av_from_text.Rd
+++ b/man/av_from_text.Rd
@@ -4,9 +4,15 @@
 \alias{av_from_text}
 \title{Retrieve Antiviral Drug Names and Doses from Clinical Text}
 \usage{
-av_from_text(text, type = c("drug", "dose", "administration"),
-  collapse = NULL, translate_av = FALSE, thorough_search = NULL,
-  info = interactive(), ...)
+av_from_text(
+  text,
+  type = c("drug", "dose", "administration"),
+  collapse = NULL,
+  translate_av = FALSE,
+  thorough_search = NULL,
+  info = interactive(),
+  ...
+)
 }
 \arguments{
 \item{text}{Text to analyse.}
--- a/man/bug_drug_combinations.Rd
+++ b/man/bug_drug_combinations.Rd
@@ -5,14 +5,26 @@
 \alias{format.bug_drug_combinations}
 \title{Determine Bug-Drug Combinations}
 \usage{
-bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname,
-  include_n_rows = FALSE, ...)
+bug_drug_combinations(
+  x,
+  col_mo = NULL,
+  FUN = mo_shortname,
+  include_n_rows = FALSE,
+  ...
+)

-\method{format}{bug_drug_combinations}(x, translate_ab = "name (ab, atc)",
-  language = get_AMR_locale(), minimum = 30, combine_SI = TRUE,
-  add_ab_group = TRUE, remove_intrinsic_resistant = FALSE,
-  decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark ==
-  ",", ".", ","), ...)
+\method{format}{bug_drug_combinations}(
+  x,
+  translate_ab = "name (ab, atc)",
+  language = get_AMR_locale(),
+  minimum = 30,
+  combine_SI = TRUE,
+  add_ab_group = TRUE,
+  remove_intrinsic_resistant = FALSE,
+  decimal.mark = getOption("OutDec"),
+  big.mark = ifelse(decimal.mark == ",", ".", ","),
+  ...
+)
 }
 \arguments{
 \item{x}{A data set with antimicrobials columns, such as \code{amox}, \code{AMX} and \code{AMC}.}
--- a/man/count.Rd
+++ b/man/count.Rd
@@ -14,11 +14,17 @@
 \alias{count_df}
 \title{Count Available Isolates}
 \usage{
-count_resistant(..., only_all_tested = FALSE,
-  guideline = getOption("AMR_guideline", "EUCAST"))
+count_resistant(
+  ...,
+  only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST")
+)

-count_susceptible(..., only_all_tested = FALSE,
-  guideline = getOption("AMR_guideline", "EUCAST"))
+count_susceptible(
+  ...,
+  only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST")
+)

 count_S(..., only_all_tested = FALSE)

@@ -34,8 +40,12 @@ count_all(..., only_all_tested = FALSE)

 n_sir(..., only_all_tested = FALSE)

