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< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 0.5.0.9017< / span >
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Conduct AMR analysis
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Predict antimicrobial resistance
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Work with WHONET data
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Create frequency tables
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Use the G-test
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< h1 > Reference< / h1 >
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< h2 id = "section-background-information" class = "hasAnchor" > < a href = "#section-background-information" class = "anchor" > < / a > Background information< / h2 >
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< p class = "section-desc" > < p > Some pages about our package and its external sources. Be sure to read our < a href = "./../articles/index.html" > How To’ < / a > for more information about how to work with functions in this package.< / p > < / p >
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< / th >
< / tr >
< tr >
< td >
< p > < code > < a href = "AMR.html" > AMR< / a > < / code > < / p >
< / td >
< td > < p > The < code > AMR< / code > Package< / p > < / td >
< / tr > < tr >
< td >
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< p > < code > < a href = "ITIS.html" > ITIS< / a > < / code > < / p >
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< / td >
< td > < p > ITIS: Integrated Taxonomic Information System< / p > < / td >
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< / tr > < tr >
< td >
< p > < code > < a href = "WHOCC.html" > WHOCC< / a > < / code > < / p >
< / td >
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< td > < p > WHOCC: WHO Collaborating Centre for Drug Statistics Methodology< / p > < / td >
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< / tr >
< / tbody > < tbody >
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< tr >
< th colspan = "2" >
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< h2 id = "section-cleaning-your-data" class = "hasAnchor" > < a href = "#section-cleaning-your-data" class = "anchor" > < / a > Cleaning your data< / h2 >
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< p class = "section-desc" > < p > 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 < a href = "http://www.eucast.org/expert_rules_and_intrinsic_resistance/" > EUCAST rules< / a > .< / p > < / p >
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< / th >
< / tr >
< tr >
< td >
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< p > < code > < a href = "as.atc.html" > as.atc()< / a > < / code > < code > < a href = "as.atc.html" > is.atc()< / a > < / code > < / p >
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< / td >
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< td > < p > Transform to ATC code< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "as.mic.html" > as.mic()< / a > < / code > < code > < a href = "as.mic.html" > is.mic()< / a > < / code > < / p >
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< / td >
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< td > < p > Class 'mic'< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "as.mo.html" > as.mo()< / a > < / code > < code > < a href = "as.mo.html" > is.mo()< / a > < / code > < code > < a href = "as.mo.html" > mo_failures()< / a > < / code > < code > < a href = "as.mo.html" > mo_uncertainties()< / a > < / code > < code > < a href = "as.mo.html" > mo_renamed()< / a > < / code > < / p >
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< / td >
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< td > < p > Transform to microorganism ID< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "as.rsi.html" > as.rsi()< / a > < / code > < code > < a href = "as.rsi.html" > is.rsi()< / a > < / code > < code > < a href = "as.rsi.html" > is.rsi.eligible()< / a > < / code > < / p >
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< / td >
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< td > < p > Class 'rsi'< / p > < / td >
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< / tr > < tr >
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< td >
< p > < code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > < code > < a href = "mo_source.html" > get_mo_source()< / a > < / code > < / p >
< / td >
< td > < p > Use predefined reference data set< / p > < / td >
< / tr > < tr >
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< td >
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< p > < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > < code > < a href = "eucast_rules.html" > EUCAST_rules()< / a > < / code > < code > < a href = "eucast_rules.html" > interpretive_reading()< / a > < / code > < / p >
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< / td >
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< td > < p > EUCAST rules< / p > < / td >
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< / tr > < tr >
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< td >
