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Summarise a Phenotype Table

Source: R/summarise.R
summarise_pheno.Rd

summarise_pheno() computes summary information for a phenotype table.

Usage

summarise_pheno(
  pheno_table,
  sample_col = "id",
  drug_col = "drug",
  mic_col = "mic",
  disk_col = "disk",
  spp_col = "spp_pheno",
  pheno_cols = NULL,
  method_cols = c("method", "platform", "guideline", "source"),
  force_ab = FALSE
)

Arguments

pheno_table

A tibble or data frame containing phenotype data, in the format output by import_pheno.

sample_col

Character. Name of the column containing sample identifiers. Default is "id".

drug_col

Character. Name of the column containing drug agent identifiers. Default is "drug". If this is of class 'ab' the entries will be annotated with their full antibiotic names, converted using AMR::as.ab. If this is desired behaviour but the class is not 'ab', set force_ab=TRUE.

mic_col

Character. Name of the column containing MIC measurements Default is "mic".

disk_col

Character. Name of the column containing disk diffusion zone measurements. Default is "disk".

spp_col

Character. Name of the column containing species names. Default is "spp_pheno".

pheno_cols

Vector. Vector giving names of columns containing categorical phenotype calls (S/I/R or NWT/WT). Default is any columns beginning with "pheno" or "ecoff".

method_cols

Vector. Vector giving names of columns containing method or source information by which to summarise MIC/disk data. Default is c("method", "platform", "guideline", "source").

force_ab

Logical. If TRUE, attempts to convert entries in drug_col to antibiotic names using AMR::as.ab even if this column is not of class "ab" Default is FALSE.

Value

A named list with the following elements:

  • uniques: A tibble of the number of unique samples, drugs, organisms, and methods detected in pheno_table.

  • drugs: A tibble listing the drugs included in the table, and the associated number of samples with MIC measures, disk measures, neither or both, for each drug and species.

  • details: A tibble listing more details of the methods of assay measurements, per drug and species.

  • pheno_counts_list: A list of tibbles, each corresponding to a unique categorical phenotype column in the input, indicating the counts of each phenotypic category per drug and species.

Details

The function automatically adapts to the presence or absence of columns in pheno_table. The force_ab parameter allows the addition of full antibiotic names using the ab_name() function even when the first column is not recognized as an "ab" object.

Examples


summarise_pheno(staph_pheno_ebi)
#> No phenotype column names provided via 'pheno_cols'
#> These are needed to summarise counts of phenotype category calls per drug.
#> Relevant columns detected in your input table are: c('pheno_provided, pheno_eucast, pheno_clsi, pheno_eucast_mic, pheno_eucast_disk, pheno_clsi_mic, pheno_clsi_disk, ecoff, ecoff_mic, ecoff_disk'). Summarising these.
#> $uniques
#> # A tibble: 7 × 2
#>   column    n_unique
#>   <chr>        <int>
#> 1 id             190
#> 2 drug             2
#> 3 spp_pheno        1
#> 4 method           3
#> 5 platform         2
#> 6 guideline        2
#> 7 source           2
#> 
#> $drugs
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno              disk   mic  none
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     3    11    70
#> 2 DOX  Doxycycline Staphylococcus aureus    NA    47    87
#> 
#> $details
#> # A tibble: 6 × 10
#>   drug drug_name   spp_pheno  method platform guideline source   mic  disk  none
#>   <ab> <chr>       <chr>      <chr>  <chr>    <chr>     <chr>  <int> <int> <int>
#> 1 AMK  Amikacin    Staphyloc… broth… Vitek    CLSI      NA         1    NA    NA
#> 2 AMK  Amikacin    Staphyloc… disk … NA       CLSI      NA        NA     3    NA
#> 3 AMK  Amikacin    Staphyloc… disk … NA       NA        27150…    NA    NA    70
#> 4 AMK  Amikacin    Staphyloc… NA     NA       NA        NA        10    NA    NA
#> 5 DOX  Doxycycline Staphyloc… broth… NA       CLSI      NA        29    NA    NA
#> 6 DOX  Doxycycline Staphyloc… NA     NA       NA        NA        18    NA    87
#> 
#> $pheno_counts_list
#> $pheno_counts_list$pheno_provided
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno                 S     R     I
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    12    72    NA
#> 2 DOX  Doxycycline Staphylococcus aureus   103    20    11
#> 
#> $pheno_counts_list$pheno_eucast
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno                 S     R  `NA`
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    12     2    70
#> 2 DOX  Doxycycline Staphylococcus aureus    38     9    87
#> 
#> $pheno_counts_list$pheno_clsi
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno              `NA`     S     I     R
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    84    NA    NA    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    87    41     5     1
#> 
#> $pheno_counts_list$pheno_eucast_mic
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno                 S     R  `NA`
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     9     2    73
#> 2 DOX  Doxycycline Staphylococcus aureus    38     9    87
#> 
#> $pheno_counts_list$pheno_eucast_disk
#> # A tibble: 2 × 5
#>   drug drug_name   spp_pheno                 S  `NA`
#>   <ab> <chr>       <chr>                 <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     3    81
#> 2 DOX  Doxycycline Staphylococcus aureus    NA   134
#> 
#> $pheno_counts_list$pheno_clsi_mic
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno              `NA`     S     I     R
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    84    NA    NA    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    87    41     5     1
#> 
#> $pheno_counts_list$pheno_clsi_disk
#> # A tibble: 2 × 4
#>   drug drug_name   spp_pheno              `NA`
#>   <ab> <chr>       <chr>                 <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    84
#> 2 DOX  Doxycycline Staphylococcus aureus   134
#> 
#> $pheno_counts_list$ecoff
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno                WT   NWT  `NA`    NI
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    12     2    70    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    NA     9    87    38
#> 
#> $pheno_counts_list$ecoff_mic
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno                WT   NWT  `NA`    NI
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     9     2    73    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    NA     9    87    38
#> 
#> $pheno_counts_list$ecoff_disk
#> # A tibble: 2 × 5
#>   drug drug_name   spp_pheno                WT  `NA`
#>   <ab> <chr>       <chr>                 <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     3    81
#> 2 DOX  Doxycycline Staphylococcus aureus    NA   134
#> 
#> 

