# filter to the top 3 species:
-top_n_microorganisms(example_isolates,
- n = 3
-)
+top_n_microorganisms(example_isolates, n = 3)
#> # A tibble: 1,015 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -130,9 +133,7 @@
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# filter to any species in the top 5 genera:
-top_n_microorganisms(example_isolates,
- n = 5, property = "genus"
-)
+top_n_microorganisms(example_isolates, n = 5, property = "genus")
#> # A tibble: 1,742 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -178,6 +179,31 @@
#> # 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>, …
+
+# filter to the top 2 genera in each of the top 3 families:
+top_n_microorganisms(example_isolates,
+ n = 3, property = "family", n_for_each = 2, property_for_each = "genus"
+)
+#> # A tibble: 1,659 × 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 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
+#> 4 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
+#> 5 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R
+#> 6 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R
+#> 7 2002-03-08 4FC193 69 M Clinical B_ESCHR_COLI R NA NA R
+#> 8 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA
+#> 9 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA
+#> 10 2002-04-23 EE2510 69 F ICU B_ESCHR_COLI R NA NA NA
+#> # ℹ 1,649 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>, …