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(v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values
This commit is contained in:
@ -1,6 +1,6 @@
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This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
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First and foremost, you are trained on version 2.1.1.9146. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9147. Remember this whenever someone asks which AMR package version you’re at.
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Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
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----------------------------------------------------------------------------------------------------
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@ -333,10 +333,12 @@ export(retrieve_wisca_parameters)
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export(rifamycins)
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export(right_join_microorganisms)
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export(scale_color_mic)
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export(scale_color_sir)
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export(scale_colour_mic)
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export(scale_colour_sir)
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export(scale_fill_mic)
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export(scale_fill_sir)
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export(scale_sir_colors)
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export(scale_sir_colours)
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export(scale_x_mic)
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export(scale_x_sir)
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@ -1650,18 +1652,19 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antibiogram.Rd':
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antibiogram(x, antibiotics = where(is.sir), mo_transform = "shortname",
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ab_transform = "name", syndromic_group = NULL, add_total_n = FALSE,
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only_all_tested = FALSE, digits = ifelse(wisca, 1, 0),
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formatting_type = getOption("AMR_antibiogram_formatting_type",
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ifelse(wisca, 14, 10)), col_mo = NULL, language = get_AMR_locale(),
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minimum = 30, combine_SI = TRUE, sep = " + ", wisca = FALSE,
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simulations = 1000, conf_interval = 0.95, interval_side = "two-tailed",
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formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
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col_mo = NULL, language = get_AMR_locale(), minimum = 30,
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combine_SI = TRUE, sep = " + ", wisca = FALSE, simulations = 1000,
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conf_interval = 0.95, interval_side = "two-tailed",
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info = interactive())
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wisca(x, antibiotics = where(is.sir), mo_transform = "shortname",
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ab_transform = "name", syndromic_group = NULL, add_total_n = FALSE,
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only_all_tested = FALSE, digits = 1,
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wisca(x, antibiotics = where(is.sir), ab_transform = "name",
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syndromic_group = NULL, add_total_n = FALSE, only_all_tested = FALSE,
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digits = 1,
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formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
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col_mo = NULL, language = get_AMR_locale(), minimum = 30,
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combine_SI = TRUE, sep = " + ", simulations = 1000,
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conf_interval = 0.95, interval_side = "two-tailed",
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info = interactive())
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retrieve_wisca_parameters(wisca_model, ...)
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@ -1684,7 +1687,7 @@ retrieve_wisca_parameters(wisca_model, ...)
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\item{syndromic_group}{a column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
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\item{add_total_n}{a \link{logical} to indicate whether total available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").}
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\item{add_total_n}{a \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
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\item{only_all_tested}{(for combination antibiograms): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see \emph{Details}}
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@ -1702,7 +1705,7 @@ retrieve_wisca_parameters(wisca_model, ...)
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\item{sep}{a separating character for antimicrobial columns in combination antibiograms}
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\item{wisca}{a \link{logical} to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is \code{FALSE}). This will use a Bayesian decision model to estimate regimen coverage probabilities using \href{https://en.wikipedia.org/wiki/Monte_Carlo_method}{Monte Carlo simulations}. Set \code{simulations} to adjust.}
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\item{wisca}{a \link{logical} to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is \code{FALSE}). This will use a Bayesian decision model to estimate regimen coverage probabilities using \href{https://en.wikipedia.org/wiki/Monte_Carlo_method}{Monte Carlo simulations}. Set \code{simulations}, \code{conf_interval}, and \code{interval_side} to adjust.}
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\item{simulations}{(for WISCA) a numerical value to set the number of Monte Carlo simulations}
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@ -1737,7 +1740,7 @@ For estimating antimicrobial coverage, especially when creating a WISCA, the out
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The numeric values of an antibiogram are stored in a long format as the \link[=attributes]{attribute} \code{long_numeric}. You can retrieve them using \code{attributes(x)$long_numeric}, where \code{x} is the outcome of \code{\link[=antibiogram]{antibiogram()}} or \code{\link[=wisca]{wisca()}}. This is ideal for e.g. advanced plotting.
