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