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These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.

count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates.


count_resistant(..., only_all_tested = FALSE)

count_susceptible(..., only_all_tested = FALSE)

count_R(..., only_all_tested = FALSE)

count_IR(..., only_all_tested = FALSE)

count_I(..., only_all_tested = FALSE)

count_SI(..., only_all_tested = FALSE)

count_S(..., only_all_tested = FALSE)

count_all(..., only_all_tested = FALSE)

n_sir(..., only_all_tested = FALSE)

  translate_ab = "name",
  language = get_AMR_locale(),
  combine_SI = TRUE



one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with as.sir() if needed.


(for combination therapies, i.e. using more than one variable for ...): a logical to indicate that isolates must be tested for all antibiotics, see section Combination Therapy below


a data.frame containing columns with class sir (see as.sir())


a column name of the antibiotics data set to translate the antibiotic abbreviations to, using ab_property()


language of the returned text - the default is the current system language (see get_AMR_locale()) and can also be set with the package option AMR_locale. Use language = NULL or language = "" to prevent translation.


a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is TRUE


An integer


These functions are meant to count isolates. Use the resistance()/susceptibility() functions to calculate microbial resistance/susceptibility.

The function count_resistant() is equal to the function count_R(). The function count_susceptible() is equal to the function count_SI().

The function n_sir() is an alias of count_all(). They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to n_distinct(). Their function is equal to count_susceptible(...) + count_resistant(...).

The function count_df() takes any variable from data that has an sir class (created with as.sir()) and counts the number of S's, I's and R's. It also supports grouped variables. The function sir_df() works exactly like count_df(), but adds the percentage of S, I and R.

Interpretation of SIR

In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (

  • S - Susceptible, standard dosing regimen
    A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

  • I - Susceptible, increased exposure
    A microorganism is categorised as "Susceptible, Increased exposure
    " when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.

  • R = Resistant
    A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.

    • Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

This AMR package honours this insight. Use susceptibility() (equal to proportion_SI()) to determine antimicrobial susceptibility and count_susceptible() (equal to count_SI()) to count susceptible isolates.

Combination Therapy

When using more than one variable for ... (= combination therapy), use only_all_tested to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how susceptibility() works to calculate the %SI:

                    only_all_tested = FALSE  only_all_tested = TRUE
                    -----------------------  -----------------------
 Drug A    Drug B   include as  include as   include as  include as
                    numerator   denominator  numerator   denominator
--------  --------  ----------  -----------  ----------  -----------
 S or I    S or I       X            X            X            X
   R       S or I       X            X            X            X
  <NA>     S or I       X            X            -            -
 S or I      R          X            X            X            X
   R         R          -            X            -            X
  <NA>       R          -            -            -            -
 S or I     <NA>        X            X            -            -
   R        <NA>        -            -            -            -
  <NA>      <NA>        -            -            -            -

Please note that, in combination therapies, for only_all_tested = TRUE applies that:

    count_S()    +   count_I()    +   count_R()    = count_all()
  proportion_S() + proportion_I() + proportion_R() = 1

and that, in combination therapies, for only_all_tested = FALSE applies that:

    count_S()    +   count_I()    +   count_R()    >= count_all()
  proportion_S() + proportion_I() + proportion_R() >= 1

Using only_all_tested has no impact when only using one antibiotic as input.

See also

proportion_* to calculate microbial resistance and susceptibility.


# example_isolates is a data set available in the AMR package.
# run ?example_isolates for more info.

# base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R"
#> [1] 804
count_susceptible(example_isolates$AMX) # counts "S" and "I"
#> [1] 546
count_all(example_isolates$AMX) # counts "S", "I" and "R"
#> [1] 1350

# be more specific
#> Using count_S() is discouraged; use count_susceptible() instead to also
#> consider "I" being susceptible. This note will be shown once for this
#> session.
#> [1] 543
#> [1] 546
#> [1] 3
#> Using count_IR() is discouraged; use count_resistant() instead to not
#> consider "I" being resistant. This note will be shown once for this
#> session.
#> [1] 807
#> [1] 804

# Count all available isolates
#> [1] 1350
#> [1] 1350

# n_sir() is an alias of count_all().
# Since it counts all available isolates, you can
# calculate back to count e.g. susceptible isolates.
# These results are the same:
#> [1] 546
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
#> [1] 546

# dplyr -------------------------------------------------------------
# \donttest{
if (require("dplyr")) {
  example_isolates %>%
    group_by(ward) %>%
      R = count_R(CIP),
      I = count_I(CIP),
      S = count_S(CIP),
      n1 = count_all(CIP), # the actual total; sum of all three
      n2 = n_sir(CIP), # same - analogous to n_distinct
      total = n()
    ) # NOT the number of tested isolates!

  # Number of available isolates for a whole antibiotic class
  # (i.e., in this data set columns GEN, TOB, AMK, KAN)
  example_isolates %>%
    group_by(ward) %>%
    summarise(across(aminoglycosides(), n_sir))

  # Count co-resistance between amoxicillin/clav acid and gentamicin,
  # so we can see that combination therapy does a lot more than mono therapy.
  # Please mind that `susceptibility()` calculates percentages right away instead.
  example_isolates %>% count_susceptible(AMC) # 1433
  example_isolates %>% count_all(AMC) # 1879

  example_isolates %>% count_susceptible(GEN) # 1399
  example_isolates %>% count_all(GEN) # 1855

  example_isolates %>% count_susceptible(AMC, GEN) # 1764
  example_isolates %>% count_all(AMC, GEN) # 1936

  # Get number of S+I vs. R immediately of selected columns
  example_isolates %>%
    select(AMX, CIP) %>%
    count_df(translate = FALSE)

  # It also supports grouping variables
  example_isolates %>%
    select(ward, AMX, CIP) %>%
    group_by(ward) %>%
    count_df(translate = FALSE)
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 12 × 4
#>    ward       antibiotic interpretation value
#>  * <chr>      <chr>      <ord>          <int>
#>  1 Clinical   AMX        SI               357
#>  2 Clinical   AMX        R                487
#>  3 Clinical   CIP        SI               741
#>  4 Clinical   CIP        R                128
#>  5 ICU        AMX        SI               158
#>  6 ICU        AMX        R                270
#>  7 ICU        CIP        SI               362
#>  8 ICU        CIP        R                 85
#>  9 Outpatient AMX        SI                31
#> 10 Outpatient AMX        R                 47
#> 11 Outpatient CIP        SI                78
#> 12 Outpatient CIP        R                 15
# }