We plot resistance trends over time for Amoxicillin.
+We plot resistance trends over time for amoxicillin.
ggplot(data_time, aes(x = year, y = res_AMX, color = gramstain)) +
geom_line() +
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index b2a32c431..36bbe9c89 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9230
+ 2.1.1.9231
Examples
-
These rules can be used to discard impossible bug-drug combinations
+
These rules can be used to discard improbable bug-drug combinations
in your data. For example, Klebsiella produces beta-lactamase
that prevents ampicillin (or amoxicillin) from working against it. In
other words, practically every strain of Klebsiella is
resistant to ampicillin.
Sometimes, laboratory data can still contain such strains with
-ampicillin being susceptible to ampicillin. This could be because an
-antibiogram is available before an identification is available, and the
-antibiogram is then not re-interpreted based on the identification
-(namely, Klebsiella). EUCAST expert rules solve this, that can
-be applied using eucast_rules():
+
Klebsiella being susceptible to ampicillin. This could be
+because an antibiogram is available before an identification is
+available, and the antibiogram is then not re-interpreted based on the
+identification. The
eucast_rules() function resolves this,
+by applying the latest ‘EUCAST Expected Resistant Phenotypes’
+guideline:
-oops <- data.frame(
+oops <- tibble::tibble(
mo = c(
- "Klebsiella",
- "Escherichia"
+ "Klebsiella pneumoniae",
+ "Escherichia coli"
),
- ampicillin = "S"
+ ampicillin = as.sir("S")
)
oops
-#> mo ampicillin
-#> 1 Klebsiella S
-#> 2 Escherichia S
+#> # A tibble: 2 × 2
+#> mo ampicillin
+#> <chr> <sir>
+#> 1 Klebsiella pneumoniae S
+#> 2 Escherichia coli S
-eucast_rules(oops, info = FALSE)
-#> mo ampicillin
-#> 1 Klebsiella S
-#> 2 Escherichia S
+
eucast_rules(oops, info = FALSE, overwrite = TRUE)
+
#> # A tibble: 2 × 2
+
#> mo ampicillin
+
#> <chr> <sir>
+
#> 1 Klebsiella pneumoniae R
+
#> 2 Escherichia coli S
mo_is_intrinsic_resistant(
- c("Klebsiella", "Escherichia"),
+ c("Klebsiella pneumoniae", "Escherichia coli"),
"ampicillin"
)
-#> [1] FALSE FALSE
+#> [1] TRUE FALSE
mo_is_intrinsic_resistant(
- "Klebsiella",
+ "Klebsiella pneumoniae",
c("ampicillin", "kanamycin")
)
-#> [1] FALSE FALSE