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AMR/reference/bug_drug_combinations.md
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# Determine Bug-Drug Combinations
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()`](https://rdrr.io/r/base/format.html) on the
result to prettify it to a publishable/printable format, see *Examples*.
## Usage
``` r
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname,
include_n_rows = FALSE, ...)
# S3 method for class '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 antimicrobials columns, such as `amox`, `AMX` and
`AMC`.
- col_mo:
Column name of the names or codes of the microorganisms (see
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)) - the default
is the first column of class
[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- FUN:
The function to call on the `mo` column to transform the microorganism
codes - the default is
[`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md).
- include_n_rows:
A [logical](https://rdrr.io/r/base/logical.html) to indicate if the
total number of rows must be included in the output.
- ...:
Arguments passed on to `FUN`.
- translate_ab:
A [character](https://rdrr.io/r/base/character.html) of length 1
containing column names of the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set.
- language:
Language of the returned text - the default is the current system
language (see
[`get_AMR_locale()`](https://amr-for-r.org/reference/translate.md))
and can also be set with the package option
[`AMR_locale`](https://amr-for-r.org/reference/AMR-options.md). Use
`language = NULL` or `language = ""` to prevent translation.
- minimum:
The minimum allowed number of available (tested) isolates. Any isolate
count lower than `minimum` will return `NA` with a warning. The
default number of `30` isolates is advised by the Clinical and
Laboratory Standards Institute (CLSI) as best practice, see *Source*.
- combine_SI:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
values S, SDD, and I should be summed, so resistance will be based on
only R - the default is `TRUE`.
- add_ab_group:
A [logical](https://rdrr.io/r/base/logical.html) to indicate where the
group of the antimicrobials must be included as a first column.
- remove_intrinsic_resistant:
[logical](https://rdrr.io/r/base/logical.html) 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.interval`
decimals *before* (hence `big`) the decimal point.
## Value
The function `bug_drug_combinations()` returns a
[data.frame](https://rdrr.io/r/base/data.frame.html) with columns "mo",
"ab", "S", "SDD", "I", "R", and "total".
## Details
The function [`format()`](https://rdrr.io/r/base/format.html) 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()`](https://rdrr.io/pkg/knitr/man/kable.html).
## Examples
``` r
# 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 × 8
#> mo ab S SDD I R NI total
#> <chr> <chr> <int> <int> <int> <int> <int> <int>
#> 1 (unknown species) AMC 15 0 0 0 0 15
#> 2 (unknown species) AMK 0 0 0 0 0 0
#> 3 (unknown species) AMP 15 0 0 1 0 16
#> 4 (unknown species) AMX 15 0 0 1 0 16
#> 5 (unknown species) AZM 3 0 0 3 0 6
#> 6 (unknown species) CAZ 0 0 0 0 0 0
#> 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 "Antimyc… Rifa… "" "100.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 6 "Beta-la… Amox… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 7 "" Amox… " 42… " 13.1% … "" " 10.3% (6/58)" "100.0% (30/30…
#> 8 "" Ampi… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 9 "" Benz… " 77… "100.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 10 "" Fluc… " 42… "" "" "" ""
#> # 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 × 8
#> mo ab S SDD I R NI total
#> <chr> <chr> <int> <int> <int> <int> <int> <int>
#> 1 Gram-negative AMC 463 0 89 174 0 726
#> 2 Gram-negative AMK 251 0 0 5 0 256
#> 3 Gram-negative AMP 226 0 0 405 0 631
#> 4 Gram-negative AMX 226 0 0 405 0 631
#> 5 Gram-negative AZM 1 0 2 696 0 699
#> 6 Gram-negative CAZ 607 0 0 27 0 634
#> 7 Gram-negative CHL 1 0 0 30 0 31
#> 8 Gram-negative CIP 610 0 11 63 0 684
#> 9 Gram-negative CLI 18 0 1 709 0 728
#> 10 Gram-negative COL 309 0 0 78 0 387
#> # 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 × 8
#> mo ab S SDD I R NI total
#> <chr> <chr> <int> <int> <int> <int> <int> <int>
#> 1 E. coli AMC 332 0 74 61 0 467
#> 2 E. coli AMK 171 0 0 0 0 171
#> 3 E. coli AMP 196 0 0 196 0 392
#> 4 E. coli AMX 196 0 0 196 0 392
#> 5 E. coli AZM 0 0 0 467 0 467
#> 6 E. coli CAZ 449 0 0 11 0 460
#> 7 E. coli CHL 0 0 0 0 0 0
#> 8 E. coli CIP 398 0 1 57 0 456
#> 9 E. coli CLI 0 0 0 467 0 467
#> 10 E. coli COL 240 0 0 0 0 240
#> # ℹ 70 more rows
#> Use 'format()' on this result to get a publishable/printable format.
# }
```
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