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big website update, licence txt update

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dr. M.S. (Matthijs) Berends
2019-01-02 23:24:07 +01:00
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commit 6b2d464f8c
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6
man/AMR-deprecated.Rd
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@@ -10,4 +10,10 @@ ratio(x, ratio)
\description{
These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.
}
\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.
}
\keyword{internal}

8
man/AMR.Rd
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@@ -11,9 +11,15 @@ This package was intended to simplify the analysis and prediction of Antimicrobi
This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
}
\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.
}
\section{Authors}{
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu Sinha[1] \cr
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{rug.nl} \url{umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}

6
man/ab_property.Rd
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@@ -40,6 +40,12 @@ A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length on
\description{
Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
}
\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{
ab_atc("amcl") # J01CR02
ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor

6
man/abname.Rd
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@@ -25,6 +25,12 @@ 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{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{
abname("AMCL")
# "Amoxicillin and beta-lactamase inhibitor"

6
man/age.Rd
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@@ -17,6 +17,12 @@ Integer (no decimals)
\description{
Calculates age in years based on a reference date, which is the sytem time at default.
}
\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.
}
\seealso{
\code{\link{age_groups}} to splits age into groups
}

6
man/age_groups.Rd
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@@ -31,6 +31,12 @@ To split ages, the input can be:
}
}
}
\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{
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)

6
man/antibiotics.Rd
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@@ -34,6 +34,12 @@ antibiotics
\description{
A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.
}
\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.
}
\seealso{
\code{\link{microorganisms}}
}

6
man/as.atc.Rd
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@@ -28,6 +28,12 @@ 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{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{
# These examples all return "J01FA01", the ATC code of Erythromycin:
as.atc("J01FA01")

6
man/as.mic.Rd
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@@ -20,6 +20,12 @@ Ordered factor with new class \code{mic}
\description{
This transforms a vector to a new class \code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
}
\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{
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
is.mic(mic_data)

18
man/as.mo.Rd
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@@ -80,6 +80,15 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\code{guess_mo} is an alias of \code{as.mo}.
}
\section{Source}{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
@@ -90,13 +99,10 @@ All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozo
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}
\section{Source}{
\section{Read more on our website!}{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
\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{

6
man/as.rsi.Rd
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@@ -24,6 +24,12 @@ This transforms a vector to a new class \code{rsi}, which is an ordered factor w
\details{
The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
}
\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{
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))

6
man/count.Rd
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@@ -58,6 +58,12 @@ These functions are meant to count isolates. Use the \code{\link{portion}_*} fun
\code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
}
\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{
# septic_patients is a data set available in the AMR package. It is true, genuine data.
?septic_patients

6
man/eucast_rules.Rd
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@@ -137,6 +137,12 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{vanc}: vancomycin (\emph{J01XA01}).
}
\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{
a <- eucast_rules(septic_patients)

6
man/first_isolate.Rd
View File

@@ -96,6 +96,12 @@ The function \code{filter_first_weighted_isolate} is essentially equal to:
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate.
}
\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{
# septic_patients is a dataset available in the AMR package. It is true, genuine data.
?septic_patients

6
man/freq.Rd
View File

@@ -107,6 +107,12 @@ In factors, all factor levels that are not existing in the input data will be dr
The function \code{top_freq} uses \code{\link[dplyr]{top_n}} internally and will include more than \code{n} rows if there are ties.
}
\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{
library(dplyr)

8
man/g.test.Rd
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@@ -100,6 +100,12 @@ where \code{df} are the degrees of freedom.
If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use \emph{G}-tests for each category, of course.
}
\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{
# = EXAMPLE 1 =
# Shivrain et al. (2006) crossed clearfield rice (which are resistant
@@ -110,7 +116,7 @@ If there are more than two categories and you want to find out which ones are si
# by a single gene with two co-dominant alleles, you would expect a 1:2:1
# ratio.
x <- c(772, 1611, 737)#'
x <- c(772, 1611, 737)
G <- g.test(x, p = c(1, 2, 1) / 4)
# G$p.value = 0.12574.

6
man/get_locale.Rd
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@@ -17,3 +17,9 @@ The system language can be overwritten with \code{\link{getOption}("AMR_locale")
Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish), \code{"it"} (Italian), \code{"fr"} (French), and \code{"pt"} (Portuguese).
}
\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.
}

6
man/ggplot_rsi.Rd
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@@ -81,6 +81,12 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
\code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
}
\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{
library(dplyr)
library(ggplot2)