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\subsection{Formatting Type}{
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The formatting of the 'cells' of the table can be set with the argument \code{formatting_type}. In these examples, \code{5} is the antimicrobial coverage (for WISCA: \code{4-6} indicates the confidence level), \code{15} the numerator, and \code{300} the denominator:
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The formatting of the 'cells' of the table can be set with the argument \code{formatting_type}. In these examples, \code{5} is the antimicrobial coverage (\code{4-6} indicates the confidence level), \code{15} the number of susceptible isolates, and \code{300} the number of tested (i.e., available) isolates:
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\enumerate{
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\item 5
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\item 15
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@ -1748,13 +1751,11 @@ The formatting of the 'cells' of the table can be set with the argument \code{fo
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\item 5 (N=300)
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\item 5\% (N=300)
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\item 5 (15/300)
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\item 5\% (15/300) - \strong{default for non-WISCA}
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\item 5\% (15/300)
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\item 5 (N=15/300)
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\item 5\% (N=15/300)
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Additional options for WISCA (using \code{antibiogram(..., wisca = TRUE)} or \code{wisca()}):
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\item 5 (4-6)
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\item 5\% (4-6\%) - \strong{default for WISCA}
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\item 5\% (4-6\%) - \strong{default}
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\item 5 (4-6,300)
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\item 5\% (4-6\%,300)
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\item 5 (4-6,N=300)
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@ -1765,7 +1766,7 @@ Additional options for WISCA (using \code{antibiogram(..., wisca = TRUE)} or \co
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\item 5\% (4-6\%,N=15/300)
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}
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The default is \code{14} for WISCA and \code{10} for non-WISCA, which can be set globally with the package option \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}. Do note that for WISCA, the numerator and denominator are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.
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The default is \code{14}, which can be set globally with the package option \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}. Do note that for WISCA, the total numbers of tested and susceptible isolates are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.
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Set \code{digits} (defaults to \code{0}) to alter the rounding of the susceptibility percentages.
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}
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@ -1774,7 +1775,7 @@ Set \code{digits} (defaults to \code{0}) to alter the rounding of the susceptibi
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There are various antibiogram types, as summarised by Klinker \emph{et al.} (2021, \doi{10.1177/20499361211011373}), and they are all supported by \code{\link[=antibiogram]{antibiogram()}}.
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\strong{Use WISCA whenever possible}, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki \emph{et al.} (2020, \doi{10.1001.jamanetworkopen.2019.21124}). See the section \emph{Explaining WISCA} on this page.
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For clinical coverage estimations, \strong{use WISCA whenever possible}, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki \emph{et al.} (2020, \doi{10.1001.jamanetworkopen.2019.21124}). See the section \emph{Explaining WISCA} on this page. Do note that WISCA is pathogen-agnostic, meaning that the outcome is not stratied by pathogen, but rather by syndrome.
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\enumerate{
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\item \strong{Traditional Antibiogram}
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@ -1844,13 +1845,16 @@ In clinical practice, antimicrobial coverage decisions evolve as more microbiolo
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At admission, no pathogen information is available.
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\itemize{
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\item Action: broad-spectrum coverage is based on local resistance patterns and syndromic antibiograms.
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\item Action: broad-spectrum coverage is based on local resistance patterns and syndromic antibiograms. Using the pathogen-agnostic yet incidence-weighted WISCA is preferred.
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\item Code example:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{antibiogram(your_data,
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antibiotics = selected_regimens,
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wisca = TRUE,
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mo_transform = NA) # all pathogens set to `NA`
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# preferred: use WISCA
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wisca(your_data,
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antibiotics = selected_regimens)
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}\if{html}{\out{</div>}}
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}
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\item \strong{Refinement with Gram Stain Results}
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@ -1862,7 +1866,6 @@ When a blood culture becomes positive, the Gram stain provides an initial and cr
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{antibiogram(your_data,
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antibiotics = selected_regimens,
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wisca = TRUE,
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mo_transform = "gramstain") # all pathogens set to Gram-pos/Gram-neg
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}\if{html}{\out{</div>}}
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}
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@ -1875,7 +1878,6 @@ After cultivation of the pathogen, full pathogen identification allows precise t
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{antibiogram(your_data,
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antibiotics = selected_regimens,
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wisca = TRUE,
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mo_transform = "shortname") # all pathogens set to 'G. species', e.g., E. coli
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}\if{html}{\out{</div>}}
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}
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@ -1919,7 +1921,7 @@ You can also use functions from specific 'table reporting' packages to transform
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\section{Explaining WISCA}{
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WISCA, as outlined by Bielicki \emph{et al.} (\doi{10.1093/jac/dkv397}), stands for Weighted-Incidence Syndromic Combination Antibiogram, which estimates the probability of adequate empirical antimicrobial regimen coverage for specific infection syndromes. This method leverages a Bayesian hierarchical logistic regression framework with random effects for pathogens and regimens, enabling robust estimates in the presence of sparse data.
