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(v1.8.1.9014) add Toxoplasma
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@ -11,12 +11,12 @@ key_antimicrobials(
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col_mo = NULL,
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universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
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"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
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gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
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"ceftazidime", "meropenem"),
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gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
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"meropenem"),
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gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
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"oxacillin", "rifampin"),
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antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
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"nystatin", "voriconazole"),
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antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
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"voriconazole"),
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only_rsi_columns = FALSE,
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...
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)
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@ -30,22 +30,20 @@ Data set containing reference data to interpret MIC and disk diffusion to R/SI v
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Overview of the data set:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
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}\if{html}{\out{</div>}}
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\if{html}{\out{<div class="sourceCode">}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
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## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
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## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
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## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
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## 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
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## 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
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## 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
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## breakpoint_S breakpoint_R uti
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## 1 1 1 FALSE
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## 2 1 1 FALSE
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## 3 1 1 FALSE
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## 4 1 1 FALSE
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## 5 1 1 FALSE
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## 6 1 1 FALSE
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#> guideline method site mo rank_index ab ref_tbl disk_dose
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#> 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
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#> 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
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#> 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
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#> 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
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#> 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
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#> 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
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#> breakpoint_S breakpoint_R uti
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#> 1 1 1 FALSE
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#> 2 1 1 FALSE
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#> 3 1 1 FALSE
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#> 4 1 1 FALSE
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#> 5 1 1 FALSE
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#> 6 1 1 FALSE
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}\if{html}{\out{</div>}}
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The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
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