P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-03-21 18:32:40 +01:00
Code Releases Activity

(v2.1.1.9081) HUGE microorganisms update for fungi!

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
DESCRIPTION
View File

@@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9080
Date: 2024-09-24
Version: 2.1.1.9081
Date: 2024-09-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
@@ -10,6 +10,7 @@ Authors@R: c(
person(family = "Souverein", c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
person(family = "Hassing", c("Erwin", "E.", "A."), role = c("aut", "ctb")),
person(family = "Albers", c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
person(family = "Bolton", c("Larisse"), role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
person(family = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
person(family = "Fonville", c("Judith", "M."), role = "ctb"),
person(family = "Friedrich", c("Alex", "W."), role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),

37
NEWS.md
View File

@@ -1,4 +1,4 @@
# AMR 2.1.1.9080
# AMR 2.1.1.9081
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
@@ -9,28 +9,27 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
## New
* One Health implementation
* Function `as.sir()` now has extensive support for animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* **One Health implementation**
* Function `as.sir()` now has extensive support for veterinary breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when `guideline` is set to CLSI)
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
* Clinical breakpoints
* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disks diffusion interpretations.
* **Major update to fungal taxonomy and tools for mycologists**
* MycoBank has now been integrated as the primary taxonomic source for fungi. The `microorganisms` data set has been enriched with new columns (`mycobank`, `mycobank_parent`, and `mycobank_renamed_to`) that provide detailed information for fungal species.
* A remarkable addition of over 20,000 new fungal records
* New function `mo_mycobank()` to retrieve the MycoBank record number, analogous to existing functions such as `mo_lpsn()` and `mo_gbif()`.
* The `as.mo()` function and all `mo_*()` functions now includes an `only_fungi` argument, allowing users to restrict results solely to fungal species. This ensures fungi are prioritised over bacteria during microorganism identification. This can also be set globally with the new `AMR_only_fungi` option.
* Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.
* **Updated clinical breakpoints**
* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
* MIC plotting and transforming
* **New forms for MIC plotting and transforming**
* New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* New function `rescale_mic()`, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
* Microbiological taxonomy (`microorganisms` data set) updated to June 2024, with some exciting new features:
* Added MycoBank as the primary taxonomic source for fungi
* The `microorganisms` data set now contains additional columns `mycobank`, `mycobank_parent`, and `mycobank_renamed_to`
* New function `mo_mycobank()` to get the MycoBank record number, analogous to existing functions `mo_lpsn()` and `mo_gbif()`
* We've welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi
* Improved support for mycologists:
* The `as.mo()` function now includes a new argument, `only_fungi` (TRUE/FALSE), which limits the results to fungi only. Normally, bacteria are often prioritised by the algorithm, but setting `only_fungi = TRUE` ensures only fungi are returned.
* You can also set this globally using the new R option `AMR_only_fungi`, e.g., `options(AMR_only_fungi = TRUE)`.
* Other
* New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that are in that group.
* New function `rescale_mic()`, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.
* **Other**
* New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that belong to that group.
## Changed
* SIR interpretation
@@ -68,9 +67,9 @@ This package now supports not only tools for AMR data analysis in clinical setti
## Other
* Greatly updated and expanded documentation
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
* Stopped support for SAS (`.xpt`) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
# Older Versions
## Older Versions
This changelog only contains changes from AMR v3.0 (October 2024) and later.

2
R/aa_amr-package.R
View File

@@ -40,7 +40,7 @@
#'
#' The `AMR` package is available in `r vector_and(vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
#' @section Reference Data Publicly Available:
#' All data sets in this `AMR` package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' All data sets in this `AMR` package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @source
#' To cite AMR in publications use:
#'

2
R/aa_helper_functions.R
View File

@@ -1563,6 +1563,8 @@ add_MO_lookup_to_AMR_env <- function() {
# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
MO_lookup$genus_lower <- tolower(MO_lookup$genus)
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
MO_lookup$species_first <- tolower(substr(MO_lookup$species, 1, 1)) # tolower for groups (Streptococcus, Salmonella)
MO_lookup$subspecies_first <- tolower(substr(MO_lookup$subspecies, 1, 1)) # tolower for Salmonella serovars

2
R/antibiogram.R
View File

@@ -42,7 +42,7 @@
#' @param 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()].
#' @param language language to translate text, which defaults to the system language (see [get_AMR_locale()])
#' @param 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*.
#' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (default is `TRUE`)
#' @param 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`)
#' @param sep a separating character for antibiotic columns in combination antibiograms
#' @param info a [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode
#' @param object an [antibiogram()] object

2
R/bug_drug_combinations.R
View File

@@ -31,7 +31,7 @@
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
#' @inheritParams eucast_rules
#' @param combine_SI a [logical] to indicate whether values S and I should be summed, so resistance will be based on only R - the default is `TRUE`
#' @param combine_SI a [logical] to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is `TRUE`
#' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the `mo` column to transform the microorganism codes - the default is [mo_shortname()]

20
R/data.R
View File

@@ -64,7 +64,7 @@
#' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
#'
#' ### Direct download
#' Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @source
#'
#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://atcddd.fhi.no/atc_ddd_index/>
@@ -136,7 +136,7 @@
#' The syntax used to transform the original data to a cleansed \R format, can be [found here](https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R).
#'
#' ### Direct download
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @source
#' Taxonomic entries were imported in this order of importance:
#' 1. `r TAXONOMY_VERSION$LPSN$name`:\cr\cr
@@ -171,7 +171,7 @@
#' - `code`\cr Commonly used code of a microorganism. ***This is a unique identifier.***
#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @seealso [as.mo()] [microorganisms]
#' @examples
#' microorganisms.codes
@@ -195,7 +195,7 @@
#' - `mo_group_name`\cr Name of the species group / microbiological complex, as retrieved with [mo_name()]
#' - `mo_name`\cr Name of the microorganism belonging in the species group / microbiological complex, as retrieved with [mo_name()]
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @seealso [as.mo()] [microorganisms]
#' @examples
#' microorganisms.groups
@@ -216,7 +216,7 @@
#' - `mo`\cr ID of microorganism created with [as.mo()], see also the [microorganisms] data set
#' - `PEN:RIF`\cr `r sum(vapply(FUN.VALUE = logical(1), example_isolates, is.sir))` different antibiotics with class [`sir`] (see [as.sir()]); these column names occur in the [antibiotics] data set and can be translated with [set_ab_names()] or [ab_name()]
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @examples
#' example_isolates
"example_isolates"
@@ -231,7 +231,7 @@
#' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
#' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.sir()]
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @examples
#' example_isolates_unclean
"example_isolates_unclean"
@@ -267,7 +267,7 @@
#' - `Date of data entry`\cr [Date] this data was entered in WHONET
#' - `AMP_ND10:CIP_EE`\cr `r sum(vapply(FUN.VALUE = logical(1), WHONET, is.sir))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.sir()].
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @examples
#' WHONET
"WHONET"
@@ -310,7 +310,7 @@
#' The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this `AMR` package.
#'
#' ### Download
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw). They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw). They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
#'
#' **NOTE:** this `AMR` package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the [microorganisms.groups] data set). It is important that this is considered when using the breakpoints for own use.
#' @seealso [intrinsic_resistant]
@@ -328,7 +328,7 @@
#' This data set is based on `r format_eucast_version_nr(3.3)`.
#'
#' ### Direct download
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#'
#' They **allow for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.
#' @examples
@@ -349,7 +349,7 @@
#' - `original_txt`\cr Original text in the PDF file of EUCAST
#' - `eucast_version`\cr Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either `r vector_or(dosage$eucast_version, quotes = FALSE, sort = TRUE, reverse = TRUE)`
#' @details
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @examples
#' dosage
"dosage"

4
R/mean_amr_distance.R
View File

@@ -32,7 +32,7 @@
#' Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.
#' @param x a vector of class [sir][as.sir()], [mic][as.mic()] or [disk][as.disk()], or a [data.frame] containing columns of any of these classes
#' @param ... variables to select (supports [tidyselect language][tidyselect::language] such as `column1:column4` and `where(is.mic)`, and can thus also be [antibiotic selectors][ab_selector()]
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is `TRUE`
#' @param combine_SI a [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is `TRUE`
#' @details The mean AMR distance is effectively [the Z-score](https://en.wikipedia.org/wiki/Standard_score); a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.
#'
#' MIC values (see [as.mic()]) are transformed with [log2()] first; their distance is thus calculated as `(log2(x) - mean(log2(x))) / sd(log2(x))`.
@@ -118,7 +118,7 @@ mean_amr_distance.disk <- function(x, ...) {
mean_amr_distance.sir <- function(x, ..., combine_SI = TRUE) {
meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1)
if (isTRUE(combine_SI)) {
x[x == "I"] <- "S"
x[x %in% c("I", "SDD")] <- "S"
}
mean_amr_distance(as.double(x))
}