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WISCA, as outlined by Bielicki \emph{et al.} (\doi{10.1093/jac/dkv397}), stands for Weighted-Incidence Syndromic Combination Antibiogram, which estimates the probability of adequate empirical antimicrobial regimen coverage for specific infection syndromes. This method leverages a Bayesian decision model with random effects for pathogen incidence and susceptibility, enabling robust estimates in the presence of sparse data.
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The Bayesian model assumes conjugate priors for parameter estimation. For example, the coverage probability \eqn{\theta} for a given antimicrobial regimen is modelled using a Beta distribution as a prior:
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@ -1953,6 +1955,8 @@ Stratified results can be provided based on covariates such as age, sex, and cli
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\deqn{\text{OR}_{\text{covariate}} = \frac{\exp(\beta_{\text{covariate}})}{\exp(\beta_0)}}
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By combining empirical data with prior knowledge, WISCA overcomes the limitations of traditional combination antibiograms, offering disease-specific, patient-stratified estimates with robust uncertainty quantification. This tool is invaluable for antimicrobial stewardship programs and empirical treatment guideline refinement.
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\strong{Note:} WISCA never gives an output on the pathogen/species level, as all incidences and susceptibilities are already weighted for all species.
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}
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\examples{
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@ -1970,14 +1974,12 @@ antibiogram(example_isolates,
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antibiogram(example_isolates,
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antibiotics = aminoglycosides(),
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ab_transform = "atc",
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mo_transform = "gramstain"
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)
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mo_transform = "gramstain")
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antibiogram(example_isolates,
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antibiotics = carbapenems(),
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ab_transform = "name",
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mo_transform = "name"
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)
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mo_transform = "name")
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# Combined antibiogram -------------------------------------------------
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@ -1985,16 +1987,14 @@ antibiogram(example_isolates,
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# combined antibiotics yield higher empiric coverage
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antibiogram(example_isolates,
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antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
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mo_transform = "gramstain"
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)
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mo_transform = "gramstain")
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# names of antibiotics do not need to resemble columns exactly:
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antibiogram(example_isolates,
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antibiotics = c("Cipro", "cipro + genta"),
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mo_transform = "gramstain",
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ab_transform = "name",
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sep = " & "
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)
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sep = " & ")
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# Syndromic antibiogram ------------------------------------------------
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@ -2002,8 +2002,7 @@ antibiogram(example_isolates,
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# the data set could contain a filter for e.g. respiratory specimens
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antibiogram(example_isolates,
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antibiotics = c(aminoglycosides(), carbapenems()),
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syndromic_group = "ward"
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)
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syndromic_group = "ward")
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# now define a data set with only E. coli
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ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
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@ -2016,27 +2015,24 @@ antibiogram(ex1,
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syndromic_group = ifelse(ex1$ward == "ICU",
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"UCI", "No UCI"
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),
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language = "es"
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)
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language = "es")
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# WISCA antibiogram ----------------------------------------------------
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# can be used for any of the above types - just add `wisca = TRUE`
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# WISCA are not stratified by species, but rather on syndromes
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antibiogram(example_isolates,
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antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
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mo_transform = "gramstain",
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wisca = TRUE
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)
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syndromic_group = "ward",
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wisca = TRUE)
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# Print the output for R Markdown / Quarto -----------------------------
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ureido <- antibiogram(example_isolates,
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antibiotics = ureidopenicillins(),
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ab_transform = "name",
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wisca = TRUE
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)
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syndromic_group = "name",
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wisca = TRUE)
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# in an Rmd file, you would just need to return `ureido` in a chunk,
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# but to be explicit here:
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@ -2049,14 +2045,11 @@ if (requireNamespace("knitr")) {
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ab1 <- antibiogram(example_isolates,
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antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
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mo_transform = "gramstain",
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wisca = TRUE
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)
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mo_transform = "gramstain")
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ab2 <- antibiogram(example_isolates,
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antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
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mo_transform = "gramstain",
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syndromic_group = "ward"
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)
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syndromic_group = "ward")
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if (requireNamespace("ggplot2")) {
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ggplot2::autoplot(ab1)
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@ -7339,6 +7332,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
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\alias{scale_fill_mic}
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\alias{scale_x_sir}
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\alias{scale_colour_sir}
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\alias{scale_color_sir}
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\alias{scale_fill_sir}
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\alias{plot.mic}
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\alias{autoplot.mic}
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@ -7349,6 +7343,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
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\alias{facet_sir}
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\alias{scale_y_percent}
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\alias{scale_sir_colours}
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\alias{scale_sir_colors}
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\alias{theme_sir}
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\alias{labels_sir_count}
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\title{Plotting Helpers for AMR Data Analysis}
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@ -7359,8 +7354,6 @@ scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_x_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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@ -7375,7 +7368,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
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"EUCAST") == "EUCAST", ...)
