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(v1.2.0.9008) ab_class improvement
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@ -190,7 +190,7 @@ Finally, we will apply [EUCAST rules](http://www.eucast.org/expert_rules_and_int
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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:
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```{r eucast, warning = FALSE, message = FALSE}
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data <- eucast_rules(data, col_mo = "bacteria")
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data <- eucast_rules(data, col_mo = "bacteria", rules = "all")
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```
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# Adding new variables
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@ -332,6 +332,41 @@ data_1st %>%
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freq(genus, species, header = TRUE)
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```
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## Overview of different bug/drug combinations
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If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the `bug_drug_combinations()` function:
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```{r bug_drg 1a, eval = FALSE}
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data_1st %>%
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bug_drug_combinations() %>%
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head() # show first 6 rows
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```
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```{r bug_drg 1b, echo = FALSE, results = 'asis'}
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knitr::kable(data_1st %>%
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bug_drug_combinations() %>%
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head(),
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align = "c")
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```
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Using [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), you can also select columns based on the antibiotic class they are in:
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```{r bug_drg 2a, eval = FALSE}
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data_1st %>%
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select(bacteria, fluoroquinolones()) %>%
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bug_drug_combinations()
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```
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```{r bug_drg 2b, echo = FALSE, results = 'asis'}
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knitr::kable(data_1st %>%
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select(bacteria, fluoroquinolones()) %>%
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bug_drug_combinations(),
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align = "c")
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```
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This will only give you the crude numbers in the data. To calculate antimicrobial resistance, we use the `resistance()` and `susceptibility()` functions.
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## Resistance percentages
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The functions `resistance()` and `susceptibility()` can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions `proportion_S()`, `proportion_SI()`, `proportion_I()`, `proportion_IR()` and `proportion_R()` can be used to determine the proportion of a specific antimicrobial outcome.
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