15
R/mo.R
View File

@@ -315,12 +315,15 @@ as.mo <- function(x,
# take out the parts, split by space
x_parts <- strsplit(gsub("-", " ", x_out, fixed = TRUE), " ", fixed = TRUE)[[1]]
# do a pre-match on first character (and if it contains a space, first chars of first two terms)
if (length(x_parts) %in% c(2, 3)) {
# for genus + species + subspecies
if (paste(x_parts[1:2], collapse = " ") %in% MO_lookup_current$fullname_lower) {
filtr <- which(MO_lookup_current$fullname_lower %like% paste(x_parts[1:2], collapse = " "))
} else if (x_parts[1] %in% MO_lookup_current$genus_lower && !paste(x_parts[1:2], collapse = " ") %in% MO_lookup_current$fullname_lower) {
# for a known genus, but unknown (sub)species
filtr <- which(MO_lookup_current$genus_lower == x_parts[1])
minimum_matching_score <- 0.05
} else if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
filtr <- which(MO_lookup_current$full_first == substr(x_parts[1], 1, 1) &
(MO_lookup_current$species_first == substr(x_parts[2], 1, 1) |
@@ -953,11 +956,15 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
),
collapse = "\n"
),
# Add note if result was coerced to accepted taxonomic name
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
paste0(
strrep(" ", nchar(x[i, ]$original_input) + 6),
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL)
ifelse(x[i, ]$keep_synonyms == FALSE,
# Add note if result was coerced to accepted taxonomic name
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
# Or add note if result is currently another taxonomic name
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
)
),
""
),

2
R/mo_matching_score.R
View File

@@ -62,7 +62,7 @@
#' - Any genus present in the **established** list also has `prevalence = 1.0` in the [microorganisms] data set;
#' - Any other genus present in the **putative** list has `prevalence = 1.25` in the [microorganisms] data set;
#' - Any other species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 1.5` in the [microorganisms] data set;
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.25` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`;
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.25` in the [microorganisms] data set: `r vector_or(MO_RELEVANT_GENERA, quotes = "*")`;
#' - All other records have `prevalence = 2.0` in the [microorganisms] data set.
#'
#' When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.

3
R/mo_property.R
View File

@@ -872,7 +872,8 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
info <- lapply(x, function(y) {
c(
list(mo = as.character(x)),
list(mo = as.character(y),
rank = mo_rank(y, language = language, keep_synonyms = keep_synonyms)),
mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms),
list(
status = mo_status(y, language = language, keep_synonyms = keep_synonyms),

4
R/proportion.R
View File

@@ -39,8 +39,8 @@
#' @param data a [data.frame] containing columns with class [`sir`] (see [as.sir()])
#' @param translate_ab a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]
#' @inheritParams ab_property
#' @param combine_SI a [logical] 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 `TRUE`
#' @param ab_result antibiotic results to test against, must be one or more values of "S", "I", or "R"
#' @param combine_SI a [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is `TRUE`
#' @param ab_result antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R"
#' @param confidence_level the confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using [binom.test()], i.e., the Clopper-Pearson method.
#' @param side the side of the confidence interval to return. The default is `"both"` for a length 2 vector, but can also be (abbreviated as) `"min"`/`"left"`/`"lower"`/`"less"` or `"max"`/`"right"`/`"higher"`/`"greater"`.
#' @param collapse a [logical] to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing

BIN
R/sysdata.rda
View File

Binary file not shown.

2
_pkgdown.yml
View File

@@ -92,7 +92,7 @@ navbar:
- text: "Work with WHONET Data"
icon: "fa-globe-americas"
href: "articles/WHONET.html"
# - text: "Import Data From SPSS/SAS/Stata"
# - text: "Import Data From SPSS/Stata"
# icon: "fa-file-upload"
# href: "articles/SPSS.html"
- text: "Apply Eucast Rules"

52
data-raw/_pre_commit_checks.R
View File

@@ -158,10 +158,11 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
"group a", "group b", "group c", "group g"
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_PREVALENT_GENERA <- c(
pre_commit_lst$MO_RELEVANT_GENERA <- c(
"Absidia",
"Acanthamoeba",
"Acremonium",
"Actinomucor",
"Aedes",
"Alternaria",
"Amoeba",
@@ -175,20 +176,31 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Aureobasidium",
"Basidiobolus",
"Beauveria",
"Bipolaris",
"Blastobotrys",
"Blastocystis",
"Blastomyces",
"Candida",
"Capillaria",
"Chaetomium",
"Chilomastix",
"Chrysonilia",
"Chrysosporium",
"Cladophialophora",
"Cladosporium",
"Clavispora",
"Coccidioides",
"Cokeromyces",
"Conidiobolus",
"Coniochaeta",
"Contracaecum",
"Cordylobia",
"Cryptococcus",
"Cryptosporidium",
"Cunninghamella",
"Curvularia",
"Cyberlindnera",
"Debaryozyma",
"Demodex",
"Dermatobia",
"Dientamoeba",
@@ -197,6 +209,8 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Echinostoma",
"Entamoeba",
"Enterobius",
"Epidermophyton",
"Exidia",
"Exophiala",
"Exserohilum",
"Fasciola",
@@ -204,6 +218,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Fusarium",
"Geotrichum",
"Giardia",
"Graphium",
"Haloarcula",
"Halobacterium",
"Halococcus",
@@ -212,16 +227,19 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Heterophyes",
"Histomonas",
"Histoplasma",
"Hortaea",
"Hymenolepis",
"Hypomyces",
"Hysterothylacium",
"Kloeckera",
"Kluyveromyces",
"Kodamaea",
"Lacazia",
"Leishmania",
"Lichtheimia",
"Lodderomyces",
"Lomentospora",
"Madurella",
"Malassezia",
"Malbranchea",
"Metagonimus",
@@ -232,6 +250,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Mortierella",
"Mucor",
"Mycocentrospora",
"Nannizzia",
"Necator",
"Nectria",
"Ochroconis",
@@ -239,8 +258,12 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Oidiodendron",
"Opisthorchis",
"Paecilomyces",
"Paracoccidioides",
"Pediculus",
"Penicillium",
"Phaeoacremonium",
"Phaeomoniella",
"Phialophora",
"Phlebotomus",
"Phoma",
"Pichia",
@@ -252,24 +275,34 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Pseudoscopulariopsis",
"Pseudoterranova",
"Pulex",
"Purpureocillium",
"Quambalaria",
"Rhinocladiella",
"Rhizomucor",
"Rhizopus",
"Rhodotorula",
"Saccharomyces",
"Saksenaea",
"Saprochaete",
"Sarcoptes",
"Scedosporium",
"Schistosoma",
"Schizosaccharomyces",
"Scolecobasidium",
"Scopulariopsis",
"Scytalidium",
"Spirometra",
"Sporobolomyces",
"Sporopachydermia",
"Sporothrix",
"Sporotrichum",
"Stachybotrys",
"Strongyloides",
"Syncephalastrum",
"Syngamus",
"Taenia",
"Talaromyces",
"Teleomorph",
"Toxocara",
"Trichinella",
"Trichobilharzia",
@@ -283,8 +316,15 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Trombicula",
"Trypanosoma",
"Tunga",
"Ulocladium",
"Ustilago",
"Verticillium",
"Wuchereria"
"Wallemia",
"Wangiella",
"Wickerhamomyces",
"Wuchereria",
"Yarrowia",
"Zygosaccharomyces"
)
# antibiotic groups
@@ -450,7 +490,6 @@ if (changed_md5(clin_break)) {
write_md5(clin_break)
try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
@@ -466,7 +505,6 @@ if (changed_md5(microorganisms)) {
mo <- microorganisms
mo$snomed <- max_50_snomed
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
try(haven::write_xpt(mo, "data-raw/microorganisms.xpt"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -481,7 +519,6 @@ if (changed_md5(microorganisms.codes)) {
write_md5(microorganisms.codes)
try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
@@ -494,7 +531,6 @@ if (changed_md5(microorganisms.groups)) {
write_md5(microorganisms.groups)
try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
@@ -507,7 +543,6 @@ if (changed_md5(ab)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
write_md5(ab)
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(ab, "data-raw/antibiotics.xpt"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -522,7 +557,6 @@ if (changed_md5(av)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
write_md5(av)
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(av, "data-raw/antivirals.xpt"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -543,7 +577,6 @@ if (changed_md5(intrinsicR)) {
write_md5(intrinsicR)
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), silent = TRUE)
try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
@@ -556,7 +589,6 @@ if (changed_md5(dosage)) {
write_md5(dosage)
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(dosage, "data-raw/dosage.xpt"), silent = TRUE)
try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)

2
data-raw/ab.md5
View File

@@ -1 +1 @@
5ad894790ad048110f8eb9207b89501f
6f6b49606c2c51f8344fbb9e186a3ad3

BIN
data-raw/antibiotics.dta
View File

Binary file not shown.