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\method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
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\method{plot}{mic}(x, mo = NULL, ab = NULL,
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guideline = getOption("AMR_guideline", "EUCAST"),
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main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
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= language),
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
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@ -7385,8 +7379,9 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{autoplot}{mic}(object, mo = NULL, ab = NULL,
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guideline = "EUCAST", title = deparse(substitute(object)),
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ylab = translate_AMR("Frequency", language = language),
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guideline = getOption("AMR_guideline", "EUCAST"),
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title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
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language = language),
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
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language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), expand = TRUE,
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@ -7396,7 +7391,7 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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\method{plot}{disk}(x, main = deparse(substitute(x)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
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mo = NULL, ab = NULL, guideline = "EUCAST",
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mo = NULL, ab = NULL, guideline = getOption("AMR_guideline", "EUCAST"),
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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@ -7405,8 +7400,9 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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\method{autoplot}{disk}(object, mo = NULL, ab = NULL,
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title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
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language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
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language = language), guideline = "EUCAST", colours_SIR = c("#3CAEA3",
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"#F6D55C", "#ED553B"), language = get_AMR_locale(), expand = TRUE,
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language = language), guideline = getOption("AMR_guideline", "EUCAST"),
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
|
||||
|
||||
@ -7499,12 +7495,12 @@ Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC
|
||||
\details{
|
||||
\subsection{The \verb{scale_*_mic()} Functions}{
|
||||
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous scale. They allow to rescale the MIC range, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
|
||||
}
|
||||
|
||||
\subsection{The \verb{scale_*_sir()} Functions}{
|
||||
|
||||
The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class (S/I/R values). They can translate the S/I/R values to any of the 20 supported languages, and set colour-blind friendly colours to the \code{colour} and \code{fill} aesthetics.
|
||||
The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 20 supported languages (use \code{language = NULL} to keep S/I/R). Also, except for \code{\link[=scale_x_sir]{scale_x_sir()}}, they set colour-blind friendly colours to the \code{colour} and \code{fill} aesthetics.