-count_df(data, translate_ab = "name", language = get_AMR_locale(),
-  combine_SI = TRUE)
+count_df(
+  data,
+  translate_ab = "name",
+  language = get_AMR_locale(),
+  combine_SI = TRUE
+)
 }
 \arguments{
 \item{...}{One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed.}
--- a/man/export_ncbi_biosample.Rd
+++ b/man/export_ncbi_biosample.Rd
@@ -4,9 +4,13 @@
 \alias{export_ncbi_biosample}
 \title{Export Data Set as NCBI BioSample Antibiogram}
 \usage{
-export_ncbi_biosample(x, filename = paste0("biosample_", format(Sys.time(),
-  "\%Y-\%m-\%d-\%H\%M\%S"), ".xlsx"), type = "pathogen MIC",
-  columns = where(is.mic), save_as_xlsx = TRUE)
+export_ncbi_biosample(
+  x,
+  filename = paste0("biosample_", format(Sys.time(), "\%Y-\%m-\%d-\%H\%M\%S"), ".xlsx"),
+  type = "pathogen MIC",
+  columns = where(is.mic),
+  save_as_xlsx = TRUE
+)
 }
 \arguments{
 \item{x}{A data set.}
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -5,18 +5,38 @@
 \alias{filter_first_isolate}
 \title{Determine First Isolates}
 \usage{
-first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
-  col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
-  col_icu = NULL, col_keyantimicrobials = NULL, episode_days = 365,
-  testcodes_exclude = NULL, icu_exclude = FALSE, specimen_group = NULL,
-  type = "points", method = c("phenotype-based", "episode-based",
-  "patient-based", "isolate-based"), ignore_I = TRUE, points_threshold = 2,
-  info = interactive(), include_unknown = FALSE,
-  include_untested_sir = TRUE, ...)
+first_isolate(
+  x = NULL,
+  col_date = NULL,
+  col_patient_id = NULL,
+  col_mo = NULL,
+  col_testcode = NULL,
+  col_specimen = NULL,
+  col_icu = NULL,
+  col_keyantimicrobials = NULL,
+  episode_days = 365,
+  testcodes_exclude = NULL,
+  icu_exclude = FALSE,
+  specimen_group = NULL,
+  type = "points",
+  method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
+  ignore_I = TRUE,
+  points_threshold = 2,
+  info = interactive(),
+  include_unknown = FALSE,
+  include_untested_sir = TRUE,
+  ...
+)

-filter_first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
-  col_mo = NULL, episode_days = 365, method = c("phenotype-based",
-  "episode-based", "patient-based", "isolate-based"), ...)
+filter_first_isolate(
+  x = NULL,
+  col_date = NULL,
+  col_patient_id = NULL,
+  col_mo = NULL,
+  episode_days = 365,
+  method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
+  ...
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
--- a/man/g.test.Rd
+++ b/man/g.test.Rd
@@ -46,7 +46,7 @@ A list with class \code{"htest"} containing the following
    \code{(observed - expected) / sqrt(expected)}.}
  \item{stdres}{standardized residuals,
    \code{(observed - expected) / sqrt(V)}, where \code{V} is the
-    residual cell variance {(\if{html}{\out{<a href="#reference+chisq.test.Rd+R+3AAgresti+3A2007" class="citation">}}Agresti 2007\if{html}{\out{</a>}}, section 2.4.5)}
+    residual cell variance (Agresti, 2007, section 2.4.5
    for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).}
 }
 \description{
--- a/man/ggplot_pca.Rd
+++ b/man/ggplot_pca.Rd
@@ -17,13 +17,30 @@ As per their GPL-2 licence that demands documentation of code changes, the chang
 }
 }
 \usage{
-ggplot_pca(x, choices = 1:2, scale = 1, pc.biplot = TRUE,
-  labels = NULL, labels_textsize = 3, labels_text_placement = 1.5,
-  groups = NULL, ellipse = TRUE, ellipse_prob = 0.68,
-  ellipse_size = 0.5, ellipse_alpha = 0.5, points_size = 2,
-  points_alpha = 0.25, arrows = TRUE, arrows_colour = "darkblue",
-  arrows_size = 0.5, arrows_textsize = 3, arrows_textangled = TRUE,
-  arrows_alpha = 0.75, base_textsize = 10, ...)
+ggplot_pca(
+  x,
+  choices = 1:2,
+  scale = 1,
+  pc.biplot = TRUE,
+  labels = NULL,
+  labels_textsize = 3,
+  labels_text_placement = 1.5,
+  groups = NULL,
+  ellipse = TRUE,
+  ellipse_prob = 0.68,
+  ellipse_size = 0.5,
+  ellipse_alpha = 0.5,
+  points_size = 2,
+  points_alpha = 0.25,
+  arrows = TRUE,
+  arrows_colour = "darkblue",
+  arrows_size = 0.5,
+  arrows_textsize = 3,
+  arrows_textangled = TRUE,
+  arrows_alpha = 0.75,
+  base_textsize = 10,
+  ...
+)
 }
 \arguments{
 \item{x}{An object returned by \code{\link[=pca]{pca()}}, \code{\link[=prcomp]{prcomp()}} or \code{\link[=princomp]{princomp()}}.}
@@ -42,9 +59,8 @@ ggplot_pca(x, choices = 1:2, scale = 1, pc.biplot = TRUE,
  }

