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(v0.9.0.9025) update as.rsi documentation

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dr. M.S. (Matthijs) Berends 2020-02-16 22:43:56 +01:00
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8
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.9.0.9024 Version: 0.9.0.9025
Date: 2020-02-14 Date: 2020-02-16
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -28,7 +28,9 @@ Authors@R: c(
person(role = "ctb", person(role = "ctb",
family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"), family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
person(role = "ctb", person(role = "ctb",
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl")) family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
person(role = "fnd",
given = "Stichting Certe Medische Diagnostiek en Advies", email = "medischedataanalyse@certe.nl"))
Description: Functions to simplify the analysis and prediction of Antimicrobial Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013) using evidence-based methods, like those defined by Leclercq et al. (2013)

6
NEWS.md
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# AMR 0.9.0.9024 # AMR 0.9.0.9025
## <small>Last updated: 14-Feb-2020</small> ## <small>Last updated: 16-Feb-2020</small>
### New ### New
* Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 2020-01-01 (use `as.rsi()` to transform MICs or disk zones) * Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 2020-01-01 (use `as.rsi()` to transform MICs and disk zones)
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. * The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
* Support for LOINC and SNOMED codes * Support for LOINC and SNOMED codes
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function: * Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:

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R/ab.R
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@ -57,9 +57,9 @@
#' #'
#' # spelling from different languages and dyslexia are no problem #' # spelling from different languages and dyslexia are no problem
#' ab_atc("ceftriaxon") #' ab_atc("ceftriaxon")
#' ab_atc("cephtriaxone") #' ab_atc("cephtriaxone") # small spelling error
#' ab_atc("cephthriaxone") #' ab_atc("cephthriaxone") # or a bit more severe
#' ab_atc("seephthriaaksone") #' ab_atc("seephthriaaksone") # and even this works
#' #'
#' # use ab_* functions to get a specific properties (see ?ab_property); #' # use ab_* functions to get a specific properties (see ?ab_property);
#' # they use as.ab() internally: #' # they use as.ab() internally:

29
R/misc.R
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@ -30,21 +30,24 @@ addin_insert_like <- function() {
} }
check_dataset_integrity <- function() { check_dataset_integrity <- function() {
if (!all(colnames(microorganisms) %in% c("mo", "fullname", "kingdom", "phylum", tryCatch({
"class", "order", "family", "genus", check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
"species", "subspecies", "rank", "class", "order", "family", "genus",
"col_id", "species_id", "source", "species", "subspecies", "rank",
"ref", "prevalence", "snomed"), "col_id", "species_id", "source",
na.rm = TRUE) | "ref", "prevalence", "snomed") %in% colnames(microorganisms),
NROW(microorganisms) != NROW(microorganismsDT) | na.rm = TRUE) & NROW(microorganisms) == NROW(microorganismsDT)
!all(colnames(antibiotics) %in% c("ab", "atc", "cid", "name", "group", check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
"atc_group1", "atc_group2", "abbreviations", "atc_group1", "atc_group2", "abbreviations",
"synonyms", "oral_ddd", "oral_units", "synonyms", "oral_ddd", "oral_units",
"iv_ddd", "iv_units", "loinc"), "iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
na.rm = TRUE)) { na.rm = TRUE)
}, error = function(e)
stop('Please use the command \'library("AMR")\' before using this function, to load the needed reference data.', call. = FALSE)
)
if (!check_microorganisms | !check_antibiotics) {
stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE) stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
} }
invisible(TRUE) invisible(TRUE)
} }

