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Evaluate expressions on metadata.

Source: R/s3_methods.r
with.Rd

with() will return the result of your expression. within() will return an rbiom object.

Usage

# S3 method for rbiom
with(biom, ...)

# S3 method for rbiom
within(biom, ..., clone = TRUE)

Arguments

biom

An rbiom object, such as from as_rbiom().

...

Passed on to base::with() or base::within().

Value

See description.

See also

Other transformations: mutate(), rarefy(), rarefy_cols(), slice(), subset()

Examples

    library(rbiom) 
    
    with(hmp50, table(`Body Site`, Sex))
#>                 Sex
#> Body Site        Male Female
#>   Anterior nares    5      5
#>   Buccal mucosa     5      5
#>   Mid vagina        0     10
#>   Saliva            5      5
#>   Stool             5      5
    
    biom <- within(hmp50, {
      age_bin = cut(Age, 5)
      bmi_bin = cut(BMI, 5)
    })
    biom$metadata
#> # A tibble: 50 × 7
#>    .sample   Age   BMI `Body Site`    Sex    bmi_bin     age_bin    
#>    <chr>   <dbl> <dbl> <fct>          <fct>  <fct>       <fct>      
#>  1 HMP01      22    20 Buccal mucosa  Female (19,21.6]   (21,24.8]  
#>  2 HMP02      24    23 Buccal mucosa  Male   (21.6,24.2] (21,24.8]  
#>  3 HMP03      28    26 Saliva         Male   (24.2,26.8] (24.8,28.6]
#>  4 HMP04      25    23 Saliva         Male   (21.6,24.2] (24.8,28.6]
#>  5 HMP05      27    24 Buccal mucosa  Female (21.6,24.2] (24.8,28.6]
#>  6 HMP06      32    25 Saliva         Male   (24.2,26.8] (28.6,32.4]
#>  7 HMP07      26    22 Buccal mucosa  Male   (21.6,24.2] (24.8,28.6]
#>  8 HMP08      27    26 Saliva         Female (24.2,26.8] (24.8,28.6]
#>  9 HMP09      33    32 Saliva         Male   (29.4,32]   (32.4,36.2]
#> 10 HMP10      22    20 Anterior nares Female (19,21.6]   (21,24.8]  
#> # ℹ 40 more rows