 \item{pc.biplot}{
-    If true, use what {\if{html}{\cite{}\out{<a href="#reference+biplot.princomp.Rd+R+3AGabriel+3A1971" class="citation">}}Gabriel (1971)\if{html}{\out{</a>}}} refers to as a
-    \dQuote{principal component biplot},
-    with \code{lambda = 1} and observations scaled up by sqrt(n) and
+    If true, use what Gabriel (1971) refers to as a "principal component
+    biplot", with \code{lambda = 1} and observations scaled up by sqrt(n) and
    variables scaled down by sqrt(n).  Then inner products between
    variables approximate covariances and distances between observations
    approximate Mahalanobis distance.
--- a/man/ggplot_sir.Rd
+++ b/man/ggplot_sir.Rd
@@ -5,18 +5,42 @@
 \alias{geom_sir}
 \title{AMR Plots with \code{ggplot2}}
 \usage{
-ggplot_sir(data, position = NULL, x = "antibiotic",
-  fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
-  limits = NULL, translate_ab = "name", combine_SI = TRUE,
-  minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
-  = "#3CAEA3", SDD = "#8FD6C4", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B",
-  R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5,
-  datalabels.colour = "grey15", title = NULL, subtitle = NULL,
-  caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...)
+ggplot_sir(
+  data,
+  position = NULL,
+  x = "antibiotic",
+  fill = "interpretation",
+  facet = NULL,
+  breaks = seq(0, 1, 0.1),
+  limits = NULL,
+  translate_ab = "name",
+  combine_SI = TRUE,
+  minimum = 30,
+  language = get_AMR_locale(),
+  nrow = NULL,
+  colours = c(S = "#3CAEA3", SDD = "#8FD6C4", SI = "#3CAEA3", I = "#F6D55C", IR =
+    "#ED553B", R = "#ED553B"),
+  datalabels = TRUE,
+  datalabels.size = 2.5,
+  datalabels.colour = "grey15",
+  title = NULL,
+  subtitle = NULL,
+  caption = NULL,
+  x.title = "Antimicrobial",
+  y.title = "Proportion",
+  ...
+)

-geom_sir(position = NULL, x = c("antibiotic", "interpretation"),
-  fill = "interpretation", translate_ab = "name", minimum = 30,
-  language = get_AMR_locale(), combine_SI = TRUE, ...)
+geom_sir(
+  position = NULL,
+  x = c("antibiotic", "interpretation"),
+  fill = "interpretation",
+  translate_ab = "name",
+  minimum = 30,
+  language = get_AMR_locale(),
+  combine_SI = TRUE,
+  ...
+)
 }
 \arguments{
 \item{data}{A \link{data.frame} with column(s) of class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}).}
--- a/man/guess_ab_col.Rd
+++ b/man/guess_ab_col.Rd
@@ -4,8 +4,12 @@
 \alias{guess_ab_col}
 \title{Guess Antibiotic Column}
 \usage{
-guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
-  only_sir_columns = FALSE)
+guess_ab_col(
+  x = NULL,
+  search_string = NULL,
+  verbose = FALSE,
+  only_sir_columns = FALSE
+)
 }
 \arguments{
 \item{x}{A \link{data.frame}.}
--- a/man/interpretive_rules.Rd
+++ b/man/interpretive_rules.Rd
@@ -8,21 +8,42 @@
 \alias{eucast_dosage}
 \title{Apply Interpretive Rules}
 \usage{
-interpretive_rules(x, col_mo = NULL, info = interactive(),
+interpretive_rules(
+  x,
+  col_mo = NULL,
+  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
-  "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
-  verbose = FALSE, version_breakpoints = 16,
-  version_expected_phenotypes = 1.2, version_expertrules = 3.3,
-  ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
-  custom_rules = NULL, overwrite = FALSE, add_if_missing = TRUE, ...)
+    "expected_phenotypes")),
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  verbose = FALSE,
+  version_breakpoints = 16,
+  version_expected_phenotypes = 1.2,
+  version_expertrules = 3.3,
+  ampc_cephalosporin_resistance = NA,
+  only_sir_columns = any(is.sir(x)),
+  custom_rules = NULL,
+  overwrite = FALSE,
+  add_if_missing = TRUE,
+  ...
+)

