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set_mo_source
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141
_pkgdown.yml
141
_pkgdown.yml
@ -19,7 +19,7 @@
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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url: https://msberends.gitlab.io/AMR
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url: 'https://msberends.gitlab.io/AMR'
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title: 'AMR (for R)'
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@ -74,74 +74,77 @@ navbar:
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href: 'LICENSE-text.html'
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reference:
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- title: 'Background information'
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desc: >
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Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
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for more information about how to work with functions in this package.
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contents:
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- '`AMR`'
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- '`ITIS`'
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- title: 'Cleaning your data'
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desc: >
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Functions for cleaning and optimising your data, to be able
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to add variables later on (like taxonomic properties) or to
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fix and extend antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
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contents:
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- starts_with("as.")
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- '`eucast_rules`'
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- '`guess_ab_col`'
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- '`read.4D`'
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- title: 'Adding variables to your data'
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desc: >
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Functions to add new data to existing data, like the determination
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of first isolates,
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contents:
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- '`first_isolate`'
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- '`mdro`'
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- '`key_antibiotics`'
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- '`mo_property`'
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- '`ab_property`'
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- '`atc_property`'
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- '`abname`'
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- '`age`'
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- '`age_groups`'
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- '`p.symbol`'
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- '`join`'
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- title: 'Analysing your data'
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desc: >
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Functions for conducting AMR analysis
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contents:
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- '`count`'
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- '`portion`'
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- '`freq`'
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- '`g.test`'
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- '`ggplot_rsi`'
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- '`kurtosis`'
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- '`resistance_predict`'
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- '`rsi`'
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- '`skewness`'
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- title: 'Included data sets'
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desc: >
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References for microorganisms and antibiotics, and even a
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genuine data set with isolates from septic patients.
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contents:
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- '`antibiotics`'
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- '`microorganisms`'
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- '`septic_patients`'
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- '`microorganisms.certe`'
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- '`microorganisms.old`'
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- '`microorganisms.umcg`'
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- '`supplementary_data`'
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- title: Other
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desc: >
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These functions are mostly for internal use, but some of
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them may also be suitable for your analysis. Especially the
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'like' function can be useful: `if (x %like% y) {...}`.
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contents:
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- '`get_locale`'
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- '`like`'
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- '`mo_failures`'
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- '`mo_renamed`'
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- title: 'Background information'
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desc: >
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Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
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for more information about how to work with functions in this package.
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contents:
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- '`AMR`'
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- '`ITIS`'
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- title: 'Cleaning your data'
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desc: >
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Functions for cleaning and optimising your data, to be able to add
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variables later on (like taxonomic properties) or to fix and extend
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antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
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contents:
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- starts_with("as.")
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- '`mo_source`'
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- '`eucast_rules`'
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- '`guess_ab_col`'
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- '`read.4D`'
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- title: 'Adding variables to your data'
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desc: >
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Functions to add new data to existing data, like the determination
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of first isolates, multi-drug resistant microorganisms (MDRO), getting
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properties of microorganisms or antibiotics and determining the age of
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patients or divide ages into age groups.
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contents:
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- '`first_isolate`'
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- '`mdro`'
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- '`key_antibiotics`'
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- '`mo_property`'
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- '`ab_property`'
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- '`atc_property`'
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- '`abname`'
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- '`age`'
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- '`age_groups`'
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- '`p.symbol`'
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- '`join`'
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- title: 'Analysing your data'
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desc: >
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Functions for conducting AMR analysis, like counting isolates, calculating
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resistance or susceptibility, creating frequency tables or make plots.
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contents:
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- '`count`'
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- '`portion`'
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- '`freq`'
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- '`g.test`'
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- '`ggplot_rsi`'
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- '`kurtosis`'
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- '`resistance_predict`'
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- '`rsi`'
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- '`skewness`'
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- title: 'Included data sets'
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desc: >
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References for microorganisms and antibiotics, and even a
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genuine data set with isolates from septic patients.
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contents:
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- '`antibiotics`'
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- '`microorganisms`'
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- '`septic_patients`'
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- '`microorganisms.codes`'
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- '`microorganisms.old`'
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- '`supplementary_data`'
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- title: Other
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desc: >
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These functions are mostly for internal use, but some of
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them may also be suitable for your analysis. Especially the
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'like' function can be useful: `if (x %like% y) {...}`.
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contents:
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- '`get_locale`'
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- '`like`'
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- '`mo_failures`'
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- '`mo_renamed`'
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authors:
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Matthijs S. Berends:
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