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new EUCAST rules algorithm
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10
R/count.R
10
R/count.R
@ -16,7 +16,7 @@
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Count isolates
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@ -74,15 +74,15 @@
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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_S` calculates percentages right away instead.
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#' count_S(septic_patients$amcl) # S = 1057 (67.1%)
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#' count_all(septic_patients$amcl) # n = 1576
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#' count_S(septic_patients$amcl) # S = 1342 (71.4%)
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#' count_all(septic_patients$amcl) # n = 1879
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#'
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#' count_S(septic_patients$gent) # S = 1372 (74.0%)
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#' count_all(septic_patients$gent) # n = 1855
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#'
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#' with(septic_patients,
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#' count_S(amcl, gent)) # S = 1396 (92.0%)
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#' with(septic_patients, # n = 1517
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#' count_S(amcl, gent)) # S = 1660 (92.3%)
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#' with(septic_patients, # n = 1798
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#' n_rsi(amcl, gent))
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#'
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#' # Get portions S/I/R immediately of all rsi columns
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