summarise_pheno(staph_pheno_ebi, pheno_cols = c("pheno_provided", "pheno_clsi", "ecoff"))
#> $uniques
#> # A tibble: 7 × 2
#>   column    n_unique
#>   <chr>        <int>
#> 1 id             190
#> 2 drug             2
#> 3 spp_pheno        1
#> 4 method           3
#> 5 platform         2
#> 6 guideline        2
#> 7 source           2
#> 
#> $drugs
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno              disk   mic  none
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus     3    11    70
#> 2 DOX  Doxycycline Staphylococcus aureus    NA    47    87
#> 
#> $details
#> # A tibble: 6 × 10
#>   drug drug_name   spp_pheno  method platform guideline source   mic  disk  none
#>   <ab> <chr>       <chr>      <chr>  <chr>    <chr>     <chr>  <int> <int> <int>
#> 1 AMK  Amikacin    Staphyloc… broth… Vitek    CLSI      NA         1    NA    NA
#> 2 AMK  Amikacin    Staphyloc… disk … NA       CLSI      NA        NA     3    NA
#> 3 AMK  Amikacin    Staphyloc… disk … NA       NA        27150…    NA    NA    70
#> 4 AMK  Amikacin    Staphyloc… NA     NA       NA        NA        10    NA    NA
#> 5 DOX  Doxycycline Staphyloc… broth… NA       CLSI      NA        29    NA    NA
#> 6 DOX  Doxycycline Staphyloc… NA     NA       NA        NA        18    NA    87
#> 
#> $pheno_counts_list
#> $pheno_counts_list$pheno_provided
#> # A tibble: 2 × 6
#>   drug drug_name   spp_pheno                 S     R     I
#>   <ab> <chr>       <chr>                 <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    12    72    NA
#> 2 DOX  Doxycycline Staphylococcus aureus   103    20    11
#> 
#> $pheno_counts_list$pheno_clsi
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno              `NA`     S     I     R
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    84    NA    NA    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    87    41     5     1
#> 
#> $pheno_counts_list$ecoff
#> # A tibble: 2 × 7
#>   drug drug_name   spp_pheno                WT   NWT  `NA`    NI
#>   <ab> <chr>       <chr>                 <int> <int> <int> <int>
#> 1 AMK  Amikacin    Staphylococcus aureus    12     2    70    NA
#> 2 DOX  Doxycycline Staphylococcus aureus    NA     9    87    38
#> 
#>