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R/rsi.R
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@ -39,7 +39,7 @@
#' #'
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter. #' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter.
#' @section Interpretation of R and S/I: #' @section Interpretation of R and S/I:
#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<http://www.eucast.org/newsiandr/>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". #' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<http://www.eucast.org/newsiandr/>).
#' #'
#' - **R = Resistant**\cr #' - **R = Resistant**\cr
#' A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. #' A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
@ -56,14 +56,9 @@
#' @seealso [as.mic()] #' @seealso [as.mic()]
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370))) #' # For INTERPRETING disk diffusion and MIC values -----------------------
#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C")) #'
#' is.rsi(rsi_data) #' # single values
#'
#' # this can also coerce combined MIC/RSI values:
#' as.rsi("<= 0.002; S") # will return S
#'
#' # interpret MIC values
#' as.rsi(x = as.mic(2), #' as.rsi(x = as.mic(2),
#' mo = as.mo("S. pneumoniae"), #' mo = as.mo("S. pneumoniae"),
#' ab = "AMP", #' ab = "AMP",
@ -73,21 +68,36 @@
#' mo = "Strep pneu", # `mo` will be coerced with as.mo() #' mo = "Strep pneu", # `mo` will be coerced with as.mo()
#' ab = "ampicillin", # and `ab` with as.ab() #' ab = "ampicillin", # and `ab` with as.ab()
#' guideline = "EUCAST") #' guideline = "EUCAST")
#'
#' # a whole data set, even with combined MIC values and disk zones
#' df <- data.frame(microorganism = "E. coli",
#' AMP = as.mic(12),
#' GEN = as.disk(18))
#' as.rsi(df)
#' #'
#'
#' # For CLEANING existing R/SI values ------------------------------------
#'
#' as.rsi(c("S", "I", "R", "A", "B", "C"))
#' as.rsi("<= 0.002; S") # will return "S"
#'
#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
#' is.rsi(rsi_data)
#' plot(rsi_data) # for percentages #' plot(rsi_data) # for percentages
#' barplot(rsi_data) # for frequencies #' barplot(rsi_data) # for frequencies
#' freq(rsi_data) # frequency table with informative header #' freq(rsi_data) # frequency table with informative header
#' #'
#' # using dplyr's mutate
#' library(dplyr) #' library(dplyr)
#' example_isolates %>% #' example_isolates %>%
#' mutate_at(vars(PEN:RIF), as.rsi) #' mutate_at(vars(PEN:RIF), as.rsi)
#' #'
#' #' # fastest way to transform all columns with already valid AMR results to class `rsi`:
#' # fastest way to transform all columns with already valid AB results to class `rsi`:
#' example_isolates %>% #' example_isolates %>%
#' mutate_if(is.rsi.eligible, #' mutate_if(is.rsi.eligible, as.rsi)
#' as.rsi) #'
#' # note: from dplyr 1.0.0 on, this will be:
#' # example_isolates %>%
#' # mutate(across(is.rsi.eligible, as.rsi))
#' #'
#' # default threshold of `is.rsi.eligible` is 5%. #' # default threshold of `is.rsi.eligible` is 5%.
#' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid #' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
@ -310,7 +320,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab()."))) message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
next next
} }
message(blue(paste0("Interpreting column `", bold(ab_cols[i]), "` (", message(blue(paste0("Interpreting MIC values of column `", bold(ab_cols[i]), "` (",
ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""), ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
ab_name(ab_col_coerced, tolower = TRUE), ")...")), ab_name(ab_col_coerced, tolower = TRUE), ")...")),
appendLF = FALSE) appendLF = FALSE)
@ -331,7 +341,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab()."))) message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
next next
} }
message(blue(paste0("Interpreting column `", bold(ab_cols[i]), "` (", message(blue(paste0("Interpreting disk zones of column `", bold(ab_cols[i]), "` (",
ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""), ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
ab_name(ab_col_coerced, tolower = TRUE), ")...")), ab_name(ab_col_coerced, tolower = TRUE), ")...")),
appendLF = FALSE) appendLF = FALSE)

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docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -240,7 +240,7 @@ Content not found. Please use links in the navbar.
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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docs/LICENSE-text.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -488,7 +488,7 @@ END OF TERMS AND CONDITIONS
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/articles/index.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -250,7 +250,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

8
docs/authors.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -302,6 +302,10 @@
<p><strong>Dennis Souverein</strong>. Contributor. <p><strong>Dennis Souverein</strong>. Contributor.
</p> </p>
</li> </li>
<li>
<p><strong>Stichting Certe Medische Diagnostiek en Advies</strong>. Funder.
</p>
</li>
</ul> </ul>
</div> </div>
@ -312,7 +316,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
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7
docs/index.html
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@ -45,7 +45,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -235,7 +235,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li> <li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li> <li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li> <li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li> <li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li> <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li> <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li> <li>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
@ -423,6 +423,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li> <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li> <li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li> <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>Stichting Certe Medische Diagnostiek en Advies <br><small class="roles"> Funder </small> </li>
<li><a href="authors.html">All authors...</a></li> <li><a href="authors.html">All authors...</a></li>
</ul> </ul>
</div> </div>
@ -432,7 +433,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<footer><div class="copyright"> <footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p> <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

