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(v0.7.1.9063) septic_patients -> example_isolates
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38
R/count.R
38
R/count.R
@ -44,29 +44,29 @@
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # septic_patients is a data set available in the AMR package. It is true, genuine data.
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#' ?septic_patients
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#' # example_isolates is a data set available in the AMR package.
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#' ?example_isolates
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#'
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#' # Count resistant isolates
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#' count_R(septic_patients$AMX)
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#' count_IR(septic_patients$AMX)
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#' count_R(example_isolates$AMX)
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#' count_IR(example_isolates$AMX)
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#'
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#' # Or susceptible isolates
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#' count_S(septic_patients$AMX)
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#' count_SI(septic_patients$AMX)
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#' count_S(example_isolates$AMX)
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#' count_SI(example_isolates$AMX)
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#'
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#' # Count all available isolates
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#' count_all(septic_patients$AMX)
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#' n_rsi(septic_patients$AMX)
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#' count_all(example_isolates$AMX)
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#' n_rsi(example_isolates$AMX)
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#'
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#' # Since n_rsi counts available isolates, you can
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#' # calculate back to count e.g. non-susceptible isolates.
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#' # This results in the same:
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#' count_SI(septic_patients$AMX)
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#' portion_SI(septic_patients$AMX) * n_rsi(septic_patients$AMX)
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#' count_SI(example_isolates$AMX)
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#' portion_SI(example_isolates$AMX) * n_rsi(example_isolates$AMX)
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#'
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#' library(dplyr)
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#' septic_patients %>%
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#' example_isolates %>%
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#' group_by(hospital_id) %>%
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#' summarise(R = count_R(CIP),
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#' I = count_I(CIP),
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@ -78,24 +78,24 @@
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#' # Count co-resistance between amoxicillin/clav acid and gentamicin,
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#' # so we can see that combination therapy does a lot more than mono therapy.
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#' # Please mind that `portion_SI` calculates percentages right away instead.
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#' count_SI(septic_patients$AMC) # 1433
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#' count_all(septic_patients$AMC) # 1879
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#' count_SI(example_isolates$AMC) # 1433
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#' count_all(example_isolates$AMC) # 1879
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#'
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#' count_SI(septic_patients$GEN) # 1399
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#' count_all(septic_patients$GEN) # 1855
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#' count_SI(example_isolates$GEN) # 1399
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#' count_all(example_isolates$GEN) # 1855
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#'
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#' with(septic_patients,
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#' with(example_isolates,
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#' count_SI(AMC, GEN)) # 1764
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#' with(septic_patients,
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#' with(example_isolates,
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#' n_rsi(AMC, GEN)) # 1936
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#'
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#' # Get portions S/I/R immediately of all rsi columns
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#' septic_patients %>%
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#' example_isolates %>%
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#' select(AMX, CIP) %>%
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#' count_df(translate = FALSE)
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#'
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#' # It also supports grouping variables
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#' septic_patients %>%
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#' example_isolates %>%
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#' select(hospital_id, AMX, CIP) %>%
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#' group_by(hospital_id) %>%
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#' count_df(translate = FALSE)
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