-eucast_rules(x, col_mo = NULL, info = interactive(),
+eucast_rules(
+  x,
+  col_mo = NULL,
+  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
-  "expected_phenotypes")), ...)
+    "expected_phenotypes")),
+  ...
+)

-clsi_rules(x, col_mo = NULL, info = interactive(),
+clsi_rules(
+  x,
+  col_mo = NULL,
+  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
-  "expected_phenotypes")), ...)
+    "expected_phenotypes")),
+  ...
+)

 eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 }
--- a/man/key_antimicrobials.Rd
+++ b/man/key_antimicrobials.Rd
@@ -6,19 +6,31 @@
 \alias{antimicrobials_equal}
 \title{(Key) Antimicrobials for First Weighted Isolates}
 \usage{
-key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
-  "amoxicillin/clavulanic acid", "cefuroxime", "piperacillin/tazobactam",
-  "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
-  gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
-  "ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
-  "tetracycline", "erythromycin", "oxacillin", "rifampin"),
-  antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
-  "nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)
+key_antimicrobials(
+  x = NULL,
+  col_mo = NULL,
+  universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
+    "piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
+  gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
+    "meropenem"),
+  gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
+    "oxacillin", "rifampin"),
+  antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
+    "voriconazole"),
+  only_sir_columns = any(is.sir(x)),
+  ...
+)

 all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)

-antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
-  ignore_I = TRUE, points_threshold = 2, ...)
+antimicrobials_equal(
+  y,
+  z,
+  type = c("points", "keyantimicrobials"),
+  ignore_I = TRUE,
+  points_threshold = 2,
+  ...
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically.}
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -15,11 +15,24 @@
 \alias{eucast_exceptional_phenotypes}
 \title{Determine Multidrug-Resistant Organisms (MDRO)}
 \usage{
-mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
-  carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
-  info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
-  verbose = FALSE, only_sir_columns = any(is.sir(x)),
-  infer_from_combinations = TRUE, ...)
+mdro(
+  x = NULL,
+  guideline = "CMI 2012",
+  col_mo = NULL,
+  esbl = NA,
+  carbapenemase = NA,
+  mecA = NA,
+  mecC = NA,
+  vanA = NA,
+  vanB = NA,
+  info = interactive(),
+  pct_required_classes = 0.5,
+  combine_SI = TRUE,
+  verbose = FALSE,
+  only_sir_columns = any(is.sir(x)),
+  infer_from_combinations = TRUE,
+  ...
+)

 brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)

@@ -27,11 +40,14 @@ mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)

 mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)

-mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
-  ...)
+mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)

-eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
-  verbose = FALSE, ...)
+eucast_exceptional_phenotypes(
+  x = NULL,
+  only_sir_columns = any(is.sir(x)),
+  verbose = FALSE,
+  ...
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
--- a/man/mo_property.Rd
+++ b/man/mo_property.Rd
@@ -41,119 +41,270 @@
 \alias{mo_url}
 \title{Get Properties of a Microorganism}
 \usage{
-mo_name(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_fullname(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_shortname(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_subspecies(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_species(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_genus(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_family(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_order(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_class(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_phylum(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_kingdom(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_domain(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_type(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_status(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_pathogenicity(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
-
-mo_gramstain(x, language = get_AMR_locale(),
+mo_name(
+  x,
+  language = get_AMR_locale(),
  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
-  add_morphology = FALSE, ...)
+  ...
+)