16
docs/news/index.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -231,19 +231,19 @@
</div> </div>
<div id="amr-0909024" class="section level1"> <div id="amr-0909025" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0909024" class="anchor"></a>AMR 0.9.0.9024<small> Unreleased </small> <a href="#amr-0909025" class="anchor"></a>AMR 0.9.0.9025<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-14-feb-2020" class="section level2"> <div id="last-updated-16-feb-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-14-feb-2020" class="anchor"></a><small>Last updated: 14-Feb-2020</small> <a href="#last-updated-16-feb-2020" class="anchor"></a><small>Last updated: 16-Feb-2020</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
<ul> <ul>
<li>Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 2020-01-01 (use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to transform MICs or disk zones)</li> <li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 2020-01-01 (use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to transform MICs and disk zones)</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</li> <li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</li>
<li>Support for LOINC and SNOMED codes <li>Support for LOINC and SNOMED codes
<ul> <ul>
@ -1462,7 +1462,7 @@
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0909024">0.9.0.9024</a></li> <li><a href="#amr-0909025">0.9.0.9025</a></li>
<li><a href="#amr-090">0.9.0</a></li> <li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li> <li><a href="#amr-080">0.8.0</a></li>
<li><a href="#amr-071">0.7.1</a></li> <li><a href="#amr-071">0.7.1</a></li>
@ -1484,7 +1484,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -307,9 +307,9 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='co'># spelling from different languages and dyslexia are no problem</span> <span class='co'># spelling from different languages and dyslexia are no problem</span>
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>) <span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>) <span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>) <span class='co'># small spelling error</span>
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>) <span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>) <span class='co'># or a bit more severe</span>
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>) <span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>) <span class='co'># and even this works</span>
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span> <span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
<span class='co'># they use as.ab() internally:</span> <span class='co'># they use as.ab() internally:</span>
@ -336,7 +336,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

40
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -298,7 +298,7 @@
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul> <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>).</p><ul>
<li><p><strong>R = Resistant</strong><br /> <li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li> A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br /> <li><p><strong>S = Susceptible</strong><br />
@ -325,14 +325,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div> <div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>))) <pre class="examples"><span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>), <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
<span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>)
<span class='co'># this can also coerce combined MIC/RSI values:</span> <span class='co'># single values</span>
<span class='fu'>as.rsi</span>(<span class='st'>"&lt;= 0.002; S"</span>) <span class='co'># will return S</span>
<span class='co'># interpret MIC values</span>
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>), <span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>), <span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMP"</span>, <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMP"</span>,
@ -343,20 +338,35 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span> <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>) <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>12</span>),
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>))
<span class='fu'>as.rsi</span>(<span class='no'>df</span>)
<span class='co'># For CLEANING existing R/SI values ------------------------------------</span>
<span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
<span class='fu'>as.rsi</span>(<span class='st'>"&lt;= 0.002; S"</span>) <span class='co'># will return "S"</span>
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span> <span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
<span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>PEN</span>:<span class='no'>RIF</span>), <span class='no'>as.rsi</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>PEN</span>:<span class='no'>RIF</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AMR results to class `rsi`:</span>
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>, <span class='no'>as.rsi</span>)
<span class='no'>as.rsi</span>)
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
<span class='co'># example_isolates %&gt;%</span>
<span class='co'># mutate(across(is.rsi.eligible, as.rsi))</span>
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span> <span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span> <span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
@ -381,7 +391,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

6
docs/reference/count.html
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@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul> <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>).</p><ul>
<li><p><strong>R = Resistant</strong><br /> <li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li> A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br /> <li><p><strong>S = Susceptible</strong><br />
@ -446,7 +446,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/reference/filter_ab_class.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -344,7 +344,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -591,7 +591,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/reference/like.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -325,7 +325,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

6
docs/reference/mdro.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -425,7 +425,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul> <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>).</p><ul>
<li><p><strong>R = Resistant</strong><br /> <li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li> A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br /> <li><p><strong>S = Susceptible</strong><br />
@ -475,7 +475,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

6
docs/reference/proportion.html
View File

@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -368,7 +368,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul> <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>).</p><ul>
<li><p><strong>R = Resistant</strong><br /> <li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li> A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br /> <li><p><strong>S = Susceptible</strong><br />
@ -490,7 +490,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

6
docs/reference/resistance_predict.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -369,7 +369,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul> <p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>).</p><ul>
<li><p><strong>R = Resistant</strong><br /> <li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li> A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br /> <li><p><strong>S = Susceptible</strong><br />
@ -458,7 +458,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/reference/rsi_translation.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
</span> </span>
</div> </div>
@ -277,7 +277,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

