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CRAN fixes for release 0.4.0

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https://cran.r-project.org/web/checks/check_results_AMR.html
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dr. M.S. (Matthijs) Berends 2018-10-09 13:53:33 +02:00
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commit 95c9fdc552
18 changed files with 142 additions and 38 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.4.0 Version: 0.4.0.9001
Date: 2018-10-01 Date: 2018-10-02
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

1
NAMESPACE
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@ -199,6 +199,7 @@ importFrom(graphics,barplot)
importFrom(graphics,hist) importFrom(graphics,hist)
importFrom(graphics,plot) importFrom(graphics,plot)
importFrom(graphics,text) importFrom(graphics,text)
importFrom(hms,is.hms)
importFrom(knitr,kable) importFrom(knitr,kable)
importFrom(rvest,html_children) importFrom(rvest,html_children)
importFrom(rvest,html_node) importFrom(rvest,html_node)

10
NEWS.md
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@ -1,4 +1,12 @@
# 0.4.0 # 0.4.0.90xx (latest development version)
#### New
#### Changed
* Check for `hms::is.hms` in frequency tables
* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
# 0.4.0 (latest stable release)
#### New #### New
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms. * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.

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R/eucast.R
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@ -20,7 +20,7 @@
#' #'
#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. #' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl} #' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_mo column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}} #' @param col_mo column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
#' @param info print progress #' @param info print progress
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations. #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
#' @param col_bactid Deprecated. Use \code{col_mo} instead. #' @param col_bactid Deprecated. Use \code{col_mo} instead.
@ -103,11 +103,12 @@
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' @examples #' @examples
#' a <- EUCAST_rules(septic_patients) #' a <- EUCAST_rules(septic_patients)
#' a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus #'
#' "ENCFAE", # Enterococcus faecalis #' a <- data.frame(mo = c("Staphylococcus aureus",
#' "ESCCOL", # Escherichia coli #' "Enterococcus faecalis",
#' "KLEPNE", # Klebsiella pneumoniae #' "Escherichia coli",
#' "PSEAER"), # Pseudomonas aeruginosa #' "Klebsiella pneumoniae",
#' "Pseudomonas aeruginosa"),
#' vanc = "-", # Vancomycin #' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin #' amox = "-", # Amoxicillin
#' coli = "-", # Colistin #' coli = "-", # Colistin
@ -116,7 +117,7 @@
#' stringsAsFactors = FALSE) #' stringsAsFactors = FALSE)
#' a #' a
#' #'
#' b <- EUCAST_rules(a) #' b <- EUCAST_rules(a) # 11 results will be forced as R due to intrinsic resistance
#' b #' b
EUCAST_rules <- function(tbl, EUCAST_rules <- function(tbl,
col_mo = 'mo', col_mo = 'mo',

3
R/freq.R
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@ -58,6 +58,7 @@
#' @importFrom grDevices boxplot.stats #' @importFrom grDevices boxplot.stats
#' @importFrom dplyr %>% select pull n_distinct group_by arrange desc mutate summarise n_distinct tibble #' @importFrom dplyr %>% select pull n_distinct group_by arrange desc mutate summarise n_distinct tibble
#' @importFrom utils browseVignettes installed.packages #' @importFrom utils browseVignettes installed.packages
#' @importFrom hms is.hms
#' @keywords summary summarise frequency freq #' @keywords summary summarise frequency freq
#' @rdname freq #' @rdname freq
#' @name freq #' @name freq
@ -366,7 +367,7 @@ frequency_tbl <- function(x,
} }
formatdates <- "%e %B %Y" # = d mmmm yyyy formatdates <- "%e %B %Y" # = d mmmm yyyy
if (any(class(x) == 'hms')) { if (is.hms(x)) {
x <- x %>% as.POSIXlt() x <- x %>% as.POSIXlt()
formatdates <- "%H:%M:%S" formatdates <- "%H:%M:%S"
} }

2
R/mo.R
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@ -63,7 +63,7 @@
#' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} #' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
#' This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). #' This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
#' #'
#' The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. #' All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
#' #'
#' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. #' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
# (source as a section, so it can be inherited by other man pages:) # (source as a section, so it can be inherited by other man pages:)

2
R/mo_property.R
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@ -22,7 +22,7 @@
#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}} #' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
#' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"} #' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
#' @param language language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese). #' @param language language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).
#' @param ... other parameters passed on to \code{/link{as.mo}} #' @param ... other parameters passed on to \code{\link{as.mo}}
#' @inheritSection as.mo ITIS #' @inheritSection as.mo ITIS
#' @inheritSection as.mo Source #' @inheritSection as.mo Source
#' @rdname mo_property #' @rdname mo_property

