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new EUCAST rules algorithm

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dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
parent 56d4b4719f
commit fbc9191b13
115 changed files with 1340 additions and 2174 deletions
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R/count.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Count isolates
@ -74,15 +74,15 @@
#' # 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_S` calculates percentages right away instead.
#' count_S(septic_patients$amcl) # S = 1057 (67.1%)
#' count_all(septic_patients$amcl) # n = 1576
#' count_S(septic_patients$amcl) # S = 1342 (71.4%)
#' count_all(septic_patients$amcl) # n = 1879
#'
#' count_S(septic_patients$gent) # S = 1372 (74.0%)
#' count_all(septic_patients$gent) # n = 1855
#'
#' with(septic_patients,
#' count_S(amcl, gent)) # S = 1396 (92.0%)
#' with(septic_patients, # n = 1517
#' count_S(amcl, gent)) # S = 1660 (92.3%)
#' with(septic_patients, # n = 1798
#' n_rsi(amcl, gent))
#'
#' # Get portions S/I/R immediately of all rsi columns