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(v0.7.1.9063) septic_patients -> example_isolates

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dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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38
R/count.R
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@ -44,29 +44,29 @@
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a data set available in the AMR package. It is true, genuine data.
#' ?septic_patients
#' # example_isolates is a data set available in the AMR package.
#' ?example_isolates
#'
#' # Count resistant isolates
#' count_R(septic_patients$AMX)
#' count_IR(septic_patients$AMX)
#' count_R(example_isolates$AMX)
#' count_IR(example_isolates$AMX)
#'
#' # Or susceptible isolates
#' count_S(septic_patients$AMX)
#' count_SI(septic_patients$AMX)
#' count_S(example_isolates$AMX)
#' count_SI(example_isolates$AMX)
#'
#' # Count all available isolates
#' count_all(septic_patients$AMX)
#' n_rsi(septic_patients$AMX)
#' count_all(example_isolates$AMX)
#' n_rsi(example_isolates$AMX)
#'
#' # Since n_rsi counts available isolates, you can
#' # calculate back to count e.g. non-susceptible isolates.
#' # This results in the same:
#' count_SI(septic_patients$AMX)
#' portion_SI(septic_patients$AMX) * n_rsi(septic_patients$AMX)
#' count_SI(example_isolates$AMX)
#' portion_SI(example_isolates$AMX) * n_rsi(example_isolates$AMX)
#'
#' library(dplyr)
#' septic_patients %>%
#' example_isolates %>%
#' group_by(hospital_id) %>%
#' summarise(R = count_R(CIP),
#' I = count_I(CIP),
@ -78,24 +78,24 @@
#' # 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 `portion_SI` calculates percentages right away instead.
#' count_SI(septic_patients$AMC) # 1433
#' count_all(septic_patients$AMC) # 1879
#' count_SI(example_isolates$AMC) # 1433
#' count_all(example_isolates$AMC) # 1879
#'
#' count_SI(septic_patients$GEN) # 1399
#' count_all(septic_patients$GEN) # 1855
#' count_SI(example_isolates$GEN) # 1399
#' count_all(example_isolates$GEN) # 1855
#'
#' with(septic_patients,
#' with(example_isolates,
#' count_SI(AMC, GEN)) # 1764
#' with(septic_patients,
#' with(example_isolates,
#' n_rsi(AMC, GEN)) # 1936
#'
#' # Get portions S/I/R immediately of all rsi columns
#' septic_patients %>%
#' example_isolates %>%
#' select(AMX, CIP) %>%
#' count_df(translate = FALSE)
#'
#' # It also supports grouping variables
#' septic_patients %>%
#' example_isolates %>%
#' select(hospital_id, AMX, CIP) %>%
#' group_by(hospital_id) %>%
#' count_df(translate = FALSE)