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reference/top_n_microorganisms.md
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reference/top_n_microorganisms.md
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# Filter Top *n* Microorganisms
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This function filters a data set to include only the top *n*
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microorganisms based on a specified property, such as taxonomic family
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or genus. For example, it can filter a data set to the top 3 species, or
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to any species in the top 5 genera, or to the top 3 species in each of
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the top 5 genera.
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## Usage
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``` r
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top_n_microorganisms(x, n, property = "species", n_for_each = NULL,
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col_mo = NULL, ...)
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```
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## Arguments
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- x:
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A data frame containing microbial data.
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- n:
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An integer specifying the maximum number of unique values of the
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`property` to include in the output.
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- property:
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A character string indicating the microorganism property to use for
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filtering. Must be one of the column names of the
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
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data set: "mo", "fullname", "status", "kingdom", "phylum", "class",
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"order", "family", "genus", "species", "subspecies", "rank", "ref",
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"oxygen_tolerance", "source", "lpsn", "lpsn_parent",
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"lpsn_renamed_to", "mycobank", "mycobank_parent",
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"mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to",
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"prevalence", or "snomed". If `NULL`, the raw values from `col_mo`
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will be used without transformation. When using `"species"` (default)
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or `"subpecies"`, the genus will be added to make sure each
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(sub)species still belongs to the right genus.
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- n_for_each:
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An optional integer specifying the maximum number of rows to retain
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for each value of the selected property. If `NULL`, all rows within
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the top *n* groups will be included.
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- col_mo:
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A character string indicating the column in `x` that contains
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microorganism names or codes. Defaults to the first column of class
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[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
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coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
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- ...:
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Additional arguments passed on to
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[`mo_property()`](https://amr-for-r.org/reference/mo_property.md) when
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`property` is not `NULL`.
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## Details
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This function is useful for preprocessing data before creating
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[antibiograms](https://amr-for-r.org/reference/antibiogram.md) or other
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analyses that require focused subsets of microbial data. For example, it
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can filter a data set to only include isolates from the top 10 species.
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## See also
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[`mo_property()`](https://amr-for-r.org/reference/mo_property.md),
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md),
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[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
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## Examples
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``` r
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# filter to the top 3 species:
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top_n_microorganisms(example_isolates,
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n = 3
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)
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#> # A tibble: 1,015 × 46
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#> date patient age gender ward mo PEN OXA FLC AMX
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#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
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#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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#> 3 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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#> 4 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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#> 5 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
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#> 6 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
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#> 7 2002-02-03 481442 76 M ICU B_STPHY_CONS R NA S NA
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#> 8 2002-02-14 067927 45 F ICU B_STPHY_CONS R NA R NA
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#> 9 2002-02-14 067927 45 F ICU B_STPHY_CONS S NA S NA
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#> 10 2002-02-21 A56499 64 M Clinical B_STPHY_CONS S NA S NA
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#> # ℹ 1,005 more rows
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#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
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#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
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#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
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#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
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#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
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#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
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# filter to any species in the top 5 genera:
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top_n_microorganisms(example_isolates,
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n = 5, property = "genus"
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)
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#> # A tibble: 1,742 × 46
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#> date patient age gender ward mo PEN OXA FLC AMX
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#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
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#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
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#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
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#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
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#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
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#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
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#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
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#> # ℹ 1,732 more rows
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#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
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#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
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#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
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#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
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#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
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#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
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# filter to the top 3 species in each of the top 5 genera:
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top_n_microorganisms(example_isolates,
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n = 5, property = "genus", n_for_each = 3
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)
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#> # A tibble: 1,497 × 46
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#> date patient age gender ward mo PEN OXA FLC AMX
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#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
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#> 1 2002-02-21 4FC193 69 M Clinical B_ENTRC_FACM NA NA NA NA
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#> 2 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA
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#> 3 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA
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#> 4 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA
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#> 5 2003-04-20 6BC362 62 M ICU B_ENTRC NA NA NA NA
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#> 6 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA
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#> 7 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA
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#> 8 2003-09-05 F35553 52 M ICU B_ENTRC NA NA NA NA
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#> 9 2003-09-05 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA
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#> 10 2003-09-28 1B0933 80 M Clinical B_ENTRC NA NA NA NA
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#> # ℹ 1,487 more rows
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#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
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#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
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#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
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#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
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#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
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#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
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```
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