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< p > < code > < a href = "guess_ab_col.html" > guess_ab_col()< / a > < / code > < / p >
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< / td >
< td > < p > Guess antibiotic column< / p > < / td >
< / tr > < tr >
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< td >
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< p > < code > < a href = "read.4D.html" > read.4D()< / a > < / code > < / p >
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< / td >
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< td > < p > Read data from 4D database< / p > < / td >
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
< h2 id = "section-adding-variables-to-your-data" class = "hasAnchor" > < a href = "#section-adding-variables-to-your-data" class = "anchor" > < / a > Adding variables to your data< / h2 >
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< p class = "section-desc" > < p > 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.< / p > < / p >
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< / th >
< / tr >
< tr >
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< td >
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< p > < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > < code > < a href = "first_isolate.html" > filter_first_isolate()< / a > < / code > < code > < a href = "first_isolate.html" > filter_first_weighted_isolate()< / a > < / code > < / p >
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< / td >
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< td > < p > Determine first (weighted) isolates< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "mdro.html" > mdro()< / a > < / code > < code > < a href = "mdro.html" > brmo()< / a > < / code > < code > < a href = "mdro.html" > mrgn()< / a > < / code > < code > < a href = "mdro.html" > eucast_exceptional_phenotypes()< / a > < / code > < / p >
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< / td >
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< td > < p > Determine multidrug-resistant organisms (MDRO)< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "key_antibiotics.html" > key_antibiotics()< / a > < / code > < code > < a href = "key_antibiotics.html" > key_antibiotics_equal()< / a > < / code > < / p >
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< / td >
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< td > < p > Key antibiotics for first < em > weighted< / em > isolates< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "mo_property.html" > mo_fullname()< / a > < / code > < code > < a href = "mo_property.html" > mo_shortname()< / a > < / code > < code > < a href = "mo_property.html" > mo_subspecies()< / a > < / code > < code > < a href = "mo_property.html" > mo_species()< / a > < / code > < code > < a href = "mo_property.html" > mo_genus()< / a > < / code > < code > < a href = "mo_property.html" > mo_family()< / a > < / code > < code > < a href = "mo_property.html" > mo_order()< / a > < / code > < code > < a href = "mo_property.html" > mo_class()< / a > < / code > < code > < a href = "mo_property.html" > mo_phylum()< / a > < / code > < code > < a href = "mo_property.html" > mo_subkingdom()< / a > < / code > < code > < a href = "mo_property.html" > mo_kingdom()< / a > < / code > < code > < a href = "mo_property.html" > mo_type()< / a > < / code > < code > < a href = "mo_property.html" > mo_gramstain()< / a > < / code > < code > < a href = "mo_property.html" > mo_TSN()< / a > < / code > < code > < a href = "mo_property.html" > mo_ref()< / a > < / code > < code > < a href = "mo_property.html" > mo_authors()< / a > < / code > < code > < a href = "mo_property.html" > mo_year()< / a > < / code > < code > < a href = "mo_property.html" > mo_taxonomy()< / a > < / code > < code > < a href = "mo_property.html" > mo_property()< / a > < / code > < / p >
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< / td >
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< td > < p > Property of a microorganism< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "atc_property.html" > atc_property()< / a > < / code > < code > < a href = "atc_property.html" > atc_official()< / a > < / code > < code > < a href = "atc_property.html" > atc_name()< / a > < / code > < code > < a href = "atc_property.html" > atc_trivial_nl()< / a > < / code > < code > < a href = "atc_property.html" > atc_certe()< / a > < / code > < code > < a href = "atc_property.html" > atc_umcg()< / a > < / code > < code > < a href = "atc_property.html" > atc_tradenames()< / a > < / code > < / p >
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< / td >
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< td > < p > Property of an antibiotic< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "atc_online.html" > atc_online_property()< / a > < / code > < code > < a href = "atc_online.html" > atc_online_groups()< / a > < / code > < code > < a href = "atc_online.html" > atc_online_ddd()< / a > < / code > < / p >
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< / td >
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< td > < p > Get ATC properties from WHOCC website< / p > < / td >