42
README.md
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@ -3,7 +3,7 @@
This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl). This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl).
:arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities. Read all changes and new functions in [NEWS.md](NEWS.md). :arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities. Read all changes and new functions in **[NEWS.md](https://github.com/msberends/AMR/blob/master/NEWS.md)**.
## Authors ## Authors
<a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Matthijs S. Berends<sup>1,2,a</sup>, <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Matthijs S. Berends<sup>1,2,a</sup>,
@ -29,6 +29,7 @@ Erwin E.A. Hassing<sup>2</sup>,
* [ITIS](#itis) * [ITIS](#itis)
* [How to get it?](#how-to-get-it) * [How to get it?](#how-to-get-it)
* [Install from CRAN](#install-from-cran) * [Install from CRAN](#install-from-cran)
* [Install from Zenodo](#install-from-zenodo)
* [Install from GitHub](#install-from-github) * [Install from GitHub](#install-from-github)
* [How to use it?](#how-to-use-it) * [How to use it?](#how-to-use-it)
* [New classes](#new-classes) * [New classes](#new-classes)
@ -80,10 +81,37 @@ The `AMR` package basically does four important things:
This package contains the **complete microbial taxonomic data** (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). This package contains the **complete microbial taxonomic data** (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).
The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.
**Get a note when a species was renamed**
```r
mo_shortname("Chlamydia psittaci")
# Note: 'Chlamydia psittaci' (Page, 1968) was renamed 'Chlamydophila psittaci' (Everett et al., 1999)
# [1] "C. psittaci"
```
**Get any property from the entire taxonomic tree for all included species**
```r
mo_class("E. coli")
# [1] "Gammaproteobacteria"
mo_family("E. coli")
# [1] "Enterobacteriaceae"
mo_ref("E. coli")
# [1] "Castellani and Chalmers, 1919"
```
**Do not get mistaken - the package only includes microorganisms**
```r
mo_phylum("C. elegans")
# [1] "Cyanobacteria" # Bacteria?!
mo_fullname("C. elegans")
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
```
## How to get it? ## How to get it?
All stable versions of this package [are published on CRAN](http://cran.r-project.org/package=AMR), the official R network with a peer-reviewed submission process. All stable versions of this package [are published on CRAN](http://cran.r-project.org/package=AMR), the official R network with a peer-reviewed submission process.
@ -99,6 +127,11 @@ All stable versions of this package [are published on CRAN](http://cran.r-projec
- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly: - <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly:
- `install.packages("AMR")` - `install.packages("AMR")`
### Install from Zenodo
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1305355.svg)](https://doi.org/10.5281/zenodo.1305355)
This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355
### Install from GitHub ### Install from GitHub
This is the latest **development version**. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green: This is the latest **development version**. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green:
@ -115,11 +148,6 @@ install.packages("devtools")
devtools::install_github("msberends/AMR") devtools::install_github("msberends/AMR")
``` ```
### Install from Zenodo
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1305355.svg)](https://doi.org/10.5281/zenodo.1305355)
This package was also published on Zenodo: https://doi.org/10.5281/zenodo.1305355
## How to use it? ## How to use it?
```r ```r
# Call it with: # Call it with:

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data/microorganisms.old.rda
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data/microorganisms.rda
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man/EUCAST.Rd
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@ -36,7 +36,7 @@ interpretive_reading(...)
\arguments{ \arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}} \item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{col_mo}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}} \item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
\item{info}{print progress} \item{info}{print progress}
@ -121,11 +121,12 @@ Abbrevations of the column containing antibiotics:
\examples{ \examples{
a <- EUCAST_rules(septic_patients) a <- EUCAST_rules(septic_patients)
a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"ENCFAE", # Enterococcus faecalis a <- data.frame(mo = c("Staphylococcus aureus",
"ESCCOL", # Escherichia coli "Enterococcus faecalis",
"KLEPNE", # Klebsiella pneumoniae "Escherichia coli",
"PSEAER"), # Pseudomonas aeruginosa "Klebsiella pneumoniae",
"Pseudomonas aeruginosa"),
vanc = "-", # Vancomycin vanc = "-", # Vancomycin
amox = "-", # Amoxicillin amox = "-", # Amoxicillin
coli = "-", # Colistin coli = "-", # Colistin
@ -134,7 +135,7 @@ a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
stringsAsFactors = FALSE) stringsAsFactors = FALSE)
a a
b <- EUCAST_rules(a) b <- EUCAST_rules(a) # 11 results will be forced as R due to intrinsic resistance
b b
} }
\keyword{eucast} \keyword{eucast}

