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2026-03-20 16:11:30 +00:00
parent ba003f3e23
commit 3560dfd611
115 changed files with 820 additions and 779 deletions
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reference/first_isolate.md
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@@ -332,11 +332,10 @@ 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 Basing inclusion on all antimicrobial results, using a points threshold
#> of 2
#> 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')
#> => Found 1,387 'phenotype-based' first isolates (69.4% of total where a
#> microbial ID was available)
#> microbial ID was available)
#> # A tibble: 1,387 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -361,6 +360,7 @@ example_isolates[first_isolate(info = TRUE), ]
# 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()`
#> (`?AMR::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>
@@ -388,11 +388,10 @@ if (require("dplyr")) {
filter(first_isolate(info = TRUE))
}
#> 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 Basing inclusion on all antimicrobial results, using a points threshold of 2
#> 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)
#> microbial ID was available)
#> # A tibble: 1,387 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -446,23 +445,19 @@ if (require("dplyr")) {
select(ward, date, patient, mo, first)
}
#> 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 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')
#> => Found 865 'phenotype-based' first isolates (70.1% of total where a
#> microbial ID was available)
#>
#> => 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')
#> => Found 452 'phenotype-based' first isolates (70.0% of total where a
#> microbial ID was available)
#>
#> => 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')
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a
#> microbial ID was available)
#> => Found 99 'phenotype-based' first isolates (82.5% of total where a microbial
#> ID was available)
#> # A tibble: 2,000 × 5
#> # Groups: ward [3]
#> ward date patient mo first