P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-02-09 12:32:56 +01:00
Code Releases Activity

Built site for AMR@3.0.1.9019: ba4c159

Browse Source
This commit is contained in:
github-actions
2026-02-08 22:40:23 +00:00
parent 0551ea51cb
commit 8b71d0eb99
255 changed files with 23625 additions and 810 deletions
Download Patch File Download Diff File Expand all files Collapse all files

78
reference/bug_drug_combinations.md
View File

@@ -102,7 +102,7 @@ format(x, translate_ab = "name (ab, atc)",
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".
"ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
## Details
@@ -143,30 +143,30 @@ example_isolates
# \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
#> # A tibble: 6 × 11
#> mo ab S SDD I R NI WT NWT NS total
#> <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1 (unknown species) AMC 15 0 0 0 0 0 0 0 15
#> 2 (unknown species) AMK 0 0 0 0 0 0 0 0 0
#> 3 (unknown species) AMP 15 0 0 1 0 0 0 0 16
#> 4 (unknown species) AMX 15 0 0 1 0 0 0 0 16
#> 5 (unknown species) AZM 3 0 0 3 0 0 0 0 6
#> 6 (unknown species) CAZ 0 0 0 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)"
#> 2 "" Gent… " 16… " 2.0% … "100.0% (39/… " 10.3% (6/58)" " 10.0% (3/30)"
#> 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 "Aminope… Amox… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 6 "" Amox… " 42… " 13.1% … "" " 10.3% (6/58)" "100.0% (30/30…
#> 6 "" Amox… " 42… " 28.9% … "" " 15.5% (9/58)" "100.0% (30/30…
#> 7 "" Ampi… " 93… " 50.0% … "" "100.0% (58/58… "100.0% (30/30…
#> 8 "Carbape… Imip… " 47… " 0.0% … " 0.0% (0/3… " 0.0% (0/51)" ""
#> 9 "" Mero… " 47… " 0.0% … "" " 0.0% (0/53)" ""
#> 10 "Cephalo… Cefa… " 47… " 2.4% … "100.0% (39/… "" "100.0% (30/30…
#> 10 "Cephalo… Cefa… " 47… " 3.7% … "100.0% (39/… "" "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>
@@ -175,19 +175,19 @@ format(x, translate_ab = "name (atc)")
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
#> # A tibble: 80 × 11
#> mo ab S SDD I R NI WT NWT NS total
#> <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1 Gram-negative AMC 463 0 89 174 0 0 0 0 726
#> 2 Gram-negative AMK 251 0 0 5 0 0 0 0 256
#> 3 Gram-negative AMP 226 0 0 405 0 0 0 0 631
#> 4 Gram-negative AMX 226 0 0 405 0 0 0 0 631
#> 5 Gram-negative AZM 1 0 2 696 0 0 0 0 699
#> 6 Gram-negative CAZ 607 0 0 27 0 0 0 0 634
#> 7 Gram-negative CHL 1 0 0 30 0 0 0 0 31
#> 8 Gram-negative CIP 610 0 11 63 0 0 0 0 684
#> 9 Gram-negative CLI 18 0 1 709 0 0 0 0 728
#> 10 Gram-negative COL 309 0 0 78 0 0 0 0 387
#> # ℹ 70 more rows
#> Use 'format()' on this result to get a publishable/printable format.
@@ -199,19 +199,19 @@ bug_drug_combinations(example_isolates,
)
}
)
#> # 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
#> # A tibble: 80 × 11
#> mo ab S SDD I R NI WT NWT NS total
#> <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1 E. coli AMC 332 0 74 61 0 0 0 0 467
#> 2 E. coli AMK 171 0 0 0 0 0 0 0 171
#> 3 E. coli AMP 196 0 0 196 0 0 0 0 392
#> 4 E. coli AMX 196 0 0 196 0 0 0 0 392
#> 5 E. coli AZM 0 0 0 467 0 0 0 0 467
#> 6 E. coli CAZ 449 0 0 11 0 0 0 0 460
#> 7 E. coli CHL 0 0 0 0 0 0 0 0 0
#> 8 E. coli CIP 398 0 1 57 0 0 0 0 456
#> 9 E. coli CLI 0 0 0 467 0 0 0 0 467
#> 10 E. coli COL 240 0 0 0 0 0 0 0 240
#> # ℹ 70 more rows
#> Use 'format()' on this result to get a publishable/printable format.
# }