2
index.md
View File

@ -45,7 +45,7 @@ This package can be used for:
* Calculating (empirical) susceptibility of both mono therapy and combination therapies ([tutorial](./articles/AMR.html)) * Calculating (empirical) susceptibility of both mono therapy and combination therapies ([tutorial](./articles/AMR.html))
* Predicting future antimicrobial resistance using regression models ([tutorial](./articles/resistance_predict.html)) * Predicting future antimicrobial resistance using regression models ([tutorial](./articles/resistance_predict.html))
* Getting properties for any microorganism (like Gram stain, species, genus or family) ([manual](./reference/mo_property.html)) * Getting properties for any microorganism (like Gram stain, species, genus or family) ([manual](./reference/mo_property.html))
* Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) ([manual](./reference/ab_property.html)) * Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) ([manual](./reference/ab_property.html))
* Plotting antimicrobial resistance ([tutorial](./articles/AMR.html)) * Plotting antimicrobial resistance ([tutorial](./articles/AMR.html))
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html)) * Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html))

6
man/as.ab.Rd
View File

@ -73,9 +73,9 @@ as.ab("Romycin") # trade name
# spelling from different languages and dyslexia are no problem # spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon") ab_atc("ceftriaxon")
ab_atc("cephtriaxone") ab_atc("cephtriaxone") # small spelling error
ab_atc("cephthriaxone") ab_atc("cephthriaxone") # or a bit more severe
ab_atc("seephthriaaksone") ab_atc("seephthriaaksone") # and even this works
# use ab_* functions to get a specific properties (see ?ab_property); # use ab_* functions to get a specific properties (see ?ab_property);
# they use as.ab() internally: # they use as.ab() internally:

36
man/as.rsi.Rd
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@ -54,7 +54,7 @@ The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRU
} }
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
\itemize{ \itemize{
\item \strong{R = Resistant}\cr \item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
@ -81,14 +81,9 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370))) # For INTERPRETING disk diffusion and MIC values -----------------------
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
is.rsi(rsi_data)
# this can also coerce combined MIC/RSI values: # single values
as.rsi("<= 0.002; S") # will return S
# interpret MIC values
as.rsi(x = as.mic(2), as.rsi(x = as.mic(2),
mo = as.mo("S. pneumoniae"), mo = as.mo("S. pneumoniae"),
ab = "AMP", ab = "AMP",
@ -98,21 +93,36 @@ as.rsi(x = as.disk(18),
mo = "Strep pneu", # `mo` will be coerced with as.mo() mo = "Strep pneu", # `mo` will be coerced with as.mo()
ab = "ampicillin", # and `ab` with as.ab() ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST") guideline = "EUCAST")
# a whole data set, even with combined MIC values and disk zones
df <- data.frame(microorganism = "E. coli",
AMP = as.mic(12),
GEN = as.disk(18))
as.rsi(df)
# For CLEANING existing R/SI values ------------------------------------
as.rsi(c("S", "I", "R", "A", "B", "C"))
as.rsi("<= 0.002; S") # will return "S"
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
is.rsi(rsi_data)
plot(rsi_data) # for percentages plot(rsi_data) # for percentages
barplot(rsi_data) # for frequencies barplot(rsi_data) # for frequencies
freq(rsi_data) # frequency table with informative header freq(rsi_data) # frequency table with informative header
# using dplyr's mutate
library(dplyr) library(dplyr)
example_isolates \%>\% example_isolates \%>\%
mutate_at(vars(PEN:RIF), as.rsi) mutate_at(vars(PEN:RIF), as.rsi)
# fastest way to transform all columns with already valid AMR results to class `rsi`:
# fastest way to transform all columns with already valid AB results to class `rsi`:
example_isolates \%>\% example_isolates \%>\%
mutate_if(is.rsi.eligible, mutate_if(is.rsi.eligible, as.rsi)
as.rsi)
# note: from dplyr 1.0.0 on, this will be:
# example_isolates \%>\%
# mutate(across(is.rsi.eligible, as.rsi))
# default threshold of `is.rsi.eligible` is 5\%. # default threshold of `is.rsi.eligible` is 5\%.
is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid

2
man/count.Rd
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@ -82,7 +82,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
\itemize{ \itemize{
\item \strong{R = Resistant}\cr \item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

2
man/mdro.Rd
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@ -187,7 +187,7 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
\itemize{ \itemize{
\item \strong{R = Resistant}\cr \item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

2
man/proportion.Rd
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@ -128,7 +128,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
\itemize{ \itemize{
\item \strong{R = Resistant}\cr \item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

2
man/resistance_predict.Rd
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@ -108,7 +108,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The u
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
\itemize{ \itemize{
\item \strong{R = Resistant}\cr \item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.