|
||||
}
|
||||
|
||||
\subsection{Additional \code{ggplot2} Functions}{
|
||||
@ -7520,7 +7516,7 @@ This package contains more functions that extend the \code{ggplot2} package, to
|
||||
|
||||
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
|
||||
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011". Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
|
||||
For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
@ -6,8 +6,8 @@ Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE 凝固酶阳性葡萄球
|
||||
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE β-溶血性链球菌 Beta-hemolytický streptokok Beta-haemolytiske streptokokker Beta-hemolytische Streptococcus Beeta-hemolyyttinen streptokokki Streptococcus Bêta-hémolytique Beta-hämolytischer Streptococcus Β-αιμολυτικός στρεπτόκοκκος Streptococcus Beta-emolitico ベータ溶血性レンサ球菌 Beta-hemolytiske streptokokker Streptococcus beta-hemolityczny Streptococcus Beta-hemolítico Streptococ beta-hemolitic Бета-гемолитический стрептококк Streptococcus Beta-hemolítico Beta-hemolytiska streptokocker Beta-hemolitik Streptokok Бета-гемолітичний стрептокок
|
||||
unknown Gram-negatives TRUE TRUE FALSE TRUE 不明革兰氏阴性菌 neznámé gramnegativní ukendte Gram-negative onbekende Gram-negatieven tuntemattomat gramnegatiiviset Gram négatifs inconnus unbekannte Gramnegativen άγνωστοι αρνητικοί κατά Gram Gram negativi sconosciuti 不明なグラム陰性菌 ukjent Gram-negative Nieznane bakterie Gram-ujemne Gram negativos desconhecidos Gram-negative necunoscute неизвестные грамотрицательные Gram negativos desconocidos okända gramnegativa bakterier bilinmeyen Gram-negatifler невідомі грамнегативні
|
||||
unknown Gram-positives TRUE TRUE FALSE TRUE 不明革兰氏阳性菌 neznámé grampozitivní ukendte Gram-positive onbekende Gram-positieven tuntemattomat grampositiiviset Gram positifs inconnus unbekannte Grampositiven άγνωστοι θετικοί κατά Gram Gram positivi sconosciuti 未知のグラム陽性菌 ukjent Gram-positive Nieznane bakterie Gram-dodatnie Gram positivos desconhecidos Gram-pozitive necunoscute неизвестные грамположительные Gram positivos desconocidos okända Gram-positiva bilinmeyen Gram-pozitifler невідомі грампозитивні
|
||||
unknown anaerobic Gram-negatives TRUE TRUE FALSE TRUE ukendte anaerobe Gram-negative onbekende anaerobe Gram-negatieven unbekannte anaerobe Gramnegativen
|
||||
unknown anaerobic Gram-positives TRUE TRUE FALSE TRUE ukendte anaerobe Gram-positive onbekende anaerobe Gram-positieven unbekannte anaerobe Grampositiven
|
||||
unknown anaerobic Gram-negatives TRUE FALSE FALSE FALSE 未知的厌氧革兰氏阴性菌 Neznámé anaerobní Gram-negativní bakterie Ukendte anaerobe Gram-negative Onbekende anaerobe Gram-negatieven Tuntemattomat anaerobiset gramnegatiivit Anaérobies à Gram négatif inconnues Unbekannte anaerobe Gram-negative Άγνωστοι αναερόβιοι Gram-αρνητικοί Sconosciuti anaerobi Gram-negativi 未知の嫌気性グラム陰性菌 Ukjente anaerobe Gram-negative Nieznane beztlenowe Gram-ujemne Anaeróbios Gram-negativos desconhecidos Necunoscuți anaerobi Gram-negativi Некоторые анаэробные Грам-отрицательные Desconocidos anaerobios Gram-negativos Okända anaeroba gramnegativa Bilinmeyen anaerobik Gram-negatif Невідомі анаеробні Грам-негативні
|
||||
unknown anaerobic Gram-positives TRUE FALSE FALSE FALSE 未知的厌氧革兰氏阳性菌 Neznámé anaerobní Gram-pozitivní bakterie Ukendte anaerobe Gram-positive Onbekende anaerobe Gram-positieven Tuntemattomat anaerobiset grampositiiviset Anaérobies à Gram positif inconnues Unbekannte anaerobe Gram-positive Άγνωστοι αναερόβιοι Gram-θετικοί Sconosciuti anaerobi Gram-positivi 未知の嫌気性グラム陽性菌 Ukjente anaerobe Gram-positive Nieznane beztlenowe Gram-dodatnie Anaeróbios Gram-positivos desconhecidos Necunoscuți anaerobi Gram-pozitivi Некоторые анаэробные Грам-положительные Desconocidos anaerobios Gram-positivos Okända anaeroba grampositiva Bilinmeyen anaerobik Gram-pozitif Невідомі анаеробні Грам-позитивні