BIN
data-raw/antibiotics.feather
View File

Binary file not shown.

BIN
data-raw/antibiotics.parquet
View File

Binary file not shown.

BIN
data-raw/antibiotics.rds
View File

Binary file not shown.

BIN
data-raw/antibiotics.sav
View File

Binary file not shown.

2
data-raw/antibiotics.txt
View File

@@ -76,7 +76,7 @@
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "NA" "" "cefetamet pivoxyl,globocef" ""
"CCL" 71719688 "Cefetecol" "Cephalosporins (4th gen.)" "NA" "cefcatacol" "cefetecol,cefetecol anhydrous" ""
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "NA" "" "cefetrizole,cefetrizolum" ""
"FDC" 77843966 "Cefiderocol" "Other antibacterials" "J01DI04" "" "cefiderocol" 6 "g" "95767-0,99280-0,99503-5"
"FDC" 77843966 "Cefiderocol" "Cephalosporins (unclassified gen.)" "J01DI04" "" "cefiderocol" 6 "g" "95767-0,99280-0,99503-5"
"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "J01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfe,cfix,cfxm,dcfm,fix,ix" "anhydrous cefixime,cefixim,cefixima,cefixime,cefixime anhydrous,cefixime hydrate,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oroken,suprax,tricef,unixime" 0.4 "g" "16567-0,18880-5,25236-1,35766-5,79-4,80-2,81-0,82-8"
"CEO" "Cefixime/ornidazole" "Other antibacterials" "J01RA15" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "J01DD05,S01AA31,S02AA18" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "bestron,cefmax,cefmenoxima,cefmenoxime,cefmenoximum" 2 "g" "32375-8,54174-8,54203-5,55641-5"

BIN
data-raw/antibiotics.xlsx
View File

Binary file not shown.

BIN
data-raw/antibiotics.xpt
View File

Binary file not shown.

BIN
data-raw/antivirals.xpt
View File

Binary file not shown.

2
data-raw/clin_break.md5
View File

@@ -1 +1 @@
c79b6e112dc3ab478b990f0689b685b6
10fd88018ca098a76a8b1e9c86d2e40c

BIN
data-raw/clinical_breakpoints.dta
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.feather
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.parquet
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.rds
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.sav
View File

Binary file not shown.

212
data-raw/clinical_breakpoints.txt
View File

@@ -1845,16 +1845,16 @@
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "RZF" "Antifungal ECOFFs" 0.016 0.016 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "Antifungal ECOFFs" 4 4 FALSE FALSE
@@ -3399,8 +3399,8 @@
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 4 4 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -4833,8 +4833,8 @@
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 4 4 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -7019,14 +7019,14 @@
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "ECOFF" 4 4 FALSE FALSE
@@ -9139,14 +9139,14 @@
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "ECOFF" 4 4 FALSE FALSE
@@ -9989,8 +9989,8 @@
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -10805,8 +10805,8 @@
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -11611,8 +11611,8 @@
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -12356,8 +12356,8 @@
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -13074,8 +13074,8 @@
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -13791,8 +13791,8 @@
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -14491,8 +14491,8 @@
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_ALBC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_GLBR" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_PRPS" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_PRPS" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE
@@ -17856,20 +17856,20 @@
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_GLBR" 2 "RZF" "M27 Table 1" 0.5 4096 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -20022,20 +20022,20 @@
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "RZF" "M27 Table 1" 0.5 4096 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -22001,19 +22001,19 @@
"CLSI 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -23602,13 +23602,13 @@
"CLSI 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE
@@ -25115,13 +25115,13 @@
"CLSI 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE
@@ -26487,13 +26487,13 @@
"CLSI 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE

BIN
data-raw/clinical_breakpoints.xlsx
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.xpt
View File

Binary file not shown.

BIN
data-raw/dosage.xpt
View File

Binary file not shown.

2
data-raw/intrinsicR.md5
View File

@@ -1 +1 @@
e8c57a559ad846e72c700c88929e880d
930e15623071edb2196fcf8b2a259380

BIN
data-raw/intrinsic_resistant.dta
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.feather
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.parquet
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.rds
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.sav
View File

Binary file not shown.

62861
data-raw/intrinsic_resistant.txt
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/intrinsic_resistant.xlsx
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.xpt
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.feather
View File

Binary file not shown.

2
data-raw/microorganisms.codes.md5
View File

@@ -1 +1 @@
c9ba186023a0003c8153215646983621
cbf15fce0784e20b87aaa33b88b97f3f

BIN
data-raw/microorganisms.codes.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.sav
View File

Binary file not shown.

