These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility.
resistance(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) susceptibility(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE) proportion_df( data, translate_ab = "name", language = get_locale(), minimum = 30, as_percent = FALSE, combine_SI = TRUE, combine_IR = FALSE ) rsi_df( data, translate_ab = "name", language = get_locale(), minimum = 30, as_percent = FALSE, combine_SI = TRUE, combine_IR = FALSE )
Arguments
| ... | one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with |
|---|---|
| minimum | the minimum allowed number of available (tested) isolates. Any isolate count lower than |
| as_percent | a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of |
| only_all_tested | (for combination therapies, i.e. using more than one variable for |
| data | a |
| translate_ab | a column name of the antibiotics data set to translate the antibiotic abbreviations to, using |
| language | language of the returned text, defaults to system language (see |
| combine_SI | 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). This used to be the parameter |
| combine_IR | a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter |
Source
M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition, 2014, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.
Value
A double or, when as_percent = TRUE, a character.
Details
The function resistance() is equal to the function proportion_R(). The function susceptibility() is equal to the function proportion_SI().
Remember that you should filter your table to let it contain only first isolates! This is needed to exclude duplicates and to reduce selection bias. Use first_isolate() to determine them in your data set.
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the count()][AMR::count()] functions to count isolates. The function susceptibility() is essentially equal to count_susceptible() / count_all(). Low counts can influence the outcome - the proportion functions may camouflage this, since they only return the proportion (albeit being dependent on the minimum parameter).
The function proportion_df() takes any variable from data that has an rsi class (created with as.rsi()) and calculates the proportions R, I and S. It also supports grouped variables. The function rsi_df() works exactly like proportion_df(), but adds the number of 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.
Stable lifecycle
The lifecycle of this function is stable. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
Interpretation of R and S/I
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (http://www.eucast.org/newsiandr/).
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.S = Susceptible
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 = Increased exposure, but still susceptible
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.
This AMR package honours this new insight. Use susceptibility() (equal to proportion_SI()) to determine antimicrobial susceptibility and count_susceptible() (equal to count_SI()) to count susceptible isolates.
Read more on our website!
On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.
See also
AMR::count() to count resistant and susceptible isolates.
Examples
# example_isolates is a data set available in the AMR package. ?example_isolates resistance(example_isolates$AMX) # determines %R susceptibility(example_isolates$AMX) # determines %S+I # be more specific proportion_S(example_isolates$AMX) proportion_SI(example_isolates$AMX) proportion_I(example_isolates$AMX) proportion_IR(example_isolates$AMX) proportion_R(example_isolates$AMX) if (require("dplyr")) { example_isolates %>% group_by(hospital_id) %>% summarise(r = resistance(CIP), n = n_rsi(CIP)) # n_rsi works like n_distinct in dplyr, see ?n_rsi example_isolates %>% group_by(hospital_id) %>% summarise(R = resistance(CIP, as_percent = TRUE), SI = susceptibility(CIP, as_percent = TRUE), n1 = count_all(CIP), # the actual total; sum of all three n2 = n_rsi(CIP), # same - analogous to n_distinct total = n()) # NOT the number of tested isolates! # Calculate co-resistance between amoxicillin/clav acid and gentamicin, # so we can see that combination therapy does a lot more than mono therapy: example_isolates %>% susceptibility(AMC) # %SI = 76.3% example_isolates %>% count_all(AMC) # n = 1879 example_isolates %>% susceptibility(GEN) # %SI = 75.4% example_isolates %>% count_all(GEN) # n = 1855 example_isolates %>% susceptibility(AMC, GEN) # %SI = 94.1% example_isolates %>% count_all(AMC, GEN) # n = 1939 # See Details on how `only_all_tested` works. Example: example_isolates %>% summarise(numerator = count_susceptible(AMC, GEN), denominator = count_all(AMC, GEN), proportion = susceptibility(AMC, GEN)) example_isolates %>% summarise(numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE), denominator = count_all(AMC, GEN, only_all_tested = TRUE), proportion = susceptibility(AMC, GEN, only_all_tested = TRUE)) example_isolates %>% group_by(hospital_id) %>% summarise(cipro_p = susceptibility(CIP, as_percent = TRUE), cipro_n = count_all(CIP), genta_p = susceptibility(GEN, as_percent = TRUE), genta_n = count_all(GEN), combination_p = susceptibility(CIP, GEN, as_percent = TRUE), combination_n = count_all(CIP, GEN)) # Get proportions S/I/R immediately of all rsi columns example_isolates %>% select(AMX, CIP) %>% proportion_df(translate = FALSE) # It also supports grouping variables example_isolates %>% select(hospital_id, AMX, CIP) %>% group_by(hospital_id) %>% proportion_df(translate = FALSE) } if (FALSE) { # calculate current empiric combination therapy of Helicobacter gastritis: my_table %>% filter(first_isolate == TRUE, genus == "Helicobacter") %>% summarise(p = susceptibility(AMX, MTR), # amoxicillin with metronidazole n = count_all(AMX, MTR)) }