c(aminoglycosides(), "AMP", "AMC")
- mo_transform
-a character to transform microorganism input - must be "name", "shortname" (default), "gramstain", or one of the column names of the microorganisms data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be NULL to not transform the input or NA to consider all microorganisms 'unknown'.
A character to transform microorganism input - must be "name", "shortname" (default), "gramstain", or one of the column names of the microorganisms data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be NULL to not transform the input or NA to consider all microorganisms 'unknown'.
- ab_transform
-a character to transform antimicrobial input - must be one of the column names of the antimicrobials data set (defaults to "name"): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be NULL to not transform the input.
A character to transform antimicrobial input - must be one of the column names of the antimicrobials data set (defaults to "name"): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be NULL to not transform the input.
- syndromic_group
-a column name of x, or values calculated to split rows of x, e.g. by using ifelse() or case_when(). See Examples.
A column name of x, or values calculated to split rows of x, e.g. by using ifelse() or case_when(). See Examples.
- add_total_n
-a logical to indicate whether n_tested available numbers per pathogen should be added to the table (default is TRUE). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for E. coli 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when wisca = TRUE; in that case, use retrieve_wisca_parameters() to get the parameters used for WISCA.
A logical to indicate whether n_tested available numbers per pathogen should be added to the table (default is TRUE). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for E. coli 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when wisca = TRUE; in that case, use retrieve_wisca_parameters() to get the parameters used for WISCA.
- only_all_tested
@@ -142,35 +142,35 @@ Adhering to previously described approaches (see Source) and especially the Baye
- digits
-number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise
Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise
- formatting_type
-numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See Details > Formatting Type for a list of options.
Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See Details > Formatting Type for a list of options.
- col_mo
-column name of the names or codes of the microorganisms (see as.mo()) - the default is the first column of class mo. Values will be coerced using as.mo().
Column name of the names or codes of the microorganisms (see as.mo()) - the default is the first column of class mo. Values will be coerced using as.mo().
- language
-language to translate text, which defaults to the system language (see get_AMR_locale())
Language to translate text, which defaults to the system language (see get_AMR_locale())
- minimum
-the minimum allowed number of available (tested) isolates. Any isolate count lower than minimum will return NA with a warning. The default number of 30 isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
The minimum allowed number of available (tested) isolates. Any isolate count lower than minimum will return NA with a warning. The default number of 30 isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
- combine_SI
-a logical to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is TRUE)
A logical to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is TRUE)
- sep
-a separating character for antimicrobial columns in combination antibiograms
A separating character for antimicrobial columns in combination antibiograms
- wisca
-a logical to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is FALSE). This will use a Bayesian decision model to estimate regimen coverage probabilities using Monte Carlo simulations. Set simulations, conf_interval, and interval_side to adjust.
A logical to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is FALSE). This will use a Bayesian decision model to estimate regimen coverage probabilities using Monte Carlo simulations. Set simulations, conf_interval, and interval_side to adjust.
- simulations
@@ -178,35 +178,35 @@ Adhering to previously described approaches (see Source) and especially the Baye
- conf_interval
-a numerical value to set confidence interval (default is 0.95)
A numerical value to set confidence interval (default is 0.95)
- interval_side
-the side of the confidence interval, either "two-tailed" (default), "left" or "right"
The side of the confidence interval, either "two-tailed" (default), "left" or "right"
- info
-a logical to indicate info should be printed - the default is TRUE only in interactive mode
A logical to indicate info should be printed - the default is TRUE only in interactive mode
- ...
-when used in R Markdown or Quarto: arguments passed on to knitr::kable() (otherwise, has no use)
When used in R Markdown or Quarto: arguments passed on to knitr::kable() (otherwise, has no use)
- wisca_model
-the outcome of wisca() or antibiogram(..., wisca = TRUE)
The outcome of wisca() or antibiogram(..., wisca = TRUE)
- object
-an antibiogram() object
An antibiogram() object
- italicise
-a logical to indicate whether the microorganism names in the knitr table should be made italic, using italicise_taxonomy().
A logical to indicate whether the microorganism names in the knitr table should be made italic, using italicise_taxonomy().
- na
-character to use for showing NA values
Character to use for showing NA values