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Add add_if_missing parameter to control NA handling in interpretive rules (#264)

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Matthijs Berends
2026-04-21 21:53:43 +02:00
committed by GitHub
parent fb8758f36b
commit 8ff5d4472a
46 changed files with 1232 additions and 1016 deletions
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26
data-raw/AMR_vet.qmd
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@@ -15,8 +15,10 @@ library(readr)
library(tidyr)
# WHONET version of 16th Feb 2024
whonet_breakpoints <- read_tsv("WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
show_col_types = FALSE, guess_max = Inf) %>%
whonet_breakpoints <- read_tsv("WHONET/Resources/Breakpoints.txt",
na = c("", "NA", "-"),
show_col_types = FALSE, guess_max = Inf
) %>%
filter(GUIDELINES %in% c("CLSI", "EUCAST"))
dim(whonet_breakpoints)
@@ -48,9 +50,9 @@ whonet_breakpoints |>
```{r}
whonet_breakpoints |>
filter(HOST == "Cats", YEAR >= 2021) |>
select(GUIDELINES, YEAR, TEST_METHOD, ORGANISM_CODE, R, S) |>
mutate(MO_NAME = AMR::mo_shortname(ORGANISM_CODE), .before = R) |>
filter(HOST == "Cats", YEAR >= 2021) |>
select(GUIDELINES, YEAR, TEST_METHOD, ORGANISM_CODE, R, S) |>
mutate(MO_NAME = AMR::mo_shortname(ORGANISM_CODE), .before = R) |>
as.data.frame()
```
@@ -58,12 +60,14 @@ whonet_breakpoints |>
```{r}
whonet_breakpoints |>
filter(HOST == "Cats", YEAR == 2023) |>
mutate(MO = AMR::mo_shortname(ORGANISM_CODE),
AB = AMR::ab_name(WHONET_ABX_CODE),
SITE_OF_INFECTION = substr(SITE_OF_INFECTION, 1, 25)) |>
arrange(MO, AB) |>
select(MO, AB, SITE_OF_INFECTION) |>
filter(HOST == "Cats", YEAR == 2023) |>
mutate(
MO = AMR::mo_shortname(ORGANISM_CODE),
AB = AMR::ab_name(WHONET_ABX_CODE),
SITE_OF_INFECTION = substr(SITE_OF_INFECTION, 1, 25)
) |>
arrange(MO, AB) |>
select(MO, AB, SITE_OF_INFECTION) |>
as.data.frame()
```