120
data-raw/microorganisms.codes.txt
View File

@@ -341,7 +341,7 @@
"7001" "F_CANDD_ALBC"
"7002" "F_CANDD_TRPC"
"7003" "F_CANDD_GLBR"
"7005" "F_CANDD_KRUS"
"7005" "F_PICHI_KDRV"
"7006" "F_MYRZY_GLLR"
"7007" "F_CANDD_DBLN"
"7110" "F_CRYPT"
@@ -393,7 +393,7 @@
"7531" "B_CTRMN_SLNR"
"7540" "F_HSTPL"
"7541" "F_HSTPL_CPSL"
"7550" "F_BLSTM"
"7550" "F_CSPRM"
"7551" "B_BLSTM_DLFL"
"7560" "B_PSYCH_CCCD"
"7561" "B_PHYTB"
@@ -429,8 +429,8 @@
"9051" "B_BFDBC_COLB"
"9070" "P_THMNS"
"9071" "P_THMNS_VAG"
"9080" "P_TXPL"
"9081" "P_TXPL_GOND"
"9080" "C_TXPL"
"9081" "C_TXPL_GOND"
"9801" "B_ACHLP"
"9802" "B_ACDMNC"
"9803" "B_ACDVR"
@@ -1014,7 +1014,7 @@
"BARHEN" "B_BRTNL_HNSL"
"BARSPP" "B_BRTNL"
"BAS" "F_BSDBL"
"BAU" "F_CRVLR_ASTR"
"BAU" "F_BPLRS_ASTR"
"BAV" "B_BRDTL_AVIM"
"BAY" "B_EXGBC_ACTY"
"BBA" "B_BRTNL_BCLL"
@@ -1099,7 +1099,7 @@
"BHA" "F_CRVLR_HWNS"
"BHE" "B_BRTNL_HNSL"
"BHM" "B_BRDTL_HLMS"
"BHO" "F_BLSTC_HMNS"
"BHO" "C_BLSTC_HMNS"
"BHR" "B_BORRL_HRMS"
"BHZ" "B_BRDTL_HINZ"
"BIF" "B_BFDBC"
@@ -1118,14 +1118,14 @@
"BILSPP" "B_BLPHL"
"BILWAD" "B_BLPHL_WDSW"
"BIN" "B_BFDBC_LNGM_INFN"
"BLA" "F_BLSTM"
"BLAHOM" "F_BLSTC_HMNS"
"BLASPP" "F_BLSTC"
"BLA" "F_CSPRM"
"BLAHOM" "C_BLSTC_HMNS"
"BLASPP" "C_BLSTC"
"BLE" "B_PRPHYR_LEVI"
"BLI" "B_BCLLS_LCHN"
"BLN" "B_LDRBR_LENT"
"BLO" "B_BFDBC_LNGM"
"BLS" "F_BLSTC"
"BLS" "C_BLSTC"
"BLT" "B_BRVBC_LTRS"
"BLTSPP" "B_BCLLS"
"BMA" "B_BRKHL_MALL"
@@ -1223,7 +1223,7 @@
"BSF" "B_STRPT_GRPF"
"BSG" "B_STRPT_GRPG"
"BSH" "B_LYSNB_SPHR"
"BSI" "F_CRVLR_SPCF"
"BSI" "F_BPLRS_SPCF"
"BSL" "B_BCLLS_SBTL"
"BSP" "B_ODRBC_SPLN"
"BSR" "B_GBCLL_STRT"
@@ -1340,13 +1340,13 @@
"CANFIR" "F_CANDD"
"CANFRE" "F_CANDD_FRYS"
"CANGLA" "F_CANDD_GLBR"
"CANGUI" "F_CANDD_GLLR"
"CANGUI" "F_MYRZY_GLLR"
"CANINC" "F_CANDD_INCN"
"CANINT" "F_CANDD_INTR"
"CANKEF" "F_CANDD_KFYR"
"CANKRU" "F_CANDD_KRUS"
"CANKRU" "F_PICHI_KDRV"
"CANLAB" "F_CANDD"
"CANLAM" "F_CANDD_LMBC"
"CANLAM" "F_PICHI_FRMN"
"CANMAR" "F_CANDD_MARS"
"CANMEL" "F_CANDD_MLBS"
"CANMEM" "F_CANDD_MMBR"
@@ -1385,7 +1385,7 @@
"CATHON" "B_CHRST_HNGK"
"CATSPP" "B_CHRST"
"CAU" "B_CTRDM_SRDN"
"CAV" "B_ANRCL_LRCM"
"CAV" "B_ANRCL_AMNV"
"CAX" "F_CANDD_ALBC-C"
"CAY" "B_CRYPH"
"CAYSPP" "B_CRYPH"
@@ -1459,14 +1459,14 @@
"CFA" "B_CTRBC_FRMR"
"CFE" "B_CMPYL_FETS"
"CFL" "B_CHLMY_FELS"
"CFN" "F_CANDD_AFRC"
"CFN" "F_CANDD_ALBC"
"CFR" "B_CTRBC_FRND"
"CFV" "B_CMPYL_FETS_VNRL"
"CFX" "B_CTRDM_FLLX"
"CGA" "F_CRYPT"
"CGASPP" "F_CRYPT"
"CGC" "B_TRRSP_GLYC"
"CGH" "B_PNCLS_GHONI"
"CGH" "B_PRCLS_GHON"
"CGI" "B_CPNCY_GNGV"
"CGL" "F_CANDD_GLBR"
"CGM" "B_CRYNB_GLTM"
@@ -1550,7 +1550,7 @@
"CHDSPP" "B_CHLMY"
"CHE" "B_CTRDM_HMLY"
"CHF" "B_TSSRL_PRCT"
"CHI" "B_HTHWY_HSTLY"
"CHI" "B_HTHWY_HSTL"
"CHL" "B_CHLMY"
"CHLSPP" "B_CHLMY"
"CHM" "B_CHRMB"
@@ -1600,7 +1600,7 @@
"CJ2" "B_CMPYL_JEJN"
"CJD" "B_CMPYL_JEJN_DOYL"
"CJK" "B_CRYNB_JEKM"
"CKR" "F_CANDD_KRUS"
"CKR" "F_PICHI_KDRV"
"CKRSPP" "F_CANDD"
"CKU" "B_CRYNB_KTSC"
"CLA" "F_CLDSP"
@@ -1615,7 +1615,7 @@
"CLL" "B_CLLLSM"
"CLLCEL" "B_CLLLSM_CLLL"
"CLLSPP" "B_CLLLSM"
"CLM" "F_CANDD_LMBC"
"CLM" "F_PICHI_FRMN"
"CLMSPP" "F_CANDD"
"CLN" "F_CRYPT"
"CLNSPP" "F_CRYPT"
@@ -1761,7 +1761,7 @@
"CORVAR" "B_CRYNB_VRBL"
"CORXER" "B_CRYNB_XRSS"
"COT" "AN_CNTRC"
"COU" "B_FCLCT_RTCM"
"COU" "B_FCLCT_ORTC"
"COX" "B_COXLL"
"COXSPP" "B_COXLL"
"CPA" "F_CANDD_PRPS"
@@ -1975,7 +1975,7 @@
"EAF" "B_CLLNS_AERF"
"EAG" "B_PANTO_AGGL"
"EAL" "B_ERWIN_AMYL"
"EAM" "B_LLLTT_NGNS"
"EAM" "B_LLLTT_AMNG"
"EAN" "B_ENTRC_ASIN"
"EAR" "B_EWNGL_AMRC"
"EAS" "B_ENTRBC_ASBR"
@@ -1994,7 +1994,7 @@
"ECI" "P_ENTMB_COLI"
"ECL" "B_ENTRBC_CLOC"
"ECM" "B_CTRDM_CMBS"
"ECN" "B_FCLCT_TRTM"
"ECN" "B_FCLCT_CNTR"
"ECO" "B_ESCHR_COLI"
"ECR" "B_EKNLL_CRRD"
"ECS" "AN_ECHNS"
@@ -2054,7 +2054,7 @@
"ELA" "B_ELZBT_ANPH"
"ELE" "B_EGGRT_LENT"
"ELI" "B_EBCTRM_LMSM"
"ELIMEN" "B_ELZBT_PTCM"
"ELIMEN" "B_ELZBT_MNNG"
"ELIMIR" "B_ELZBT_MRCL"
"ELISPP" "B_ELZBT"
"ELZ" "B_ELZBT"
@@ -2163,14 +2163,14 @@
"EPO" "P_ENTMB_PLCK"
"EPS" "B_ENTRC_PSDV"
"ERA" "B_ENTRC_RFFN"
"ERE" "B_AGTHB_RECTL"
"ERE" "B_AGTHB_RCTL"
"ERH" "B_ERYSP_RHSP"
"ERO" "F_EXPHL"
"EROSPP" "F_EXPHL"
"ERU" "B_EHRLC_RMNN"
"ERW" "B_ERWIN"
"ERWAMY" "B_ERWIN_AMYL"
"ERWANA" "B_ERWIN_ANNT"
"ERWANA" "B_PANTO_ANNT"
"ERWCAR" "B_PCTBC_CRTV"
"ERWCHR" "B_DICKY_CHRY"
"ERWCYP" "B_ERWIN"
@@ -2378,7 +2378,7 @@
"FOD" "B_MYRDS_DRTS"
"FON" "F_FONSC"
"FOR" "B_PSDMN_ORYZ"
"FPA" "F_FUSRM_PLLD"
"FPA" "F_FUSRM_INCR"
"FPD" "F_FONSC_PDRS"
"FPE" "B_FSBCTR_PRDN"
"FPH" "B_FRNCS_PHLM"
@@ -2728,7 +2728,7 @@
"KOCKRI" "B_ROTHI_KRST"
"KOCPAL" "B_KOCUR_PLST"
"KOCRHI" "B_KOCUR_RHZP"
"KOCROS" "B_KOCUR_ROSS"
"KOCROS" "B_KOCUR_ROSE"
"KOCSPP" "B_KOCUR"
"KOCVAR" "B_KOCUR_VRNS"
"KOL" "B_KGLLA_ORLS"
@@ -2756,7 +2756,7 @@
"LAC" "B_LCTBC"
"LACACI" "B_LCTBC_ACDPH"
"LACCAS" "B_LCTCS_CASE"
"LACCAT" "B_LCTBC_CTNFR"
"LACCAT" "B_ERTHA_CTNF"
"LACCRI" "B_LCTBC_CRSP"
"LACCUR" "B_LTLCT_CRVT"
"LACDEL" "B_LCTBC_DLBR"
