your_data %>% mutate_if(is.disk, as.sir)
@@ -810,16 +816,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> # A tibble: 65 × 16
#> datetime index ab_given mo_given host_given ab mo
#> <dttm> <int> <chr> <chr> <chr> <ab> <mo>
-#> 1 2025-03-14 16:26:44 1 ampicillin Strep p… human AMP B_STRPT_PNMN
-#> 2 2025-03-14 16:26:44 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
-#> 3 2025-03-14 16:26:44 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
+#> 1 2025-03-15 12:31:12 1 ampicillin Strep p… human AMP B_STRPT_PNMN
+#> 2 2025-03-15 12:31:12 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
+#> 3 2025-03-15 12:31:12 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
#> 4 NA NA NA NA NA NA NA
-#> 5 2025-03-14 16:26:44 1 GEN Escheri… human GEN B_[ORD]_ENTRBC…
-#> 6 2025-03-14 16:26:45 1 TOB Escheri… human TOB B_[ORD]_ENTRBC…
-#> 7 2025-03-14 16:26:45 1 AMX B_STRPT… human AMX B_STRPT_PNMN
-#> 8 2025-03-14 16:26:46 1 AMX B_STRPT… human AMX B_STRPT_PNMN
-#> 9 2025-03-14 16:26:46 2 AMX B_STRPT… human AMX B_STRPT_PNMN
-#> 10 2025-03-14 16:26:46 3 AMX B_STRPT… human AMX B_STRPT_PNMN
+#> 5 2025-03-15 12:31:12 1 GEN Escheri… human GEN B_[ORD]_ENTRBC…
+#> 6 2025-03-15 12:31:12 1 TOB Escheri… human TOB B_[ORD]_ENTRBC…
+#> 7 2025-03-15 12:31:13 1 AMX B_STRPT… human AMX B_STRPT_PNMN
+#> 8 2025-03-15 12:31:13 1 AMX B_STRPT… human AMX B_STRPT_PNMN
+#> 9 2025-03-15 12:31:13 2 AMX B_STRPT… human AMX B_STRPT_PNMN
+#> 10 2025-03-15 12:31:13 3 AMX B_STRPT… human AMX B_STRPT_PNMN
#> # ℹ 55 more rows
#> # ℹ 9 more variables: host <chr>, method <chr>, input <chr>, outcome <sir>,
#> # notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
@@ -895,7 +901,26 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
# example_isolates %>%
# mutate(across(where(is_sir_eligible), as.sir))
}
-#> Error: object 'PEN' not found
+#> # A tibble: 2,000 × 46
+#> date patient age gender ward mo PEN OXA FLC AMX
+#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
+#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
+#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
+#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
+#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
+#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
+#> # ℹ 1,990 more rows
+#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
+#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
+#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
+#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
+#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
+#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# }