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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>, …