This R package was intended to make microbial epidemiology easier. Most functions contain extensive help pages to get started.
This AMR
package basically does four important things:
It cleanses existing data, by transforming it to reproducible and profound classes, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:
as.mo
to get an ID of a microorganism. The IDs are quite obvious - the ID of E. coli is “ESCCOL” and the ID of S. aureus is “STAAUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even as.mo("MRSA")
will return the ID of S. aureus. Moreover, it can group all coagulase negative and positive Staphylococci, and can transform Streptococci into Lancefield groups. To find bacteria based on your input, this package contains a freely available database of almost 3,000 different (potential) human pathogenic microorganisms.as.rsi
to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.as.mic
to cleanse your MIC values. It produces a so-called factor (called ordinal in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.as.atc
to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.It enhances existing data and adds new data from data sets included in this package.
EUCAST_rules
to apply EUCAST expert rules to isolates.first_isolate
to identify the first isolates of every patient using guidelines from the CLSI (Clinical and Laboratory Standards Institute).
MDRO
(abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.microorganisms
contains the taxonomic properties of almost 3,000 potential human pathogenic microorganisms (bacteria, fungi/yeasts and parasites). Taxonomic names were downloaded from ITIS (Integrated Taxonomic Information System, http://www.itis.gov). Furhermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like mo_genus
, mo_family
, mo_gramstain
or even mo_phylum
. As they use as.mo
internally, they also use artificial intelligence. For example, mo_genus("MRSA")
and mo_genus("S. aureus")
will both return "Staphylococcus"
. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese. These functions can be used to add new variables to your data.antibiotics
contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like ab_name
and ab_tradenames
to look up values. The ab_*
functions use as.atc
internally so they support AI to guess your expected result. For example, ab_name("Fluclox")
, ab_name("Floxapen")
and ab_name("J01CF05")
will all return "Flucloxacillin"
. These functions can again be used to add new variables to your data.It analyses the data with convenient functions that use well-known methods.
portion_R
, portion_IR
, portion_I
, portion_SI
and portion_S
functions. Similarly, the amount of isolates can be determined with the count_R
, count_IR
, count_I
, count_SI
and count_S
functions. All these functions can be used with the dplyr
package (e.g. in conjunction with summarise
)geom_rsi
, a function made for the ggplot2
packageresistance_predict
functionIt teaches the user how to use all the above actions.
septic_patients
. This data set contains:
AMR, (c) 2018, https://github.com/msberends/AMR
Licensed under the GNU General Public License v2.0.