@@ -2866,7 +2866,7 @@
"LEIMEX" "P_LSHMN_MXCN"
"LEITRO" "P_LSHMN_TRPC"
"LEL" "B_LLLTT"
"LELAMN" "B_LLLTT_NGNS"
"LELAMN" "B_LLLTT_AMNG"
"LELNIM" "B_LLLTT_NMPR"
"LELSPP" "B_LLLTT"
"LEM" "B_LMNRL"
@@ -3024,7 +3024,7 @@
"MCT" "B_MYCBC_CHIT"
"MCU" "B_MBLNC_CRTS"
"MDE" "B_MYCBC_DRNH"
"MDI" "F_MCRSP_DSTR"
"MDI" "F_MCRSP_EQNM"
"MDU" "B_MYCBC_DUVL"
"MEA" "AN_MTGNM"
"MEASPP" "AN_MTGNM"
@@ -3098,9 +3098,9 @@
"MIO" "F_CANDD_PLML"
"MIP" "B_NOCRD"
"MIPAUD" "F_MCRSP_AUDN"
"MIPBOU" "F_MCRSP_BLLR"
"MIPBOU" "F_MCRSP_FLVM"
"MIPCAN" "F_MCRSP_CANS"
"MIPDIS" "F_MCRSP_DSTR"
"MIPDIS" "F_MCRSP_EQNM"
"MIPFER" "F_MCRSP_FRRG"
"MIPFUL" "F_MCRSP_FLVM"
"MIPGYP" "F_MCRSP_GYPS"
@@ -3108,7 +3108,7 @@
"MIPPRA" "F_MCRSP_PRCX"
"MIPRAC" "F_MCRSP_RCMS"
"MIPSPP" "F_MCRSP"
"MIPVAN" "F_MCRSP_VNBR"
"MIPVAN" "F_MCRSP_GLLN"
"MIR" "B_MCRBC"
"MIRARB" "B_MCRBC_ARBR"
"MIRAUR" "B_MCRBC_AURM"
@@ -3164,7 +3164,7 @@
"MOISPP" "B_MRTLL"
"MOO" "B_MRXLL_OVIS"
"MOR" "B_MRGNL"
"MORANA" "B_MRXLL_TFRA"
"MORANA" "B_RMRLL_TFRA"
"MORATL" "B_MRXLL_ATLN"
"MORBOV" "B_MRXLL_BOVS"
"MORCAN" "B_MRXLL_CANS"
@@ -3243,7 +3243,7 @@
"MUT" "B_MRXLL"
"MUTSPP" "B_MRXLL"
"MVA" "B_MYCBC_VACC"
"MVB" "F_MCRSP_VNBR"
"MVB" "F_MCRSP_GLLN"
"MVI" "B_MRTLL_VSCS"
"MWI" "B_MLLRL_WSCN"
"MXC" "B_MRXLL_CANS"
@@ -3349,7 +3349,7 @@
"MYPSPP" "B_MYCPLS"
"MYR" "B_MYRDS"
"MYRODM" "B_MYRDS_ODRT"
"MYRODO" "B_MYRDS_DRTM"
"MYRODO" "B_MYRDS_DRTS"
"MYRSPE" "B_MYRDS"
"MYRSPP" "B_MYRDS"
"MYS" "B_MYCBC_TBRC"
@@ -3359,7 +3359,7 @@
"MZC" "F_MYRZY_CRBB"
"NAE" "P_NAGLR"
"NAEFOW" "P_NAGLR_FWLR"
"NAM" "AN_NECTR_AMRC"
"NAM" "F_NECATR_AMRC"
"NAS" "B_NOCRD_ASTR"
"NBR" "B_NOCRD_BRSL"
"NCA" "B_NESSR_CANS"
@@ -3376,7 +3376,7 @@
"NDGPR" "B_GRAMP"
"NE-" "B_NESSR"
"NEC" "F_NECATR"
"NECAME" "AN_NECTR_AMRC"
"NECAME" "F_NECATR_AMRC"
"NECSPP" "F_NECATR"
"NEI" "B_NESSR"
"NEICAN" "B_NESSR_CANS"
@@ -3639,7 +3639,7 @@
"PEU" "AN_PDCLS"
"PEX" "F_EXPHL_EXPH"
"PFL" "B_PSDMN_FLRS"
"PFN" "F_PICHI_FRNS"
"PFN" "F_MLLRZ_FRNS"
"PFNSPP" "F_PICHI"
"PFR" "B_PRPNB_FRDN"
"PFX" "B_PSDMN_FLRS-C"
@@ -3734,7 +3734,7 @@
"PPI" "B_RLSTN_PCKT"
"PPL" "B_PSDMN_OLVR"
"PPM" "B_BRKHL_PSDM"
"PPN" "B_RDNTB_PNMTR"
"PPN" "B_RDNTB_PNMT"
"PPNGOR" "B_PPTNP"
"PPNHAR" "B_PPTNP"
"PPNIND" "B_PPTNP_INDL"
@@ -3968,7 +3968,7 @@
"RHDSPP" "F_RHDTR"
"RHI" "F_RHZMC"
"RHIMIC" "F_RHZPS_MCRS"
"RHIORY" "F_RHZPS_ORYZ"
"RHIORY" "F_RHZPS_ARRH"
"RHIRAD" "B_AGRBCT_RDBC"
"RHISPE" "F_RHZPS"
"RHISPP" "F_RHZPS"
@@ -4125,7 +4125,7 @@
"SCOSPP" "F_SCPLR"
"SCP" "B_STPHY_CAPR"
"SCR" "B_LCTCC_CRMR"
"SCS" "F_SCLCB_CNST"
"SCS" "F_OCHRC_CNST"
"SCT" "B_STRPT_CNST"
"SCU" "B_STPHY_CRNS"
"SCY" "F_SCYTL"
@@ -4250,7 +4250,7 @@
"SHO" "B_STPHY_HMNS"
"SHR" "B_SLMNL_ENTR_ENTR"
"SHT" "B_SLMNL_ENTR_HOTN"
"SHU" "F_SCLCB_HMCL"
"SHU" "F_OCHRC_HMCL"
"SHWPUT" "B_SHWNL_PTRF"
"SHY" "B_STPHY_HYCS"
"SIA" "B_STRPT_INFN"
@@ -4663,35 +4663,35 @@
"TCTSPP" "B_TRPNM"
"TDE" "B_TRPNM_DNTC"
"TEN" "B_TRPNM_PRLS"
"TEQ" "F_TRCHP_EQNM"
"TEQ" "F_TRCHP_TNSR"
"TER" "B_TRRBCL"
"TERSPP" "B_TRRBCL"
"TFO" "P_TRTRC_SUIS"
"TGA" "P_THMNS_GLLN"
"TGASPP" "F_TRCHD_NTHS"
"TGO" "P_TXPL_GOND"
"TGO" "C_TXPL_GOND"
"TGU" "B_TRBLS_GMNS"
"THA" "F_CANDD_HMLN"
"THM" "B_SLMNL_ENTR_ENTR"
"THO" "F_TRCHD_NTHS"
"THOSPP" "F_TRCHD_NTHS"
"THS" "F_CANDD_PSDH"
"THX" "B_CANDD_HMLN-C"
"THX" "F_CANDD_HMLN-C"
"TIN" "F_CANDD_INCN"
"TIS" "B_TSSRL"
"TISPRA" "B_TSSRL_PRCT"
"TISSPP" "B_TSSRL"
"TME" "F_TRCHP_MNTG"
"TMG" "F_TRCHP_MGNN"
"TMG" "F_TRCHP_RBRM"
"TMU" "F_TRCHS"
"TMUSPP" "F_TRCHS"
"TNB" "B_TNCBC"
"TNM" "B_TNCBC_MRTM"
"TNS" "B_SLMNL_ENTR_ENTR"
"TOP" "P_TXPL"
"TOP" "C_TXPL"
"TOT" "B_CRYNB_OTTD"
"TOX" "AN_TOXCR"
"TOXGON" "P_TXPL_GOND"
"TOXGON" "C_TXPL_GOND"
"TPA" "B_TRPNM_PRLS"
"TPH" "B_TRPNM_PHGD"
"TPHSPP" "B_TRPNM"
@@ -4734,24 +4734,24 @@
"TRICHO" "F_TRCHP"
"TRICON" "F_TRCHP_CNCN"
"TRICSP" "F_TRCHS"
"TRIEQU" "F_TRCHP_EQNM"
"TRIFIS" "F_TRCHP_FSCH"
"TRIEQU" "F_TRCHP_TNSR"
"TRIFIS" "F_TRCHP_RBRM"
"TRIFLA" "F_TRCHP_FLVS"
"TRIFLU" "F_TRCHP_FLVM"
"TRIFLU" "F_TRCHP_RBRM"
"TRIGEO" "F_TRCHP_GLOR"
"TRIGLO" "F_TRCHP_GLOR"
"TRIGOU" "F_TRCHP_GRVL"
"TRIINT" "F_TRCHP_MNTG"
"TRIKAN" "F_TRCHP_KANE"
"TRILON" "F_TRCHP_LNGF"
"TRIMEG" "F_TRCHP_MGNN"
"TRIKAN" "F_TRCHP_RBRM"
"TRILON" "F_ADRMA_FLVM"
"TRIMEG" "F_TRCHP_RBRM"
"TRIMEN" "F_TRCHP_MNTG"
"TRIPRO" "F_TRCHP_PRLF"
"TRIRAU" "F_TRCHP_RBTS"
"TRIRAU" "F_TRCHP_RBRM"
"TRIRUB" "F_TRCHP_RBRM"
"TRISCH" "F_TRCHP_SCHN"
"TRISIM" "F_TRCHP_SIMI"
"TRISOU" "F_TRCHP_SDNN"
"TRISOU" "F_TRCHP_VLCM"
"TRISPI" "AN_TRCHN_SPRL"
"TRISPP" "F_TRCHP"
"TRITER" "F_TRCHP_TRRS"
@@ -4761,7 +4761,7 @@
"TRIVER" "F_TRCHP_VRRC"
"TRIVIO" "F_TRCHP_VLCM"
"TRIVIR" "F_TRCHD_VIRD"
"TRIYAO" "F_TRCHP_YAND"
"TRIYAO" "F_TRCHP_VLCM"
"TRL" "B_TRPRL"
"TRLSPI" "AN_TRCHN_SPRL"
"TRLSPP" "AN_TRCHN"
@@ -4793,7 +4793,7 @@
"TSO" "AN_TAENI_SOLM"
"TSOSPP" "AN_TAENI"
"TSP" "AN_TRCHN_SPRL"
"TSU" "F_TRCHP_SDNN"
"TSU" "F_TRCHP_VLCM"
"TTC" "P_TRTRC"
"TTE" "F_TRCHP_TRRS"
"TTN" "P_THMNS_TENX"

