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(v1.8.1.9014) add Toxoplasma

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dr. M.S. (Matthijs) Berends
2022-08-12 23:27:15 +02:00
parent 7f981e7778
commit ab97268f4c
20 changed files with 808 additions and 728 deletions
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8
man/key_antimicrobials.Rd
View File

@ -11,12 +11,12 @@ key_antimicrobials(
col_mo = NULL,
universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
"ceftazidime", "meropenem"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
"meropenem"),
gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
"oxacillin", "rifampin"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
"nystatin", "voriconazole"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
"voriconazole"),
only_rsi_columns = FALSE,
...
)

30
man/rsi_translation.Rd
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@ -30,22 +30,20 @@ Data set containing reference data to interpret MIC and disk diffusion to R/SI v
Overview of the data set:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
}\if{html}{\out{</div>}}
\if{html}{\out{<div class="sourceCode">}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
## 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
## 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
## 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
## breakpoint_S breakpoint_R uti
## 1 1 1 FALSE
## 2 1 1 FALSE
## 3 1 1 FALSE
## 4 1 1 FALSE
## 5 1 1 FALSE
## 6 1 1 FALSE
#> guideline method site mo rank_index ab ref_tbl disk_dose
#> 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
#> 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
#> 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
#> 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
#> 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
#> 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
#> breakpoint_S breakpoint_R uti
#> 1 1 1 FALSE
#> 2 1 1 FALSE
#> 3 1 1 FALSE
#> 4 1 1 FALSE
#> 5 1 1 FALSE
#> 6 1 1 FALSE
}\if{html}{\out{</div>}}
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.