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 publishable/printable format, see Examples.
Usage
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
# S3 method for bug_drug_combinations
format(
x,
translate_ab = "name (ab, atc)",
language = get_AMR_locale(),
minimum = 30,
combine_SI = TRUE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...
)Arguments
- x
a data set with antibiotic columns, such as
amox,AMXandAMC- col_mo
column name of the names or codes of the microorganisms (see
as.mo()) - the default is the first column of classmo. Values will be coerced usingas.mo().- FUN
the function to call on the
mocolumn to transform the microorganism codes - the default ismo_shortname()- ...
arguments passed on to
FUN- translate_ab
a character of length 1 containing column names of the antibiotics data set
- language
language of the returned text - the default is the current system language (see
get_AMR_locale()) and can also be set with the package optionAMR_locale. Uselanguage = NULLorlanguage = ""to prevent translation.- minimum
the minimum allowed number of available (tested) isolates. Any isolate count lower than
minimumwill returnNAwith a warning. The default number of30isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.- combine_SI
a logical to indicate whether values S and I should be summed, so resistance will be based on only R - the default is
TRUE- add_ab_group
a 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
big.intervaldecimals before (hencebig) the decimal point.
Value
The function bug_drug_combinations() returns a data.frame with columns "mo", "ab", "S", "SDD", "I", "R", and "total".
Details
The function format() calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use combine_SI = TRUE (default) to test R vs. S+I and combine_SI = FALSE to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. knitr::kable().
Examples
# example_isolates is a data set available in the AMR package.
# run ?example_isolates for more info.
example_isolates
#> # A tibble: 2,000 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
#> # ℹ 1,990 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# \donttest{
x <- bug_drug_combinations(example_isolates)
head(x)
#> # A tibble: 6 × 9
#> mo ab S SDD I R NI total N
#> <chr> <chr> <int> <int> <int> <int> <int> <int> <lgl>
#> 1 (unknown species) AMC 15 0 0 0 0 15 NA
#> 2 (unknown species) AMK 0 0 0 0 0 0 NA
#> 3 (unknown species) AMP 15 0 0 1 0 16 NA
#> 4 (unknown species) AMX 15 0 0 1 0 16 NA
#> 5 (unknown species) AZM 3 0 0 3 0 6 NA
#> 6 (unknown species) CAZ 0 0 0 0 0 0 NA
#> Use 'format()' on this result to get a publishable/printable format.
format(x, translate_ab = "name (atc)")
#> # A tibble: 39 × 12
#> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 "Aminogl… Amik… "100… " 0.0% … "100.0% (39/… "" ""
#> 2 "" Gent… " 13… " 2.0% … "100.0% (39/… " 10.3% (6/58)" " 0.0% (0/30)"
#> 3 "" Kana… "100… "" "100.0% (39/… "" "100.0% (30/30…
#> 4 "" Tobr… " 78… " 2.6% … "100.0% (39/… " 10.3% (6/58)" " 0.0% (0/30)"
#> 5 "Ampheni… Chlo… "" "" "" "" "100.0% (30/30…
#> 6 "Antimyc… Rifa… "" "100.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 7 "Beta-la… Amox… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 8 "" Amox… " 42… " 13.1% … "" " 10.3% (6/58)" "100.0% (30/30…
#> 9 "" Ampi… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 10 "" Benz… " 77… "100.0% … "" "100.0% (58/58… "100.0% (30/30…
#> # ℹ 29 more rows
#> # ℹ 5 more variables: `P. mirabilis` <chr>, `S. aureus` <chr>,
#> # `S. epidermidis` <chr>, `S. hominis` <chr>, `S. pneumoniae` <chr>
# Use FUN to change to transformation of microorganism codes
bug_drug_combinations(example_isolates,
FUN = mo_gramstain
)
#> # A tibble: 80 × 9
#> mo ab S SDD I R NI total N
#> * <chr> <chr> <int> <int> <int> <int> <int> <int> <lgl>
#> 1 Gram-negative AMC 463 0 89 174 0 726 NA
#> 2 Gram-negative AMK 251 0 0 5 0 256 NA
#> 3 Gram-negative AMP 226 0 0 405 0 631 NA
#> 4 Gram-negative AMX 226 0 0 405 0 631 NA
#> 5 Gram-negative AZM 1 0 2 696 0 699 NA
#> 6 Gram-negative CAZ 607 0 0 27 0 634 NA
#> 7 Gram-negative CHL 1 0 0 30 0 31 NA
#> 8 Gram-negative CIP 610 0 11 63 0 684 NA
#> 9 Gram-negative CLI 18 0 1 709 0 728 NA
#> 10 Gram-negative COL 309 0 0 78 0 387 NA
#> # ℹ 70 more rows
#> Use 'format()' on this result to get a publishable/printable format.
bug_drug_combinations(example_isolates,
FUN = function(x) {
ifelse(x == as.mo("Escherichia coli"),
"E. coli",
"Others"
)
}
)
#> # A tibble: 80 × 9
#> mo ab S SDD I R NI total N
#> * <chr> <chr> <int> <int> <int> <int> <int> <int> <lgl>
#> 1 E. coli AMC 332 0 74 61 0 467 NA
#> 2 E. coli AMK 171 0 0 0 0 171 NA
#> 3 E. coli AMP 196 0 0 196 0 392 NA
#> 4 E. coli AMX 196 0 0 196 0 392 NA
#> 5 E. coli AZM 0 0 0 467 0 467 NA
#> 6 E. coli CAZ 449 0 0 11 0 460 NA
#> 7 E. coli CHL 0 0 0 0 0 0 NA
#> 8 E. coli CIP 398 0 1 57 0 456 NA
#> 9 E. coli CLI 0 0 0 467 0 467 NA
#> 10 E. coli COL 240 0 0 0 0 240 NA
#> # ℹ 70 more rows
#> Use 'format()' on this result to get a publishable/printable format.
# }