BIN
data-raw/microorganisms.codes.xlsx
View File

Binary file not shown.

0
data-raw/microorganisms.codes.xpt
View File

BIN
data-raw/microorganisms.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.feather
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.feather
View File

Binary file not shown.

2
data-raw/microorganisms.groups.md5
View File

@@ -1 +1 @@
c296aff21039582a1c2d3c092ccf848c
a16b8db2140952b8a5848989afdccb53

BIN
data-raw/microorganisms.groups.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.sav
View File

Binary file not shown.

170
data-raw/microorganisms.groups.txt
View File

@@ -1,14 +1,14 @@
"mo_group" "mo" "mo_group_name" "mo_name"
"B_ACNTB_BMNN-C" "B_ACNTB_BMNN" "Acinetobacter baumannii complex" "Acinetobacter baumannii"
"B_ACNTB_BMNN-C" "B_ACNTB_CLCC" "Acinetobacter baumannii complex" "Acinetobacter calcoaceticus"
"B_ACNTB_BMNN-C" "B_ACNTB_DJKS" "Acinetobacter baumannii complex" "Acinetobacter dijkshoorniae"
"B_ACNTB_BMNN-C" "B_ACNTB_LCTC" "Acinetobacter baumannii complex" "Acinetobacter dijkshoorniae"
"B_ACNTB_BMNN-C" "B_ACNTB_NSCM" "Acinetobacter baumannii complex" "Acinetobacter nosocomialis"
"B_ACNTB_BMNN-C" "B_ACNTB_PITT" "Acinetobacter baumannii complex" "Acinetobacter pittii"
"B_ACNTB_BMNN-C" "B_ACNTB_SFRT" "Acinetobacter baumannii complex" "Acinetobacter seifertii"
"B_BCTRD_FRGL-C" "B_BCTRD_FRGL" "Bacteroides fragilis complex" "Bacteroides fragilis"
"B_BCTRD_FRGL-C" "B_BCTRD_OVTS" "Bacteroides fragilis complex" "Bacteroides ovatus"
"B_BCTRD_FRGL-C" "B_BCTRD_THTT" "Bacteroides fragilis complex" "Bacteroides thetaiotaomicron"
"B_BCTRD_FRGL-C" "B_BCTRD_VLGT" "Bacteroides fragilis complex" "Bacteroides vulgatus"
"B_BCTRD_FRGL-C" "B_PHCCL_VLGT" "Bacteroides fragilis complex" "Bacteroides vulgatus"
"B_BCTRD_FRGL-C" "B_PRBCT_DSTS" "Bacteroides fragilis complex" "Parabacteroides distasonis"
"B_STRPT_HAEM" "B_STRPT_GRPA" "Beta-haemolytic Streptococcus" "Streptococcus Group A"
"B_STRPT_HAEM" "B_STRPT_ABCG" "Beta-haemolytic Streptococcus" "Streptococcus Group A, B, C, G"
@@ -43,8 +43,8 @@
"B_STRPT_HAEM" "B_STRPT_PRCN" "Beta-haemolytic Streptococcus" "Streptococcus porcinus"
"B_STRPT_HAEM" "B_STRPT_PYGN" "Beta-haemolytic Streptococcus" "Streptococcus pyogenes"
"B_STRPT_HAEM" "B_STRPT_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius"
"B_STRPT_HAEM" "B_STRPT_SLVR_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius salivarius"
"B_STRPT_HAEM" "B_STRPT_SLVR_THRM" "Beta-haemolytic Streptococcus" "Streptococcus salivarius thermophilus"
"B_STRPT_HAEM" "B_STRPT_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius salivarius"
"B_STRPT_HAEM" "B_STRPT_THRM" "Beta-haemolytic Streptococcus" "Streptococcus salivarius thermophilus"
"B_STRPT_HAEM" "B_STRPT_SNGN" "Beta-haemolytic Streptococcus" "Streptococcus sanguinis"
"B_BRKHL_CEPC-C" "B_BRKHL_AMBF" "Burkholderia cepacia complex" "Burkholderia ambifaria"
"B_BRKHL_CEPC-C" "B_BRKHL_ANTH" "Burkholderia cepacia complex" "Burkholderia anthina"
@@ -56,15 +56,15 @@
"B_BRKHL_CEPC-C" "B_BRKHL_STBL" "Burkholderia cepacia complex" "Burkholderia stabilis"
"B_BRKHL_CEPC-C" "B_BRKHL_UBNN" "Burkholderia cepacia complex" "Burkholderia ubonensis"
"B_BRKHL_CEPC-C" "B_BRKHL_VTNM" "Burkholderia cepacia complex" "Burkholderia vietnamiensis"
"F_CANDD_ALBC-C" "F_CANDD_AFRC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_CLSS" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_MTLN" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_NNLQ" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_STLL" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_VLLM" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_DBLN" "Candida albicans complex" "Candida dubliniensis"
"F_CANDD_GLBR-C" "F_CANDD_BRCR" "Candida glabrata complex" "Candida bracarensis"
"F_CANDD_GLBR-C" "F_CANDD_GLBR" "Candida glabrata complex" "Candida glabrata"
@@ -72,14 +72,14 @@
"F_CANDD_PRPS-C" "F_CANDD_MTPS" "Candida parapsilosis complex" "Candida metapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_ORTH" "Candida parapsilosis complex" "Candida orthopsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_HOKK" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_INTR" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QURC" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_MLBS" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_MLBS" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QRCS" "Candida parapsilosis complex" "Candida parapsilosis quercus"
"P_CHLMS" "F_CANDD_DBSH" "Chilomastix" "Candida duobushaemulonii"
"P_CHLMS" "F_CANDD_HMLN" "Chilomastix" "Candida haemulonii"
"P_CHLMS" "B_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
"P_CHLMS" "F_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
"B_CTRBC_AMLN-C" "B_CTRBC_AMLN" "Citrobacter amalonaticus complex" "Citrobacter amalonaticus"
"B_CTRBC_AMLN-C" "B_CTRBC_FRMR" "Citrobacter amalonaticus complex" "Citrobacter farmeri"
"B_CTRBC_AMLN-C" "B_CTRBC_SDLK" "Citrobacter amalonaticus complex" "Citrobacter sedlakii"
@@ -101,18 +101,18 @@
"B_STPHY_CONS" "B_STPHY_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis"
"B_STPHY_CONS" "B_STPHY_CPTS_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis capitis"
"B_STPHY_CONS" "B_STPHY_CPTS_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis urealyticus"
"B_STPHY_CONS" "B_STPHY_CPTS_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis ureolyticus"
"B_STPHY_CONS" "B_STPHY_CPTS_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis ureolyticus"
"B_STPHY_CONS" "B_STPHY_CAPR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caprae"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS_UTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus utilis"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus utilis"
"B_STPHY_CONS" "B_STPHY_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus casei"
"B_STPHY_CONS" "B_STPHY_CSLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caseolyticus"
"B_STPHY_CONS" "B_MCRCC_CSLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caseolyticus"
"B_STPHY_CONS" "B_STPHY_CHRM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus chromogenes"
"B_STPHY_CONS" "B_STPHY_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii"
"B_STPHY_CONS" "B_STPHY_COHN_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii cohnii"
"B_STPHY_CONS" "B_STPHY_COHN_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticum"
"B_STPHY_CONS" "B_STPHY_COHN_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticus"
"B_STPHY_CONS" "B_STPHY_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii cohnii"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticum"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticus"
"B_STPHY_CONS" "B_STPHY_CNDM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus condimenti"
"B_STPHY_CONS" "B_STPHY_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus croceilyticus"
"B_STPHY_CONS" "B_STPHY_DBCK" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus debuckii"
@@ -130,7 +130,7 @@
"B_STPHY_CONS" "B_STPHY_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis"
"B_STPHY_CONS" "B_STPHY_HMNS_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis hominis"
"B_STPHY_CONS" "B_STPHY_HMNS_NVBS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis novobiosepticus"
"B_STPHY_CONS" "B_STPHY_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus jettensis"
"B_STPHY_CONS" "B_STPHY_KLOS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus kloosii"
"B_STPHY_CONS" "B_STPHY_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lentus"
"B_STPHY_CONS" "B_STPHY_LLYD" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lloydii"
@@ -141,40 +141,40 @@
"B_STPHY_CONS" "B_STPHY_NPLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus nepalensis"
"B_STPHY_CONS" "B_STPHY_PSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pasteuri"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii"
"B_STPHY_CONS" "B_STPHY_PTRS_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii croceilyticus"
"B_STPHY_CONS" "B_STPHY_PTRS_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii petrasii"
"B_STPHY_CONS" "B_STPHY_PTRS_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii pragensis"
"B_STPHY_CONS" "B_STPHY_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii croceilyticus"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii petrasii"
"B_STPHY_CONS" "B_STPHY_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii pragensis"
"B_STPHY_CONS" "B_STPHY_PTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pettenkoferi"
"B_STPHY_CONS" "B_STPHY_PSCF" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus piscifermentans"
"B_STPHY_CONS" "B_STPHY_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pragensis"
"B_STPHY_CONS" "B_STPHY_PSDX" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pseudoxylosus"
"B_STPHY_CONS" "B_STPHY_PLVR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pulvereri"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pulvereri"
"B_STPHY_CONS" "B_STPHY_RATT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ratti"
"B_STPHY_CONS" "B_STPHY_RSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus rostri"
"B_STPHY_CONS" "B_STPHY_SCCH" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saccharolyticus"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SPRP_BOVS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi"
"B_STPHY_CONS" "B_STPHY_SCHL_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR_CRNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
"B_STPHY_CONS" "B_STPHY_SCIR_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri lentus"
"B_STPHY_CONS" "B_STPHY_SCIR_RDNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri rodentium"
"B_STPHY_CONS" "B_STPHY_SCIR_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
"B_STPHY_CONS" "B_STPHY_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri lentus"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri rodentium"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri sciuri"
"B_STPHY_CONS" "B_STPHY_SMLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus simulans"
"B_STPHY_CONS" "B_STPHY_STPN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus stepanovicii"
"B_STPHY_CONS" "B_STPHY_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus"
"B_STPHY_CONS" "B_STPHY_SCCN_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus casei"
"B_STPHY_CONS" "B_STPHY_SCCN_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus succinus"
"B_STPHY_CONS" "B_STPHY_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus casei"
"B_STPHY_CONS" "B_STPHY_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus succinus"
"B_STPHY_CONS" "B_STPHY_TWNN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus taiwanensis"
"B_STPHY_CONS" "B_STPHY_URLYT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus urealyticus"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ureilyticus"
"B_STPHY_CONS" "B_STPHY_VRTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus veratri"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulinus"
"B_STPHY_CONS" "B_STPHY_VTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulus"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulus"
"B_STPHY_CONS" "B_STPHY_WRNR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus warneri"
"B_STPHY_CONS" "B_STPHY_XYLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus xylosus"
"B_STPHY_COPS" "B_STPHY_AGNT" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus agnetis"