2
man/MDRO.Rd
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@ -36,7 +36,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).} \item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
\item{col_mo}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}} \item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
\item{info}{print progress} \item{info}{print progress}

2
man/as.mo.Rd
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@ -70,7 +70,7 @@ This means that looking up human pathogenic microorganisms takes less time than
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
} }

2
man/microorganisms.Rd
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@ -36,7 +36,7 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria,
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
} }

2
man/microorganisms.old.Rd
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@ -25,7 +25,7 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
} }

4
man/mo_property.Rd
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@ -56,7 +56,7 @@ mo_taxonomy(x, ...)
\item{language}{language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).} \item{language}{language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
\item{...}{other parameters passed on to \code{/link{as.mo}}} \item{...}{other parameters passed on to \code{\link{as.mo}}}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}} \item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
} }
@ -71,7 +71,7 @@ Use these functions to return a specific property of a microorganism from the \c
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
} }

29
tests/testthat/test-data.R
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@ -4,4 +4,33 @@ test_that("data sets are valid", {
# IDs should always be unique # IDs should always be unique
expect_identical(nrow(antibiotics), length(unique(antibiotics$atc))) expect_identical(nrow(antibiotics), length(unique(antibiotics$atc)))
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo))) expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
# there should be no diacritics (i.e. non ASCII) characters in the datasets
library(dplyr)
# check only character variables:
test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
# and compare them with their transformed version:
expect_identical(test_microorganisms,
test_microorganisms %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_microorganisms.old,
test_microorganisms.old %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_antibiotics,
test_antibiotics %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_septic_patients,
test_septic_patients %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
}) })

45
vignettes/AMR.Rmd
View File

@ -3,7 +3,7 @@ title: "Introduction to the AMR package"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: false
vignette: > vignette: >
%\VignetteIndexEntry{Introduction to the AMR package} %\VignetteIndexEntry{Introduction to the AMR package}
%\VignetteEngine{knitr::rmarkdown} %\VignetteEngine{knitr::rmarkdown}
@ -17,13 +17,13 @@ knitr::opts_chunk$set(
) )
``` ```
This R package was intended to make microbial epidemiology easier. Most functions contain extensive help pages to get started. 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: The `AMR` package basically does four important things:
1. 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: 1. 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:
* Use `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. * Use `as.mo` to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of *Klebsiella pneumoniae* is "B_KLBSL_PNE" (B stands for Bacteria) and the ID of *S. aureus* is "B_STPHY_AUR". 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, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.
* Use `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". * Use `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".
* Use `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". * Use `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".
* Use `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. * Use `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.
@ -34,7 +34,7 @@ This `AMR` package basically does four important things:
* Use `first_isolate` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute). * Use `first_isolate` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute).
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them. * You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
* Use `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. * Use `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.
* The data set `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. * The data set `microorganisms` contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, 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.
* The data set `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. * The data set `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.
3. It **analyses the data** with convenient functions that use well-known methods. 3. It **analyses the data** with convenient functions that use well-known methods.
@ -52,6 +52,41 @@ This `AMR` package basically does four important things:
* Results of 40 antibiotics (each antibiotic in its own column) with a total of 38,414 antimicrobial results * Results of 40 antibiotics (each antibiotic in its own column) with a total of 38,414 antimicrobial results
* Real and genuine data * Real and genuine data
### ITIS
This package contains the **complete microbial taxonomic data** (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).
All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all 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.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.
**Get a note when a species was renamed**
```r
mo_shortname("Chlamydia psittaci")
# Note: 'Chlamydia psittaci' (Page, 1968) was renamed 'Chlamydophila psittaci' (Everett et al., 1999)
# [1] "C. psittaci"
```
**Get any property from the entire taxonomic tree for all included species**
```r
mo_class("E. coli")
# [1] "Gammaproteobacteria"
mo_family("E. coli")
# [1] "Enterobacteriaceae"
mo_ref("E. coli")
# [1] "Castellani and Chalmers, 1919"
```
**Do not get mistaken - the package only includes microorganisms**
```r
mo_phylum("C. elegans")
# [1] "Cyanobacteria" # Bacteria?!
mo_fullname("C. elegans")
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
```
---- ----
```{r, echo = FALSE} ```{r, echo = FALSE}
# this will print "2018" in 2018, and "2018-yyyy" after 2018. # this will print "2018" in 2018, and "2018-yyyy" after 2018.