# Antimicrobial Resistance Analysis

## Documentation for package ‘AMR’ version 0.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C E F G I J K L M N P R S T misc

## -- A --

abname | Name of an antibiotic
ab_atc | Property of an antibiotic
ab_certe | Property of an antibiotic
ab_name | Property of an antibiotic
ab_official | Property of an antibiotic
ab_property | Property of an antibiotic
ab_tradenames | Property of an antibiotic
ab_trivial_nl | Property of an antibiotic
ab_umcg | Property of an antibiotic
AMR | The 'AMR' Package
antibiotics | Data set with 423 antibiotics
anti_join_microorganisms | Join a table with 'microorganisms'
as.atc | Transform to ATC code
as.mic | Class 'mic'
as.mo | Transform to microorganism ID
as.rsi | Class 'rsi'
atc | Transform to ATC code
atc_ddd | Properties of an ATC code
atc_groups | Properties of an ATC code
atc_property | Properties of an ATC code

## -- B --

brmo | Determine multidrug-resistant organisms (MDRO)

## -- C --

count | Count isolates
count_all | Count isolates
count_df | Count isolates
count_I | Count isolates
count_IR | Count isolates
count_R | Count isolates
count_S | Count isolates
count_SI | Count isolates

## -- E --

eucast_exceptional_phenotypes | Determine multidrug-resistant organisms (MDRO)
EUCAST_rules | EUCAST rules
eucast_rules | EUCAST rules

## -- F --

facet_rsi | AMR bar plots with 'ggplot'
first_isolate | Determine first (weighted) isolates
freq | Frequency table
frequency_tbl | Frequency table
full_join_microorganisms | Join a table with 'microorganisms'

## -- G --

g.test | _G_-test for Count Data
geom_rsi | AMR bar plots with 'ggplot'
get_locale | Get language for AMR
ggplot_rsi | AMR bar plots with 'ggplot'
guess_atc | Transform to ATC code
guess_mo | Transform to microorganism ID

## -- I --

inner_join | Join a table with 'microorganisms'
inner_join_microorganisms | Join a table with 'microorganisms'
interpretive_reading | EUCAST rules
is.atc | Transform to ATC code
is.mic | Class 'mic'
is.mo | Transform to microorganism ID
is.rsi | Class 'rsi'
is.rsi.eligible | Class 'rsi'

## -- J --

join | Join a table with 'microorganisms'

## -- K --

key_antibiotics | Key antibiotics for first _weighted_ isolates
key_antibiotics_equal | Key antibiotics for first _weighted_ isolates
kurtosis | Kurtosis of the sample
kurtosis.data.frame | Kurtosis of the sample
kurtosis.default | Kurtosis of the sample
kurtosis.matrix | Kurtosis of the sample

## -- L --

labels_rsi_count | AMR bar plots with 'ggplot'
left_join_microorganisms | Join a table with 'microorganisms'
like | Pattern Matching

## -- M --

mdro | Determine multidrug-resistant organisms (MDRO)
microorganisms | Data set with taxonomic data from ITIS
microorganisms.certe | Translation table for Certe
microorganisms.old | Data set with old taxonomic data from ITIS
microorganisms.oldDT | Supplementary Data
microorganisms.prevDT | Supplementary Data
microorganisms.umcg | Translation table for UMCG
microorganisms.unprevDT | Supplementary Data
microorganismsDT | Supplementary Data
mo | Transform to microorganism ID
mo_authors | Property of a microorganism
mo_class | Property of a microorganism
mo_family | Property of a microorganism
mo_fullname | Property of a microorganism
mo_genus | Property of a microorganism
mo_gramstain | Property of a microorganism
mo_kingdom | Property of a microorganism
mo_order | Property of a microorganism
mo_phylum | Property of a microorganism
mo_property | Property of a microorganism
mo_ref | Property of a microorganism
mo_shortname | Property of a microorganism
mo_species | Property of a microorganism
mo_subkingdom | Property of a microorganism
mo_subspecies | Property of a microorganism
mo_taxonomy | Property of a microorganism
mo_TSN | Property of a microorganism
mo_type | Property of a microorganism
mo_year | Property of a microorganism
mrgn | Determine multidrug-resistant organisms (MDRO)

## -- N --

n_rsi | Count isolates

## -- P --

p.symbol | Symbol of a p value
portion | Calculate resistance of isolates
portion_df | Calculate resistance of isolates
portion_I | Calculate resistance of isolates
portion_IR | Calculate resistance of isolates
portion_R | Calculate resistance of isolates
portion_S | Calculate resistance of isolates
portion_SI | Calculate resistance of isolates
print.frequency_tbl | Frequency table

## -- R --

read.4D | Read data from 4D database
resistance_predict | Predict antimicrobial resistance
right_join_microorganisms | Join a table with 'microorganisms'
rsi | Calculate resistance of isolates
rsi_predict | Predict antimicrobial resistance

## -- S --

scale_rsi_colours | AMR bar plots with 'ggplot'
scale_y_percent | AMR bar plots with 'ggplot'
semi_join_microorganisms | Join a table with 'microorganisms'
septic_patients | Data set with 2000 blood culture isolates of septic patients
skewness | Skewness of the sample
skewness.data.frame | Skewness of the sample
skewness.default | Skewness of the sample
skewness.matrix | Skewness of the sample
supplementary_data | Supplementary Data

## -- T --

theme_rsi | AMR bar plots with 'ggplot'
top_freq | Frequency table

## -- misc --

%like% | Pattern Matching