@@ -183,13 +183,13 @@
"B_STPHY_COPS" "B_STPHY_CRNB" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus cornubiensis"
"B_STPHY_COPS" "B_STPHY_DLPH" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus delphini"
"B_STPHY_COPS" "B_STPHY_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus"
"B_STPHY_COPS" "B_STPHY_HYCS_CHRM" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus chromogenes"
"B_STPHY_COPS" "B_STPHY_HYCS_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus hyicus"
"B_STPHY_COPS" "B_STPHY_CHRM" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus chromogenes"
"B_STPHY_COPS" "B_STPHY_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus hyicus"
"B_STPHY_COPS" "B_STPHY_INTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus intermedius"
"B_STPHY_COPS" "B_STPHY_LUTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus lutrae"
"B_STPHY_COPS" "B_STPHY_PSDN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus pseudintermedius"
"B_STPHY_COPS" "B_STPHY_RTRD" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus roterodami"
"B_STPHY_COPS" "B_STPHY_SCHL_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_COPS" "B_STPHY_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_COPS" "B_STPHY_SCHW" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schweitzeri"
"B_STPHY_COPS" "B_STPHY_SIMI" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus simiae"
"B_STPHY_COPS" "B_STPHY_SNGP" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus singaporensis"
@@ -252,8 +252,8 @@
"B_CORYNF" "B_TRPRL" "Coryneform bacterium" "Trueperella"
"B_CORYNF" "B_TRPRL_BRNR" "Coryneform bacterium" "Trueperella bernardiae"
"B_CORYNF" "B_TRPRL_PYGN" "Coryneform bacterium" "Trueperella pyogenes"
"B_CORYNF" "B_TRCLL" "Coryneform bacterium" "Turicella"
"B_CORYNF" "B_TRCLL_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_CORYNF" "B_CRYNB" "Coryneform bacterium" "Turicella"
"B_CORYNF" "B_CRYNB_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_ASBR" "Enterobacter cloacae complex" "Enterobacter asburiae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae cloacae"
@@ -266,59 +266,59 @@
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_XNGF" "Enterobacter cloacae complex" "Enterobacter hormaechei xiangfangensis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_KOBE" "Enterobacter cloacae complex" "Enterobacter kobei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_LDWG" "Enterobacter cloacae complex" "Enterobacter ludwigii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
"B_HACEK" "B_ACTNB_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Actinobacillus actinomycetemcomitans"
"B_ENTRBC_CLOC-C" "B_LLLTT_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Actinobacillus actinomycetemcomitans"
"B_HACEK" "B_AGGRG" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter actinomycetemcomitans"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter aphrophilus"
"B_HACEK" "B_AGGRG_KILN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter kilianii"
"B_HACEK" "B_AGGRG_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter paraphrophilus"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter paraphrophilus"
"B_HACEK" "B_AGGRG_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter segnis"
"B_HACEK" "B_CRDBC_HMNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Cardiobacterium hominis"
"B_HACEK" "B_EKNLL_CRRD" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Eikenella corrodens"
"B_HACEK" "B_HMPHL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus"
"B_HACEK" "B_HMPHL_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus actinomycetemcomitans"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus actinomycetemcomitans"
"B_HACEK" "B_HMPHL_AEGY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aegyptius"
"B_HACEK" "B_HMPHL_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aphrophilus"
"B_HACEK" "B_HMPHL_AVIM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus avium"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aphrophilus"
"B_HACEK" "B_AVBCT_AVIM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus avium"
"B_HACEK" "B_HMPHL_DCRY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus ducreyi"
"B_HACEK" "B_HMPHL_EQGN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus equigenitalis"
"B_HACEK" "B_TYLRL_EQGN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus equigenitalis"
"B_HACEK" "B_HMPHL_FELS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus felis"
"B_HACEK" "B_HMPHL_HMGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemoglobinophilus"
"B_HACEK" "B_CANCL_HMGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemoglobinophilus"
"B_HACEK" "B_HMPHL_HMLY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemolyticus"
"B_HACEK" "B_HMPHL_INFL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus influenzae"
"B_HACEK" "B_HMPHL_MSSL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus massiliensis"
"B_HACEK" "B_HMPHL_PRCN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paracuniculus"
"B_HACEK" "B_HMPHL_PRGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paragallinarum"
"B_HACEK" "B_AVBCT_PRGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paragallinarum"
"B_HACEK" "B_HMPHL_PRHM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parahaemolyticus"
"B_HACEK" "B_HMPHL_PRNF" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parainfluenzae"
"B_HACEK" "B_HMPHL_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrohaemolyticus"
"B_HACEK" "B_HMPHL_PHLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrophilus"
"B_HACEK" "B_HMPHL_PRSS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parasuis"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrophilus"
"B_HACEK" "B_GLSSR_PRSS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parasuis"
"B_HACEK" "B_HMPHL_PSCM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus piscium"
"B_HACEK" "B_HMPHL_PTTM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pittmaniae"
"B_HACEK" "B_HMPHL_PLRP" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pleuropneumoniae"
"B_HACEK" "B_ACTNB_PLRP" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pleuropneumoniae"
"B_HACEK" "B_HMPHL_QNTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus quentini"
"B_HACEK" "B_HMPHL_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus segnis"
"B_HACEK" "B_AGGRG_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus segnis"
"B_HACEK" "B_HMPHL_SMNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus seminalis"
"B_HACEK" "B_HMPHL_SPTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus sputorum"
"B_HACEK" "B_HMPHL_VGNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus vaginalis"
"B_HACEK" "B_GRDNR_VGNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus vaginalis"
"B_HACEK" "B_KGLLA" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella"
"B_HACEK" "B_KGLLA_DNTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella denitrificans"
"B_HACEK" "B_KGLLA_INDL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella indologenes"
"B_HACEK" "B_STTNL_INDL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella indologenes"
"B_HACEK" "B_KGLLA_KING" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella kingae"
"B_HACEK" "B_KGLLA_NGVN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella negevensis"
"B_HACEK" "B_KGLLA_ORAL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella oralis"
"B_HACEK" "B_KGLLA_POTS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella potus"
"F_MYRZY_GLLR-C" "F_CANDD_FRMN" "Meyerozyma guilliermondii complex" "Candida fermentati"
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_JPNC" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_MUHR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_PSDG" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_PRTB" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium paratuberculosis"
@@ -326,19 +326,19 @@
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare chimaera"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_INTR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_YNGN" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_AFRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_MCRT" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_TBRC-C" "B_MYCBC_MUNG" "Mycobacterium tuberculosis complex" "Mycobacterium mungi"
"B_MYCBC_TBRC-C" "B_MYCBC_ORYG" "Mycobacterium tuberculosis complex" "Mycobacterium orygis"
"B_MYCBC_TBRC-C" "B_MYCBC_PNNP" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_PSDMN_FLRS-C" "B_PSDMN_FLRS" "Pseudomonas fluorescens complex" "Pseudomonas fluorescens"
"B_MYCBC_RGM" "B_MYCBC_ABSC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus abscessus"
"B_MYCBC_RGM" "B_MYCBC_ABSC_BLLT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus bolletii"
@@ -361,8 +361,8 @@
"B_MYCBC_RGM" "B_MYCBC_CNRS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium canariasense"
"B_MYCBC_RGM" "B_MYCBC_CLRF" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium celeriflavum"
"B_MYCBC_RGM" "B_MYCBC_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BOVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BVST" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_CHLN_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_GWNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae gwanakae"
"B_MYCBC_RGM" "B_MYCBC_CHIT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chitae"
@@ -428,7 +428,7 @@
"B_MYCBC_RGM" "B_MYCBC_THRM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium thermoresistibile"
"B_MYCBC_RGM" "B_MYCBC_TKNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium tokaiense"
"B_MYCBC_RGM" "B_MYCBC_VACC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vaccae"
"B_MYCBC_RGM" "B_MYCBC_VNBL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vanbaalenii"
"B_MYCBC_RGM" "B_MYCBC_ASTR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vanbaalenii"
"B_MYCBC_RGM" "B_MYCBC_WLNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium wolinskyi"
"B_MYCBC_SGM" "B_MYCBC_FRCN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium farcinogenes"
"B_MYCBC_SGM" "B_MYCBC_GSTR" "Slowly growing Mycobacterium (SGM)" "Mycobacterium gastri"
@@ -476,8 +476,8 @@
"B_STRPT_GRPG" "B_STRPT_DYSG_EQSM" "Streptococcus Group G" "Streptococcus dysgalactiae equisimilis"
"B_STRPT_GRPH" "B_STRPT_SNGN" "Streptococcus Group H" "Streptococcus sanguinis"
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPL" "B_STRPT_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_EQSM" "Streptococcus Group L" "Streptococcus dysgalactiae equisimilis"
@@ -507,8 +507,8 @@
"B_STRPT_VIRI" "B_STRPT_PRSN" "Viridans Group Streptococcus (VGS)" "Streptococcus parasanguinis"
"B_STRPT_VIRI" "B_STRPT_RATT" "Viridans Group Streptococcus (VGS)" "Streptococcus ratti"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SNGN" "Viridans Group Streptococcus (VGS)" "Streptococcus sanguinis"
"B_STRPT_VIRI" "B_STRPT_SBRN" "Viridans Group Streptococcus (VGS)" "Streptococcus sobrinus"
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"
@@ -516,7 +516,7 @@
"B_STRPT_VIRI" "B_STRPT_VSTB" "Viridans Group Streptococcus (VGS)" "Streptococcus vestibularis"
"B_YERSN_PSDT-C" "B_YERSN_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_SMLS" "Yersinia pseudotuberculosis complex" "Yersinia similis"
"B_YERSN_PSDT-C" "B_YERSN_WTRS" "Yersinia pseudotuberculosis complex" "Yersinia wautersii"