|
||||
unknown protozoan TRUE TRUE FALSE TRUE 未知原生动物 neznámý prvok ukendt protozo onbekend protozoön tuntematon alkueläin protozoaire inconnu unbekanntes Protozoon άγνωστο πρωτόζωο protozoo sconosciuto 未知の原生動物 ukjent protozo nieznany pierwotniak protozoário desconhecido protozoar necunoscut неизвестное простейшее protozoo desconocido okänd protozo bilinmeyen protozoa невідоме найпростіше
|
||||
unknown fungus TRUE TRUE FALSE TRUE 未知真菌 neznámé houby ukendt svamp onbekende schimmel tuntematon sieni champignon inconnu unbekannter Pilze άγνωστος μύκητας fungo sconosciuto 未知真菌 ukjent sopp Nieznany grzyb fungo desconhecido ciuperci necunoscute неизвестный грибок hongo desconocido Okänd svamp bilinmeyen mantar невідомий гриб
|
||||
unknown yeast TRUE TRUE FALSE TRUE 未知酵母菌 neznámé kvasinky ukendt gær onbekende gist tuntematon hiiva levure inconnue unbekannte Hefe άγνωστος ζυμομύκητας lievito sconosciuto 未知酵母 ukjent gjær Nieznany drożdżak levedura desconhecida drojdie necunoscută неизвестные дрожжи levadura desconocida Okänd jäst bilinmeyen maya невідомі дріжджі
|
||||
@ -39,13 +39,13 @@ vegetative TRUE TRUE FALSE FALSE 无性系 vegetativní vegetativ vegetatief kas
|
||||
([([ ]*?)Group TRUE TRUE FALSE FALSE ([([]*?)组 \\1Skupina \\1Gruppe \\1Groep \\1Ryhmä \\1Groupe \\1Gruppe ([([ ]*;)ομάδα \\1Gruppo \\1グループ \\1Gruppe ([([ ]*?)Grupa \\1Grupo \\1Grup \\1Группа \\1Grupo \\1Grupp ([([ ]*?)Grup \\1Група
|
||||
no .*growth FALSE FALSE FALSE FALSE 无.*生长 žádný .*růst ingen .*vækst geen .*groei ei .*kasvua pas .*croissance keine(|n|m|r|s)|nicht .*wachstum όχι .*αύξηση sem .*crescimento 成長なし nei .*vekst brak .*wzrostu sem .*crescimento fără creștere отсутствие.*роста no .*crecimientonon ingen .*tillväxt büyüme yok відсутність .*росту
|
||||
no|not FALSE FALSE FALSE FALSE 不|不 ne nej|ikke geen|niet ei non keine? no|not sem no|ない nei|ikke nie|nie sem nu нет? no|sin nej|inte hayır|değil|hayir|degil ні
|
||||
Intermediate TRUE FALSE FALSE FALSE 中级 Meziprodukt Mellemliggende Intermediair Väliaikainen Mittlere Ενδιάμεση 中間体 Mellomliggende Pośrednia Intermediar Intermedio Mellanliggande Orta seviye Знижена чутливість
|
||||
Susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，暴露增加 Vnímavý, zvýš. expozice Modtagelig, øget eksp. Gevoelig bij verh. blootstelling Altis, lisääntynyt altist. Empfindlich, erh Belastung Ευάλωτος, αυξημένη έκθεση 感受性、曝露量増加 Mottakelig, økt eksp. Podatne, zwiększone narażenie Susceptibil, exp. crescută Susceptible, mayor exposición Mottaglig, inkr. exponering Duyarlı, enk. maruziyet Чутливий до підвищеної експозиції
|
||||
susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，接触增加 náchylná,zvýš. Expozice modtagelig, øget eksp. gevoelig bij verh. blootstelling altis, lisääntynyt altist. empfindlich, erh Belastung Ευαίσθητος, αυξημένη έκθεση 影響を受けやすい、露出が増える mottakelig, økt eksp. podatny, zwiększone narażenie susceptibil, exp. crescută susceptible, mayor exposición mottaglig, inkr. exponering duyarlı, enk. maruziyet чутливий до підвищеної експозиції
|
||||
Susceptible TRUE FALSE FALSE FALSE 易受影响 Susceptible Modtagelig Gevoelig Altis Empfindlich Ευαίσθητο 影響を受けやすい Mottakelig Podatny Susceptibil Susceptible Mottaglig Duyarlı Чутливий
|
||||
Incr. exposure TRUE FALSE FALSE FALSE 暴露增加 zvýšená expozice Øget eksponering 'Incr. exposure' Lisääntynyt altistuminen Empfindlich, erh Belastung Αυξημένη έκθεση 曝露量増加 Økt eksp. Większe narażenie Exp. crescută Mayor exposición Inkr. exponering Enk. maruziyet Підвищена експозиція
|
||||
Resistant TRUE FALSE FALSE FALSE 耐药性 Rezistentní Resistent Resistent Kestävä Resistent Ανθεκτικός 耐性 Resistent Odporny Rezistent Resistente Resistent Dayanıklı Стійкий
|
||||
