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AMR/reference/top_n_microorganisms.md
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# 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
``` r
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](https://amr-for-r.org/reference/microorganisms.md)
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](https://amr-for-r.org/reference/microorganisms.md)
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`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- ...:
Additional arguments passed on to
[`mo_property()`](https://amr-for-r.org/reference/mo_property.md) when
`property` is not `NULL`.
## Details
This function is useful for preprocessing data before creating
[antibiograms](https://amr-for-r.org/reference/antibiogram.md) or other
analyses that require focused subsets of microbial data.
## See also
[`mo_property()`](https://amr-for-r.org/reference/mo_property.md),
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md),
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
## Examples
``` r
# 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>, …
```
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