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< / tr > < tr >
< td >
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< p > < code > < a href = "abname.html" > abname()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Name of an antibiotic< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "age.html" > age()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Age in years of individuals< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "age_groups.html" > age_groups()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Split ages into age groups< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "p.symbol.html" > p.symbol()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Symbol of a p value< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "join.html" > inner_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > left_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > right_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > full_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > semi_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > anti_join_microorganisms()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Join a table with < code > microorganisms< / code > < / p > < / td >
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
2018-12-30 10:27:28 +01:00
< h2 id = "section-analysing-your-data" class = "hasAnchor" > < a href = "#section-analysing-your-data" class = "anchor" > < / a > Analysing your data< / h2 >
2019-01-21 15:53:01 +01:00
< p class = "section-desc" > < p > Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.< / p > < / p >
2018-12-29 22:24:19 +01:00
< / th >
< / tr >
< tr >
2018-12-23 21:26:21 +01:00
2019-02-08 16:06:54 +01:00
< td >
< p > < code > < a href = "availability.html" > availability()< / a > < / code > < / p >
< / td >
< td > < p > Check availability of columns< / p > < / td >
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "count.html" > count_R()< / a > < / code > < code > < a href = "count.html" > count_IR()< / a > < / code > < code > < a href = "count.html" > count_I()< / a > < / code > < code > < a href = "count.html" > count_SI()< / a > < / code > < code > < a href = "count.html" > count_S()< / a > < / code > < code > < a href = "count.html" > count_all()< / a > < / code > < code > < a href = "count.html" > n_rsi()< / a > < / code > < code > < a href = "count.html" > count_df()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Count isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "portion.html" > portion_R()< / a > < / code > < code > < a href = "portion.html" > portion_IR()< / a > < / code > < code > < a href = "portion.html" > portion_I()< / a > < / code > < code > < a href = "portion.html" > portion_SI()< / a > < / code > < code > < a href = "portion.html" > portion_S()< / a > < / code > < code > < a href = "portion.html" > portion_df()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Calculate resistance of isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "freq.html" > frequency_tbl()< / a > < / code > < code > < a href = "freq.html" > freq()< / a > < / code > < code > < a href = "freq.html" > top_freq()< / a > < / code > < code > < a href = "freq.html" > header()< / a > < / code > < code > < a href = "freq.html" > print(< i > < frequency_tbl> < / i > )< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Frequency table< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "g.test.html" > g.test()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > < em > G< / em > -test for Count Data< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "ggplot_rsi.html" > ggplot_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > geom_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > facet_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > scale_y_percent()< / a > < / code > < code > < a href = "ggplot_rsi.html" > scale_rsi_colours()< / a > < / code > < code > < a href = "ggplot_rsi.html" > theme_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > labels_rsi_count()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-27 19:30:40 +01:00
< td > < p > AMR plots with < code > ggplot2< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "kurtosis.html" > kurtosis()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Kurtosis of the sample< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2019-01-15 12:45:24 +01:00
< p > < code > < a href = "resistance_predict.html" > resistance_predict()< / a > < / code > < code > < a href = "resistance_predict.html" > rsi_predict()< / a > < / code > < code > < a href = "resistance_predict.html" > plot(< i > < resistance_predict> < / i > )< / a > < / code > < code > < a href = "resistance_predict.html" > ggplot_rsi_predict()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Predict antimicrobial resistance< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "rsi.html" > rsi()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Calculate resistance of isolates< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "skewness.html" > skewness()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Skewness of the sample< / p > < / td >
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