Not interpretable TRUE FALSE FALSE FALSE 无法解释 Nelze interpretovat Ufortolkelig Niet interpreteerbaar Ei tulkittavissa Non interprétable Nicht interpretierbar Μη ερμηνεύσιμο Non interpretabile 解釈不可 Utolkelig ikke Niemożliwe do interpretacji Neinterpretabil Непереводимо No interpretable Inte tolkningsbar Yorumlanamaz Непридатний до інтерпретації
|
||||
Intermediate TRUE FALSE FALSE FALSE 中级 Meziprodukt Mellemliggende Intermediair Väliaikainen Intermédiaire Mittlere Ενδιάμεση Intermedio 中間体 Mellomliggende Pośrednia Intermediário Intermediar Проміжний Intermedio Mellanliggande Orta seviye Знижена чутливість
|
||||
Susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，暴露增加 Vnímavý, zvýšená expozice Modtagelig, øget eksponering Gevoelig bij verhoogde blootstelling Altis, lisääntynyt altistuminen Sensible, exposition accrue Empfindlich, erhöhte Belastung Ευάλωτος, αυξημένη έκθεση Sensibile, esposizione aumentata 感受性、曝露量増加 Mottakelig, økt eksponering Podatne, zwiększone narażenie Suscetível, exposição aumentada Susceptibil, expunere crescută Чутливий, підвищена експозиція Susceptible, mayor exposición Mottaglig, ökad exponering Duyarlı, artmış maruziyet Чутливий до підвищеної експозиції
|
||||
susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，接触增加 Vnímavý, zvýšená expozice Modtagelig, øget eksponering Gevoelig bij verhoogde blootstelling Altis, lisääntynyt altistuminen Sensible, exposition accrue Empfindlich, erhöhte Belastung Ευαίσθητος, αυξημένη έκθεση Sensibile, esposizione aumentata 影響を受けやすい、露出が増える Mottakelig, økt eksponering Podatne, zwiększone narażenie Suscetível, exposição aumentada Susceptibil, expunere crescută Чутливий, підвищена експозиція Susceptible, mayor exposición Mottaglig, ökad exponering Duyarlı, artmış maruziyet Чутливий до підвищеної експозиції
|
||||
Susceptible TRUE FALSE FALSE FALSE 易受影响 Vnímavý Modtagelig Gevoelig Altis Sensible Empfindlich Ευαίσθητο Sensibile 影響を受けやすい Mottakelig Podatny Suscetível Susceptibil Чутливий Susceptible Mottaglig Duyarlı Чутливий
|
||||
Incr. exposure TRUE FALSE FALSE FALSE 暴露增加 Zvýšená expozice Øget eksponering Verhoogde blootstelling Lisääntynyt altistuminen Exposition accrue Erhöhte Belastung Αυξημένη έκθεση Esposizione aumentata 曝露量増加 Økt eksponering Większe narażenie Exposição aumentada Expunere crescută Підвищена експозиція Mayor exposición Ökad exponering Artmış maruziyet Підвищена експозиція
|
||||
Resistant TRUE FALSE FALSE FALSE 耐药性 Rezistentní Resistent Resistent Kestävä Résistant Resistent Ανθεκτικός Resistente 耐性 Resistent Odporny Resistente Rezistent Стійкий Resistente Resistent Dayanıklı Стійкий
|
||||
Not interpretable TRUE FALSE FALSE FALSE 无法解释 Nelze interpretovat Ufortolkelig Niet interpreteerbaar Ei tulkittavissa Non interprétable Nicht interpretierbar Μη ερμηνεύσιμο Non interpretabile 解釈不可 Utolkelig ikke Niemożliwe do interpretacji Não interpretável Neinterpretabil Непереводимо No interpretable Inte tolkningsbar Yorumlanamaz Непридатний до інтерпретації
|
||||
antibiotic TRUE TRUE FALSE FALSE 抗生素 antibiotikum antibiotikum antibioticum antibiootti antibiotique Antibiotikum αντιβιοτικό antibiotico 抗生物質 Antibiotikum antybiotyk antibiótico antibiotic антибиотик antibiótico antibiotika Antibiyotik антибіотик
|
||||
Antibiotic TRUE TRUE FALSE FALSE 抗生素 Antibiotikum Antibiotikum Antibioticum Antibiootti Antibiotique Antibiotikum Αντιβιοτικό Antibiotico 抗生物質 Antibiotikum Antybiotyk Antibiótico Antibiotic Антибиотик Antibiótico Antibiotika Antibiyotik Антибіотик
|
||||
Drug TRUE TRUE FALSE FALSE 药物 Lék Lægemiddel Middel Lääke Médicament Medikament Φάρμακο Droga 薬剤 Legemiddel Lek Droga Medicament Лекарство Fármaco Läkemedel İlaç Лікарський засіб
|
||||
|
||||
|
Can't render this file because it has a wrong number of fields in line 48.
|
Reference in New Issue
Block a user