diff --git a/404.html b/404.html index d4052a65c..9ce965421 100644 --- a/404.html +++ b/404.html @@ -30,7 +30,7 @@ AMR (for R) - 2.1.1.9125 + 2.1.1.9133 + + + + + +
+
+
+

Filter Top n Microorganisms

+ Source: R/top_n_microorganisms.R +
top_n_microorganisms.Rd
+
+ +
+

This function filters a data set to include only the top n microorganisms based on a specified property, such as taxonomic family or genus. For example, it can filter a data set to the top 3 species, or to any species in the top 5 genera, or to the top 3 species in each of the top 5 genera.

+
+ +
+

Usage

+ 
top_n_microorganisms(x, n, property = "fullname", n_for_each = NULL,
+  col_mo = NULL, ...)
+
+ +
+

Arguments

+ + +
x
+

a data frame containing microbial data

+ + +
n
+

an integer specifying the maximum number of unique values of the property to include in the output

+ + +
property
+

a character string indicating the microorganism property to use for filtering. Must be one of the column names of the microorganisms data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". If NULL, the raw values from col_mo will be used without transformation.

+ + +
n_for_each
+

an optional integer specifying the maximum number of rows to retain for each value of the selected property. If NULL, all rows within the top n groups will be included.

+ + +
col_mo
+

A character string indicating the column in x that contains microorganism names or codes. Defaults to the first column of class mo. Values will be coerced using as.mo().

+ + +
...
+

Additional arguments passed on to mo_property() when property is not NULL.

+ +
+
+

Details

+

This function is useful for preprocessing data before creating antibiograms or other analyses that require focused subsets of microbial data. For example, it can filter a data set to only include isolates from the top 10 species.

+
+
+

See also

+

mo_property(), as.mo(), antibiogram()

+
+ +
+

Examples

+ 
# filter to the top 3 species:
+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>
+#>  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 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    
+#>  4 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    
+#>  5 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   
+#>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   
+#>  7 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   
+#>  8 2002-02-14 067927     45 F      ICU      B_STPHY_CONS R     NA    R     NA   
+#>  9 2002-02-14 067927     45 F      ICU      B_STPHY_CONS S     NA    S     NA   
+#> 10 2002-02-21 A56499     64 M      Clinical B_STPHY_CONS S     NA    S     NA   
+#> # ℹ 1,005 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>, …
+
+# filter to any species in the top 5 genera:
+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>
+#>  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 1,732 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>, …
+
+# filter to the top 3 species in each of the top 5 genera:
+top_n_microorganisms(example_isolates,
+                     n = 5, property = "genus", n_for_each = 3)
+#> # A tibble: 1,497 × 46
+#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
+#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
+#>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
+#>  2 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
+#>  3 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   
+#>  4 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   
+#>  5 2003-04-20 6BC362     62 M      ICU      B_ENTRC      NA    NA    NA    NA   
+#>  6 2003-04-21 6BC362     62 M      ICU      B_ENTRC      NA    NA    NA    NA   
+#>  7 2003-08-13 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
+#>  8 2003-09-05 F35553     52 M      ICU      B_ENTRC      NA    NA    NA    NA   
+#>  9 2003-09-05 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
+#> 10 2003-09-28 1B0933     80 M      Clinical B_ENTRC      NA    NA    NA    NA   
+#> # ℹ 1,487 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>, …
+
+
+
+ + +
+ + + + + + + diff --git a/reference/translate.html b/reference/translate.html index 43627e76a..a142d013a 100644 --- a/reference/translate.html +++ b/reference/translate.html @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9125 + 2.1.1.9133