< h2 id = "section-included-data-sets" class = "hasAnchor" > < a href = "#section-included-data-sets" class = "anchor" > < / a > Included data sets< / h2 >
< p class = "section-desc" > < p > References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.< / p > < / p >
< / th >
< / tr >
< tr >
2018-12-23 21:26:21 +01:00
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "antibiotics.html" > antibiotics< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-25 13:18:41 +01:00
< td > < p > Data set with ~500 antibiotics< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "microorganisms.html" > microorganisms< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-25 13:18:41 +01:00
< td > < p > Data set with ~20,000 microorganisms< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "septic_patients.html" > septic_patients< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-25 13:18:41 +01:00
< td > < p > Data set with 2,000 blood culture isolates from septic patients< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2019-01-29 20:20:09 +01:00
< td >
< p > < code > < a href = "WHONET.html" > WHONET< / a > < / code > < / p >
< / td >
< td > < p > Data set with 500 isolates - WHONET example< / p > < / td >
< / tr > < tr >
2018-12-23 21:26:21 +01:00
< td >
2019-01-21 15:53:01 +01:00
< p > < code > < a href = "microorganisms.codes.html" > microorganisms.codes< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-21 15:53:01 +01:00
< td > < p > Translation table for microorganism codes< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "microorganisms.old.html" > microorganisms.old< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2019-01-25 13:18:41 +01:00
< td > < p > Data set with previously accepted taxonomic names< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "supplementary_data.html" > microorganismsDT< / a > < / code > < code > < a href = "supplementary_data.html" > microorganisms.prevDT< / a > < / code > < code > < a href = "supplementary_data.html" > microorganisms.unprevDT< / a > < / code > < code > < a href = "supplementary_data.html" > microorganisms.oldDT< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Supplementary Data< / p > < / td >
< / tr >
< / tbody > < tbody >
< tr >
< th colspan = "2" >
< h2 id = "section-other" class = "hasAnchor" > < a href = "#section-other" class = "anchor" > < / a > Other< / h2 >
2019-01-11 20:37:23 +01:00
< p class = "section-desc" > < p > These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘ ’ < code > if (x %like% y) {...}< / code > .< / p > < / p >
2018-12-29 22:24:19 +01:00
< / th >
< / tr >
< tr >
2018-12-23 21:26:21 +01:00
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "get_locale.html" > get_locale()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Get language for AMR< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
< td >
2018-12-29 22:24:19 +01:00
< p > < code > < a href = "like.html" > like()< / a > < / code > < code > < a href = "like.html" > `%like%`< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2018-12-29 22:24:19 +01:00
< td > < p > Pattern Matching< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr > < tr >
2019-01-26 23:22:56 +01:00
< td >
2019-01-27 13:33:43 +01:00
< p > < code > < a href = "AMR-deprecated.html" > ratio()< / a > < / code > < code > < a href = "AMR-deprecated.html" > guess_mo()< / a > < / code > < code > < a href = "AMR-deprecated.html" > guess_atc()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_property()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_atc()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_official()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_name()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_trivial_nl()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_certe()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_umcg()< / a > < / code > < code > < a href = "AMR-deprecated.html" > ab_tradenames()< / a > < / code > < code > < a href = "AMR-deprecated.html" > atc_ddd()< / a > < / code > < code > < a href = "AMR-deprecated.html" > atc_groups()< / a > < / code > < / p >
2019-01-26 23:22:56 +01:00
< / td >
< td > < p > Deprecated functions< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / tbody >
< / table >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
2019-01-08 16:23:45 +01:00
< li > < a href = "#section-background-information" > Background information< / a > < / li >
2018-12-29 22:24:19 +01:00
< li > < a href = "#section-cleaning-your-data" > Cleaning your data< / a > < / li >
< li > < a href = "#section-adding-variables-to-your-data" > Adding variables to your data< / a > < / li >
2018-12-30 10:27:28 +01:00
< li > < a href = "#section-analysing-your-data" > Analysing your data< / a > < / li >
2018-12-29 22:24:19 +01:00
< li > < a href = "#section-included-data-sets" > Included data sets< / a > < / li >
< li > < a href = "#section-other" > Other< / a > < / li >
2018-12-23 21:26:21 +01:00
< / ul >
< / div >
< / div >
< footer >
< div class = "copyright" >
2018-12-29 22:24:19 +01:00
< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
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< / footer >
< / div >
2018-12-29 22:24:19 +01:00
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