-mo_is_gram_negative(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_fullname(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_is_gram_positive(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_shortname(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_is_yeast(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_subspecies(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_species(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_oxygen_tolerance(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_genus(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_is_anaerobic(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_family(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_morphology(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_order(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_snomed(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_class(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_ref(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_phylum(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_authors(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_kingdom(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_year(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_domain(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_lpsn(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_type(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_mycobank(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_status(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_gbif(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_pathogenicity(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_rank(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_gramstain(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  add_morphology = FALSE,
+  ...
+)

-mo_taxonomy(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_is_gram_negative(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_synonyms(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_is_gram_positive(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_is_yeast(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_is_intrinsic_resistant(
+  x,
+  ab,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_oxygen_tolerance(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_is_anaerobic(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_morphology(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_snomed(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_ref(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_authors(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_year(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_lpsn(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_mycobank(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_gbif(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_rank(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_taxonomy(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
+
+mo_synonyms(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

 mo_current(x, language = get_AMR_locale(), ...)

-mo_group_members(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_group_members(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_info(x, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_info(
+  x,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_url(x, open = FALSE, language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_url(
+  x,
+  open = FALSE,
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)

-mo_property(x, property = "fullname", language = get_AMR_locale(),
-  keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
+mo_property(
+  x,
+  property = "fullname",
+  language = get_AMR_locale(),
+  keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
+  ...
+)
 }
 \arguments{
 \item{x}{Any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
--- a/man/mo_source.Rd
+++ b/man/mo_source.Rd
@@ -6,8 +6,10 @@
 \alias{get_mo_source}
 \title{User-Defined Reference Data Set for Microorganisms}
 \usage{
-set_mo_source(path, destination = getOption("AMR_mo_source",
-  "~/mo_source.rds"))
+set_mo_source(
+  path,
+  destination = getOption("AMR_mo_source", "~/mo_source.rds")
+)

 get_mo_source(destination = getOption("AMR_mo_source", "~/mo_source.rds"))
 }
--- a/man/pca.Rd
+++ b/man/pca.Rd
@@ -4,8 +4,15 @@
 \alias{pca}
 \title{Principal Component Analysis (for AMR)}
 \usage{
-pca(x, ..., retx = TRUE, center = TRUE, scale. = TRUE, tol = NULL,
-  rank. = NULL)
+pca(
+  x,
+  ...,
+  retx = TRUE,
+  center = TRUE,
+  scale. = TRUE,
+  tol = NULL,
+  rank. = NULL
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} containing \link{numeric} columns.}
--- a/man/plot.Rd
+++ b/man/plot.Rd
@@ -33,80 +33,135 @@ scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)

 scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)

-scale_x_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  = "#ED553B"), language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
+scale_x_sir(
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  ...
+)

-scale_colour_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I =
-  "#F6D55C", R = "#ED553B"), language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
+scale_colour_sir(
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  ...
+)

-scale_fill_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C",
-  R = "#ED553B"), language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
+scale_fill_sir(
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  ...
+)

-\method{plot}{mic}(x, mo = NULL, ab = NULL,
+\method{plot}{mic}(
+  x,
+  mo = NULL,
+  ab = NULL,
  guideline = getOption("AMR_guideline", "EUCAST"),
-  main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
-  = language),
-  xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
-  language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  = "#ED553B"), language = get_AMR_locale(), expand = TRUE,
+  main = deparse(substitute(x)),
+  ylab = translate_AMR("Frequency", language = language),
+  xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  ...
+)

-\method{autoplot}{mic}(object, mo = NULL, ab = NULL,
+\method{autoplot}{mic}(
+  object,
+  mo = NULL,
+  ab = NULL,
  guideline = getOption("AMR_guideline", "EUCAST"),
-  title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
-  language = language),
-  xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
-  language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  = "#ED553B"), language = get_AMR_locale(), expand = TRUE,
+  title = deparse(substitute(object)),
+  ylab = translate_AMR("Frequency", language = language),
+  xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  ...
+)

-\method{plot}{disk}(x, main = deparse(substitute(x)),
+\method{plot}{disk}(
+  x,
+  main = deparse(substitute(x)),
  ylab = translate_AMR("Frequency", language = language),
  xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
-  mo = NULL, ab = NULL, guideline = getOption("AMR_guideline", "EUCAST"),
-  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
-  "#ED553B"), language = get_AMR_locale(), expand = TRUE,
+  mo = NULL,
+  ab = NULL,
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  ...
+)

