bug_drug_combinations
Determine Bug-Drug Combinations
Description
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples.
Usage
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
## S3 method for class 'bug_drug_combinations'
format(
x,
translate_ab = "name (ab, atc)",
language = get_locale(),
minimum = 30,
combine_SI = TRUE,
combine_IR = FALSE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...
)Arguments
x |
data with antibiotic columns, such as |
col_mo |
column name of the IDs of the microorganisms (see |
FUN |
function to call on the |
... |
arguments passed on to |
translate_ab |
character of length 1 containing column names of the antibiotics data set |
language |
language of the returned text, defaults to system language (see |
minimum |
the minimum allowed number of available (tested) isolates. Any isolate count lower than |
combine_SI |
a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument |
combine_IR |
logical to indicate whether values R and I should be summed |
add_ab_group |
logical to indicate where the group of the antimicrobials must be included as a first column |
remove_intrinsic_resistant |
logical to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table |
decimal.mark |
the character to be used to indicate the numeric decimal point. |
big.mark |
character; if not empty used as mark between every
|
Details
The function format() calculates the resistance per bug-drug combination. Use combine_IR = FALSE (default) to test R vs. S+I and combine_IR = TRUE to test R+I vs. S.
Value
The function bug_drug_combinations() returns a data.frame with columns "mo", "ab", "S", "I", "R" and "total".
Stable Lifecycle
The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
Read more on Our Website!
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
Source
M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition, 2014, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.
Examples
x <- bug_drug_combinations(example_isolates)
x
format(x, translate_ab = "name (atc)")
# Use FUN to change to transformation of microorganism codes
bug_drug_combinations(example_isolates,
FUN = mo_gramstain)
bug_drug_combinations(example_isolates,
FUN = function(x) ifelse(x == as.mo("E. coli"),
"E. coli",
"Others"))