BIN
data-raw/microorganisms.groups.xlsx
View File

Binary file not shown.

0
data-raw/microorganisms.groups.xpt
View File

2
data-raw/microorganisms.md5
View File

@@ -1 +1 @@
f6957ab7c3022dfcdb686f70453a9795
f1cbe414851c1eee08ff5440a47af76c

BIN
data-raw/microorganisms.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.sav
View File

Binary file not shown.

39589
data-raw/microorganisms.txt
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/microorganisms.xlsx
View File

Binary file not shown.

BIN
data-raw/microorganisms.xpt
View File

Binary file not shown.

620
data-raw/reproduction_of_microorganisms.R
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/taxonomy0.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy1.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy0b.rds → data-raw/taxonomy1b.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy1c.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy2.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy2b.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy2c.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy3.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy3b.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy_gbif.rds
View File

Binary file not shown.

BIN
data/antibiotics.rda
View File

Binary file not shown.

BIN
data/clinical_breakpoints.rda
View File

Binary file not shown.

BIN
data/intrinsic_resistant.rda
View File

Binary file not shown.

BIN
data/microorganisms.codes.rda
View File

Binary file not shown.

BIN
data/microorganisms.groups.rda
View File

Binary file not shown.

BIN
data/microorganisms.rda
View File

Binary file not shown.

5
man/AMR.Rd
View File

@@ -32,13 +32,13 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~71 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\seealso{
@@ -62,6 +62,7 @@ Authors:
Other contributors:
\itemize{
\item Casper J. Albers (\href{https://orcid.org/0000-0002-9213-6743}{ORCID}) [thesis advisor]
\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
\item Judith M. Fonville [contributor]
\item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]

2
man/WHONET.Rd
View File

@@ -42,7 +42,7 @@ WHONET
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our \link{example_isolates} data set. All patient names were created using online surname generators and are only in place for practice purposes.
}
\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
WHONET

2
man/ab_property.Rd
View File

@@ -104,7 +104,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/antibiogram.Rd
View File

@@ -69,7 +69,7 @@ antibiogram(
\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 or I, instead of only S (default is \code{TRUE})}
\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 antibiotic columns in combination antibiograms}

6
man/antibiotic_class_selectors.Rd
View File

@@ -148,9 +148,9 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
\item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
@@ -176,7 +176,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/antibiotics.Rd
View File

@@ -64,7 +64,7 @@ Properties that are based on an ATC code are only available when an ATC is avail
Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column \code{cid}) and consequently only available where a CID is available.
\subsection{Direct download}{
Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
}
\section{WHOCC}{

2
man/as.ab.Rd
View File

@@ -62,7 +62,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/as.av.Rd
View File

@@ -60,7 +60,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

4
man/as.mo.Rd
View File

@@ -200,7 +200,7 @@ Furthermore,
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.0} in the \link{microorganisms} data set;
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Verticillium}, or \emph{Wuchereria};
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Actinomucor}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bipolaris}, \emph{Blastobotrys}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chilomastix}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Clavispora}, \emph{Coccidioides}, \emph{Cokeromyces}, \emph{Conidiobolus}, \emph{Coniochaeta}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Cryptosporidium}, \emph{Cunninghamella}, \emph{Curvularia}, \emph{Cyberlindnera}, \emph{Debaryozyma}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Epidermophyton}, \emph{Exidia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Graphium}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hansenula}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hortaea}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kluyveromyces}, \emph{Kodamaea}, \emph{Lacazia}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Lomentospora}, \emph{Madurella}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Nannizzia}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Paracoccidioides}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phaeoacremonium}, \emph{Phaeomoniella}, \emph{Phialophora}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoscopulariopsis}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Purpureocillium}, \emph{Quambalaria}, \emph{Rhinocladiella}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saksenaea}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Schistosoma}, \emph{Schizosaccharomyces}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporopachydermia}, \emph{Sporothrix}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syncephalastrum}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Teleomorph}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ulocladium}, \emph{Ustilago}, \emph{Verticillium}, \emph{Wallemia}, \emph{Wangiella}, \emph{Wickerhamomyces}, \emph{Wuchereria}, \emph{Yarrowia}, or \emph{Zygosaccharomyces};
\item All other records have \code{prevalence = 2.0} in the \link{microorganisms} data set.
}
@@ -211,7 +211,7 @@ All matches are sorted descending on their matching score and for all user input
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/as.sir.Rd
View File

@@ -253,7 +253,7 @@ This AMR package honours this insight. Use \code{\link[=susceptibility]{suscepti
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/av_property.Rd
View File

@@ -79,7 +79,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/bug_drug_combinations.Rd
View File

@@ -35,7 +35,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\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 values S and I should be summed, so resistance will be based on only R - the default is \code{TRUE}}
\item{combine_SI}{a \link{logical} to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is \code{TRUE}}
\item{add_ab_group}{a \link{logical} to indicate where the group of the antimicrobials must be included as a first column}

Some files were not shown because too many files have changed in this diff Show More