-\method{autoplot}{disk}(object, mo = NULL, ab = NULL,
-  title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
-  language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
-  language = language), guideline = getOption("AMR_guideline", "EUCAST"),
-  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
-  "#ED553B"), language = get_AMR_locale(), expand = TRUE,
+\method{autoplot}{disk}(
+  object,
+  mo = NULL,
+  ab = NULL,
+  title = deparse(substitute(object)),
+  ylab = translate_AMR("Frequency", language = language),
+  xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
-  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
+  breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+  ...
+)

-\method{plot}{sir}(x, ylab = translate_AMR("Percentage", language =
-  language), xlab = translate_AMR("Antimicrobial Interpretation", language =
-  language), main = deparse(substitute(x)), language = get_AMR_locale(),
-  ...)
-
-\method{autoplot}{sir}(object, title = deparse(substitute(object)),
+\method{plot}{sir}(
+  x,
+  ylab = translate_AMR("Percentage", language = language),
  xlab = translate_AMR("Antimicrobial Interpretation", language = language),
-  ylab = translate_AMR("Frequency", language = language), colours_SIR = c(S
-  = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
-  language = get_AMR_locale(), ...)
+  main = deparse(substitute(x)),
+  language = get_AMR_locale(),
+  ...
+)
+
+\method{autoplot}{sir}(
+  object,
+  title = deparse(substitute(object)),
+  xlab = translate_AMR("Antimicrobial Interpretation", language = language),
+  ylab = translate_AMR("Frequency", language = language),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
+  language = get_AMR_locale(),
+  ...
+)

 facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)

-scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
-  limits = c(0, NA))
+scale_y_percent(
+  breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
+  limits = c(0, NA)
+)

-scale_sir_colours(..., aesthetics, colours_SIR = c(S = "#3CAEA3", SDD =
-  "#8FD6C4", I = "#F6D55C", R = "#ED553B"))
+scale_sir_colours(
+  ...,
+  aesthetics,
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B")
+)

 theme_sir()

-labels_sir_count(position = NULL, x = "antibiotic",
-  translate_ab = "name", minimum = 30, language = get_AMR_locale(),
-  combine_SI = TRUE, datalabels.size = 3, datalabels.colour = "grey15")
+labels_sir_count(
+  position = NULL,
+  x = "antibiotic",
+  translate_ab = "name",
+  minimum = 30,
+  language = get_AMR_locale(),
+  combine_SI = TRUE,
+  datalabels.size = 3,
+  datalabels.colour = "grey15"
+)
 }
 \arguments{
 \item{keep_operators}{A \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
--- a/man/proportion.Rd
+++ b/man/proportion.Rd
@@ -15,40 +15,62 @@
 \alias{sir_df}
 \title{Calculate Antimicrobial Resistance}
 \usage{
-resistance(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
-  "EUCAST"))
+resistance(
+  ...,
+  minimum = 30,
+  as_percent = FALSE,
+  only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST")
+)

-susceptibility(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
-  "EUCAST"))
+susceptibility(
+  ...,
+  minimum = 30,
+  as_percent = FALSE,
+  only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST")
+)

-sir_confidence_interval(..., ab_result = "R", minimum = 30,
-  as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
-  side = "both", collapse = FALSE)
+sir_confidence_interval(
+  ...,
+  ab_result = "R",
+  minimum = 30,
+  as_percent = FALSE,
+  only_all_tested = FALSE,
+  confidence_level = 0.95,
+  side = "both",
+  collapse = FALSE
+)

-proportion_R(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)

-proportion_IR(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)

-proportion_I(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)

-proportion_SI(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)

-proportion_S(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)

