Add columns to taxmap() objects

Add columns to tables in obj$data in taxmap() objects. See dplyr::mutate() for the inspiration for this function and more information. Calling the function using the obj$mutate_obs(...) style edits "obj" in place, unlike most R functions. However, calling the function using the mutate_obs(obj, ...) imitates R's traditional copy-on-modify semantics, so "obj" would not be changed; instead a changed version would be returned, like most R functions.

obj$mutate_obs(data, ...)
mutate_obs(obj, data, ...)

Arguments

obj	An object of type taxmap()
data	Dataset name, index, or a logical vector that indicates which dataset in obj$data to add columns to.
...	One or more named columns to add. Newly created columns can be referenced in the same function call. Any variable name that appears in all_names() can be used as if it was a vector on its own.
target	DEPRECIATED. use "data" instead.

Value

An object of type taxmap()

See also

Other taxmap manipulation functions: arrange_obs(), arrange_taxa(), filter_obs(), filter_taxa(), sample_frac_obs(), sample_frac_taxa(), sample_n_obs(), sample_n_taxa(), select_obs(), transmute_obs()

Examples

# Add column to existing tables
mutate_obs(ex_taxmap, "info",
           new_col = "Im new",
           newer_col = paste0(new_col, "er!"))
#> <Taxmap>
#>   17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
#>   17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
#>   4 data sets:
#>     info:
#>       # A tibble: 6 x 6
#>         taxon_id name  n_legs dangerous new_col newer_col
#>         <chr>    <chr>  <dbl> <lgl>     <chr>   <chr>    
#>       1 m        tiger      4 TRUE      Im new  Im newer!
#>       2 n        cat        4 FALSE     Im new  Im newer!
#>       3 o        mole       4 FALSE     Im new  Im newer!
#>       # … with 3 more rows
#>     phylopic_ids: a named vector of 'character' with 6 items
#>        m. e148eabb-f138-43[truncated] ... r. 63604565-0406-46[truncated]
#>     foods: a list of 6 items named by taxa:
#>        m, n, o, p, q, r
#>     abund:
#>       # A tibble: 8 x 5
#>         taxon_id code  sample_id count taxon_index
#>         <chr>    <fct> <fct>     <dbl>       <int>
#>       1 m        T     A             1           1
#>       2 n        C     A             2           2
#>       3 o        M     B             5           3
#>       # … with 5 more rows
#>   1 functions:
#>     reaction

# Create columns in a new table
mutate_obs(ex_taxmap, "new_table",
           nums = 1:10,
           squared = nums ^ 2)
#> Adding a new 10 x 2 table called "new_table"
#> <Taxmap>
#>   17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
#>   17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
#>   5 data sets:
#>     info:
#>       # A tibble: 6 x 4
#>         taxon_id name  n_legs dangerous
#>         <chr>    <chr>  <dbl> <lgl>    
#>       1 m        tiger      4 TRUE     
#>       2 n        cat        4 FALSE    
#>       3 o        mole       4 FALSE    
#>       # … with 3 more rows
#>     phylopic_ids: a named vector of 'character' with 6 items
#>        m. e148eabb-f138-43[truncated] ... r. 63604565-0406-46[truncated]
#>     foods: a list of 6 items named by taxa:
#>        m, n, o, p, q, r
#>     abund:
#>       # A tibble: 8 x 5
#>         taxon_id code  sample_id count taxon_index
#>         <chr>    <fct> <fct>     <dbl>       <int>
#>       1 m        T     A             1           1
#>       2 n        C     A             2           2
#>       3 o        M     B             5           3
#>       # … with 5 more rows
#>     new_table:
#>       # A tibble: 10 x 2
#>          nums squared
#>         <int>   <dbl>
#>       1     1       1
#>       2     2       4
#>       3     3       9
#>       # … with 7 more rows
#>   1 functions:
#>     reaction

# Add a new vector
mutate_obs(ex_taxmap, "new_vector", 1:10)
#> Adding a new "integer" vector of length 10.
#> <Taxmap>
#>   17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
#>   17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
#>   5 data sets:
#>     info:
#>       # A tibble: 6 x 4
#>         taxon_id name  n_legs dangerous
#>         <chr>    <chr>  <dbl> <lgl>    
#>       1 m        tiger      4 TRUE     
#>       2 n        cat        4 FALSE    
#>       3 o        mole       4 FALSE    
#>       # … with 3 more rows
#>     phylopic_ids: a named vector of 'character' with 6 items
#>        m. e148eabb-f138-43[truncated] ... r. 63604565-0406-46[truncated]
#>     foods: a list of 6 items named by taxa:
#>        m, n, o, p, q, r
#>     abund:
#>       # A tibble: 8 x 5
#>         taxon_id code  sample_id count taxon_index
#>         <chr>    <fct> <fct>     <dbl>       <int>
#>       1 m        T     A             1           1
#>       2 n        C     A             2           2
#>       3 o        M     B             5           3
#>       # … with 5 more rows
#>     new_vector: a vector of 'integer' with 10 items
#>        1, 2, 3, 4, 5, 6, 7, 8, 9, 10
#>   1 functions:
#>     reaction

# Add a new list
mutate_obs(ex_taxmap, "new_list", list(1, 2))
#> Adding a new "list" vector of length 2.
#> <Taxmap>
#>   17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
#>   17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
#>   5 data sets:
#>     info:
#>       # A tibble: 6 x 4
#>         taxon_id name  n_legs dangerous
#>         <chr>    <chr>  <dbl> <lgl>    
#>       1 m        tiger      4 TRUE     
#>       2 n        cat        4 FALSE    
#>       3 o        mole       4 FALSE    
#>       # … with 3 more rows
#>     phylopic_ids: a named vector of 'character' with 6 items
#>        m. e148eabb-f138-43[truncated] ... r. 63604565-0406-46[truncated]
#>     foods: a list of 6 items named by taxa:
#>        m, n, o, p, q, r
#>     abund:
#>       # A tibble: 8 x 5
#>         taxon_id code  sample_id count taxon_index
#>         <chr>    <fct> <fct>     <dbl>       <int>
#>       1 m        T     A             1           1
#>       2 n        C     A             2           2
#>       3 o        M     B             5           3
#>       # … with 5 more rows
#>     new_list: a list of 2 items
#>   1 functions:
#>     reaction