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(v1.4.0) matching score update

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dr. M.S. (Matthijs) Berends
2020-10-08 11:16:03 +02:00
parent c04dc852cf
commit 28e77680c5
261 changed files with 1488 additions and 1171 deletions
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4
vignettes/AMR.Rmd
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@ -185,7 +185,7 @@ data <- data %>%
mutate_at(vars(AMX:GEN), as.rsi)
```
Finally, we will apply [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the `eucast_rules()` function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.
Finally, we will apply [EUCAST rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the `eucast_rules()` function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.
Because the amoxicillin (column `AMX`) and amoxicillin/clavulanic acid (column `AMC`) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The `eucast_rules()` fixes this:
@ -206,7 +206,7 @@ data <- data %>%
## First isolates
We also need to know which isolates we can *actually* use for analysis.
To conduct an analysis of antimicrobial resistance, you must [only include the first isolate of every patient per episode](https://www.ncbi.nlm.nih.gov/pubmed/17304462) (Hindler *et al.*, Clin Infect Dis. 2007). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following weeks (yes, some countries like the Netherlands have these blood drawing policies). The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would clearly be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
To conduct an analysis of antimicrobial resistance, you must [only include the first isolate of every patient per episode](https:/pubmed.ncbi.nlm.nih.gov/17304462/) (Hindler *et al.*, Clin Infect Dis. 2007). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following weeks (yes, some countries like the Netherlands have these blood drawing policies). The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would clearly be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
The Clinical and Laboratory Standards Institute (CLSI) appoints this as follows:

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vignettes/EUCAST.Rmd
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@ -24,7 +24,7 @@ library(AMR)
## Introduction
What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states [on their website](http://www.eucast.org/expert_rules_and_intrinsic_resistance/):
What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states [on their website](https://www.eucast.org/expert_rules_and_intrinsic_resistance/):
> *EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.*

2
vignettes/MDR.Rmd
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@ -36,7 +36,7 @@ The function support multiple guidelines. You can select a guideline with the `g
Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext))
* `guideline = "EUCAST"`
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" ([link](http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf))
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf))
* `guideline = "TB"`
The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/tb/publications/pmdt_companionhandbook/en/))

2
vignettes/datasets.Rmd
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@ -45,7 +45,7 @@ structure_txt <- function(dataset) {
download_txt <- function(filename) {
msg <- paste0("It was last updated on ",
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z")),
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", filename, ".html).\n")
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n")
github_base <- "https://github.com/msberends/AMR/raw/master/data-raw/"
filename <- paste0("../data-raw/", filename)
txt <- paste0(filename, ".txt")