-proportion_df(data, translate_ab = "name", language = get_AMR_locale(),
-  minimum = 30, as_percent = FALSE, combine_SI = TRUE,
-  confidence_level = 0.95)
+proportion_df(
+  data,
+  translate_ab = "name",
+  language = get_AMR_locale(),
+  minimum = 30,
+  as_percent = FALSE,
+  combine_SI = TRUE,
+  confidence_level = 0.95
+)

-sir_df(data, translate_ab = "name", language = get_AMR_locale(),
-  minimum = 30, as_percent = FALSE, combine_SI = TRUE,
-  confidence_level = 0.95)
+sir_df(
+  data,
+  translate_ab = "name",
+  language = get_AMR_locale(),
+  minimum = 30,
+  as_percent = FALSE,
+  combine_SI = TRUE,
+  confidence_level = 0.95
+)
 }
 \arguments{
 \item{...}{One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See \emph{Examples}.}
--- a/man/random.Rd
+++ b/man/random.Rd
@@ -7,11 +7,23 @@
 \alias{random_sir}
 \title{Random MIC Values/Disk Zones/SIR Generation}
 \usage{
-random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
-  severity = 1, ...)
+random_mic(
+  size = NULL,
+  mo = NULL,
+  ab = NULL,
+  skew = "right",
+  severity = 1,
+  ...
+)

-random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
-  severity = 1, ...)
+random_disk(
+  size = NULL,
+  mo = NULL,
+  ab = NULL,
+  skew = "left",
+  severity = 1,
+  ...
+)

 random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
 }
--- a/man/resistance_predict.Rd
+++ b/man/resistance_predict.Rd
@@ -8,22 +8,51 @@
 \alias{autoplot.resistance_predict}
 \title{Predict Antimicrobial Resistance}
 \usage{
-resistance_predict(x, col_ab, col_date = NULL, year_min = NULL,
-  year_max = NULL, year_every = 1, minimum = 30, model = NULL,
-  I_as_S = TRUE, preserve_measurements = TRUE, info = interactive(), ...)
+resistance_predict(
+  x,
+  col_ab,
+  col_date = NULL,
+  year_min = NULL,
+  year_max = NULL,
+  year_every = 1,
+  minimum = 30,
+  model = NULL,
+  I_as_S = TRUE,
+  preserve_measurements = TRUE,
+  info = interactive(),
+  ...
+)

-sir_predict(x, col_ab, col_date = NULL, year_min = NULL, year_max = NULL,
-  year_every = 1, minimum = 30, model = NULL, I_as_S = TRUE,
-  preserve_measurements = TRUE, info = interactive(), ...)
+sir_predict(
+  x,
+  col_ab,
+  col_date = NULL,
+  year_min = NULL,
+  year_max = NULL,
+  year_every = 1,
+  minimum = 30,
+  model = NULL,
+  I_as_S = TRUE,
+  preserve_measurements = TRUE,
+  info = interactive(),
+  ...
+)

-\method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of",
-  x_name), ...)
+\method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...)

-ggplot_sir_predict(x, main = paste("Resistance Prediction of", x_name),
-  ribbon = TRUE, ...)
+ggplot_sir_predict(
+  x,
+  main = paste("Resistance Prediction of", x_name),
+  ribbon = TRUE,
+  ...
+)

-\method{autoplot}{resistance_predict}(object,
-  main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)
+\method{autoplot}{resistance_predict}(
+  object,
+  main = paste("Resistance Prediction of", x_name),
+  ribbon = TRUE,
+  ...
+)
 }
 \arguments{
 \item{x}{A \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
--- a/man/top_n_microorganisms.Rd
+++ b/man/top_n_microorganisms.Rd
@@ -4,8 +4,14 @@
 \alias{top_n_microorganisms}
 \title{Filter Top \emph{n} Microorganisms}
 \usage{
-top_n_microorganisms(x, n, property = "species", n_for_each = NULL,
-  col_mo = NULL, ...)
+top_n_microorganisms(
+  x,
+  n,
+  property = "species",
+  n_for_each = NULL,
+  col_mo = NULL,
+  ...
+)
 }
 \arguments{
 \item{x}{A data frame containing microbial data.}