P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-03-29 14:55:55 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9040: 9c95aa4

Browse Source
This commit is contained in:
github-actions
2026-03-24 12:34:17 +00:00
parent 330f1a9dfe
commit d55d073ae9
109 changed files with 762 additions and 777 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
reference/first_isolate.md
View File

@@ -330,10 +330,10 @@ method is applied at default.
example_isolates[first_isolate(info = TRUE), ]
#> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Using column 'date' as input for `col_date`.
#> ℹ Using column 'patient' as input for `col_patient_id`.
#> ℹ Using column date as input for `col_date`.
#> ℹ Using column patient as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
#> microbial ID was available)
#> # A tibble: 1,387 × 46
@@ -359,7 +359,7 @@ example_isolates[first_isolate(info = TRUE), ]
# \donttest{
# get all first Gram-negatives
example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
#> ℹ Using column 'mo' as input for `?mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> # A tibble: 441 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -388,7 +388,7 @@ if (require("dplyr")) {
}
#> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
#> ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
#> microbial ID was available)
#> # A tibble: 1,387 × 46
@@ -446,15 +446,15 @@ if (require("dplyr")) {
#> ℹ Determining first isolates using an episode length of 365 days
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> Group: ward = "Clinical"
#> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
#> ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 865 'phenotype-based' first isolates (70.1% of total where a microbial
#> ID was available)
#> Group: ward = "ICU"
#> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
#> ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 452 'phenotype-based' first isolates (70.0% of total where a microbial
#> ID was available)
#> Group: ward = "Outpatient"
#> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo')
#> ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column mo)
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial
#> ID was available)
#> # A tibble: 2,000 × 5