P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:02:38 +02:00
Code Releases Activity

WHO update, antibiotics update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-01-25 13:18:41 +01:00
parent 3ec44b6e0c
commit f4ff98b470
99 changed files with 1363 additions and 737 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/ITIS.Rd
View File

@ -8,10 +8,10 @@ All taxonomic names of all microorganisms are included in this package, using th
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

30
man/WHOCC.Rd Normal file
View File

@ -0,0 +1,30 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/whocc.R
\name{WHOCC}
\alias{WHOCC}
\title{WHO Collaborating Centre for Drug Statistics Methodology}
\description{
All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
}
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~500 antimicrobial drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD)} from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
}
\examples{
as.atc("meropenem")
ab_name("J01DH02")
ab_tradenames("flucloxacillin")
}

10
man/abname.Rd
View File

@ -25,6 +25,16 @@ Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice ver
\details{
\strong{The \code{\link{ab_property}} functions are faster and more concise}, but do not support concatenated strings, like \code{abname("AMCL+GENT"}.
}
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~500 antimicrobial drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD)} from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}

4
man/age.Rd
View File

@ -23,6 +23,10 @@ Calculates age in years based on a reference date, which is the sytem date at de
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
}
\examples{
df <- data.frame(birth_date = Sys.Date() - runif(100) * 25000)
df$age <- age(df$birth_date)
}
\seealso{
\code{\link{age_groups}} to split age into age groups
}

12
man/antibiotics.Rd
View File

@ -3,8 +3,8 @@
\docType{data}
\name{antibiotics}
\alias{antibiotics}
\title{Data set with 423 antibiotics}
\format{A \code{\link{data.frame}} with 423 observations and 18 variables:
\title{Data set with ~500 antibiotics}
\format{A \code{\link{data.frame}} with 488 observations and 16 variables:
\describe{
\item{\code{atc}}{ATC code, like \code{J01CR02}}
\item{\code{certe}}{Certe code, like \code{amcl}}
@ -20,13 +20,15 @@
\item{\code{iv_units}}{Units of \code{iv_ddd}}
\item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
\item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
\item{\code{atc_group1_nl}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
\item{\code{atc_group2_nl}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
\item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
\item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
}}
\source{
- World Health Organization: \url{https://www.whocc.no/atc_ddd_index/} \cr - EUCAST - Expert rules intrinsic exceptional V3.1 \cr - MOLIS (LIS of Certe): \url{https://www.certe.nl} \cr - GLIMS (LIS of UMCG): \url{https://www.umcg.nl}
- World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
}
\usage{
antibiotics

10
man/as.atc.Rd
View File

@ -28,6 +28,16 @@ Use the \code{\link{ab_property}} functions to get properties based on the retur
In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
Source: \url{https://www.whocc.no/atc/structure_and_principles/}
}
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~500 antimicrobial drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD)} from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}

4
man/as.mo.Rd
View File

@ -85,10 +85,10 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

BIN
man/figures/logo_certe.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 17 KiB

BIN
man/figures/logo_eh1h.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 11 KiB

BIN
man/figures/logo_interreg.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 11 KiB

0
man/figures/itis_logo.jpg → man/figures/logo_itis.jpg
View File

Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 16 KiB

After

Width:  |  Height:  |  Size: 16 KiB

BIN
man/figures/logo_rug.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 9.4 KiB

BIN
man/figures/logo_umcg.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 11 KiB

BIN
man/figures/logo_who.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 22 KiB

10
man/microorganisms.Rd
View File

@ -3,7 +3,7 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with taxonomic data from ITIS}
\title{Data set with ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
@ -23,20 +23,20 @@
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
Integrated Taxonomic Information System (ITIS) public online database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}
\description{
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}.
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

6
man/microorganisms.old.Rd
View File

@ -3,7 +3,7 @@
\docType{data}
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with old taxonomic data from ITIS}
\title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 2,383 observations and 4 variables:
\describe{
\item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
@ -22,10 +22,10 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

4
man/mo_property.Rd
View File

@ -94,10 +94,10 @@ Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/septic_patients.Rd
View File

@ -3,7 +3,7 @@
\docType{data}
\name{septic_patients}
\alias{septic_patients}
\title{Data set with 2000 blood culture isolates of septic patients}
\title{Data set with 2,000 blood culture isolates from septic patients}
\format{A \code{\link{data.frame}} with 2,000 observations and 49 variables:
\describe{
\item{\code{date}}{date of receipt at the laboratory}