P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-29 18:56:19 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9077: f7d3533

Browse Source
This commit is contained in:
github-actions
2026-06-26 19:49:26 +00:00
parent 108afaca6f
commit 169659837d
93 changed files with 368 additions and 239 deletions
Download Patch File Download Diff File Expand all files Collapse all files

71
reference/top_n_microorganisms.md
View File

@@ -1,10 +1,9 @@
# Filter Top *n* Microorganisms
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.
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
@@ -14,6 +13,7 @@ top_n_microorganisms(
n,
property = "species",
n_for_each = NULL,
property_for_each = "species",
col_mo = NULL,
...
)
@@ -27,8 +27,8 @@ top_n_microorganisms(
- n:
An integer specifying the maximum number of unique values of the
`property` to include in the output.
A positive whole number specifying the maximum number of unique values
of `property` to include in the output.
- property:
@@ -43,14 +43,25 @@ top_n_microorganisms(
`"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 `"subpecies"`, the genus will be added to
make sure each (sub)species still belongs to the right genus.
`"species"` (default) or `"subspecies"`, the genus is prepended to
ensure each name is unambiguous.
- 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.
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:
@@ -69,8 +80,7 @@ top_n_microorganisms(
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. For example, it
can filter a data set to only include isolates from the top 10 species.
analyses that require focused subsets of microbial data.
## See also
@@ -82,9 +92,7 @@ can filter a data set to only include isolates from the top 10 species.
``` r
# filter to the top 3 species:
top_n_microorganisms(example_isolates,
n = 3
)
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>
@@ -107,9 +115,7 @@ top_n_microorganisms(example_isolates,
#> # 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"
)
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>
@@ -155,4 +161,29 @@ top_n_microorganisms(example_isolates,
#> # 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>, …
```