P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-29 06:56:20 +02:00
Code Releases Activity
Files
169659837d0a67a559fe70560892db5ceb42beb1
AMR/reference/top_n_microorganisms.md
github-actions 169659837d Built site for AMR@3.0.1.9077: f7d3533
2026-06-26 19:49:26 +00:00

9.4 KiB
Raw Blame History

Filter Top n Microorganisms

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, 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 = "species",
  n_for_each = NULL,
  property_for_each = "species",
  col_mo = NULL,
  ...
)

Arguments

  • x:

    A data frame containing microbial data.

  • n:

    A positive whole number specifying the maximum number of unique values of 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", "domain", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "morphology", "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. When using "species" (default) or "subspecies", the genus is prepended to ensure each name is unambiguous.

  • n_for_each:

    An optional positive whole number specifying the maximum number of distinct microorganism groups at the level of property_for_each to retain within each of the top n groups. Only used when property_for_each is also set.

  • property_for_each:

    The microorganism property to use for sub-grouping within each top n group. Must be one of the column names of the microorganisms data set and at a strictly lower taxonomic rank than property (allowed order: domain > kingdom > phylum > class > order > family > genus > species > subspecies). Defaults to "species". Only relevant when n_for_each is set.

  • 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.

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>, …

# 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>, …