52
man/itis.Rd Normal file
View File

@@ -0,0 +1,52 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/itis.R
\name{itis}
\alias{itis}
\title{ITIS: Integrated Taxonomic Information System}
\description{
All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS).
}
\section{ITIS}{
\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 nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{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. 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].
}
\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{
# Get a note when a species was renamed
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
mo_class("E. coli")
# [1] "Gammaproteobacteria"
mo_family("E. coli")
# [1] "Enterobacteriaceae"
mo_subkingdom("E. coli")
# [1] "Negibacteria"
mo_gramstain("E. coli") # based on subkingdom
# [1] "Gram negative"
mo_ref("E. coli")
# [1] "Castellani and Chalmers, 1919"
# Do not get mistaken - the package only includes microorganisms
mo_phylum("C. elegans")
# [1] "Cyanobacteria" # Bacteria?!
mo_fullname("C. elegans")
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
}

6
man/join.Rd
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@@ -38,6 +38,12 @@ Join the dataset \code{\link{microorganisms}} easily to an existing table or cha
\details{
\strong{Note:} As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
}
\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{
left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNE")

6
man/key_antibiotics.Rd
View File

@@ -67,6 +67,12 @@ The function \code{key_antibiotics} returns a character vector with 12 antibioti
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate.
}
\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{
# septic_patients is a dataset available in the AMR package
?septic_patients

6
man/kurtosis.Rd
View File

@@ -23,6 +23,12 @@ kurtosis(x, na.rm = FALSE)
\description{
Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
}
\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.
}
\seealso{
\code{\link{skewness}}
}

6
man/like.Rd
View File

@@ -34,6 +34,12 @@ Convenient wrapper around \code{\link[base]{grep}} to match a pattern: \code{a \
\details{
Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools > Modify Keyboard Shortcuts...).
}
\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{
# simple test
a <- "This is a test"

6
man/mdro.Rd
View File

@@ -240,6 +240,12 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{vanc}: vancomycin (\emph{J01XA01}).
}
\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{
library(dplyr)

6
man/microorganisms.Rd
View File

@@ -41,6 +41,12 @@ All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozo
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}
\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.
}
\seealso{
\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
}

6
man/microorganisms.certe.Rd
View File

@@ -15,6 +15,12 @@ microorganisms.certe
\description{
A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
}
\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.
}
\seealso{
\code{\link{as.mo}} \code{\link{microorganisms}}
}

6
man/microorganisms.old.Rd
View File

@@ -30,6 +30,12 @@ All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozo
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}
\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.
}
\seealso{
\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
}

6
man/microorganisms.umcg.Rd
View File

@@ -15,6 +15,12 @@ microorganisms.umcg
\description{
A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
}
\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.
}
\seealso{
\code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
}

6
man/mo_property.Rd
View File

@@ -111,6 +111,12 @@ ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic spec
[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
}
\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{
# All properties of Escherichia coli
## taxonomic properties

6
man/p.symbol.Rd
View File

@@ -17,3 +17,9 @@ Text
\description{
Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above \code{p = 1} will return \code{NA}.
}
\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.
}

6
man/portion.Rd
View File

@@ -79,6 +79,12 @@ The old \code{\link{rsi}} function is still available for backwards compatibilit
And so on.
}
}
\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{
# septic_patients is a data set available in the AMR package. It is true, genuine data.
?septic_patients

6
man/read.4D.Rd
View File

@@ -122,3 +122,9 @@ This function is only useful for the MMB department of the UMCG. Use this functi
\details{
Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
}
\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.
}

6
man/resistance_predict.Rd
View File

@@ -52,6 +52,12 @@ rsi_predict(tbl, col_ab, col_date, year_min = NULL, year_max = NULL,
\description{
Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See Examples for a real live example.
}
\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{
\dontrun{
# use it with base R:

44
man/septic_patients.Rd
View File

@@ -21,46 +21,12 @@
septic_patients
}
\description{
An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
}
\examples{
# ----------- #
# PREPARATION #
# ----------- #
\section{Read more on our website!}{
# Save this example data set to an object, so we can edit it:
my_data <- septic_patients
# load the dplyr package to make data science A LOT easier
library(dplyr)
# Add first isolates to our data set:
my_data <- my_data \%>\%
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "mo"))
# -------- #
# ANALYSIS #
# -------- #
# 1. Get the amoxicillin resistance percentages (p)
# and numbers (n) of E. coli, divided by hospital:
my_data \%>\%
filter(mo == guess_mo("E. coli"),
first_isolates == TRUE) \%>\%
group_by(hospital_id) \%>\%
summarise(n = n_rsi(amox),
p = portion_IR(amox))
# 2. Get the amoxicillin/clavulanic acid resistance
# percentages of E. coli, trend over the years:
my_data \%>\%
filter(mo == guess_mo("E. coli"),
first_isolates == TRUE) \%>\%
group_by(year = format(date, "\%Y")) \%>\%
summarise(n = n_rsi(amcl),
p = portion_IR(amcl, minimum = 20))
\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.
}
\keyword{datasets}

6
man/skewness.Rd
View File

@@ -25,6 +25,12 @@ Skewness is a measure of the asymmetry of the probability distribution of a real
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.
}
\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.
}
\seealso{
\code{\link{kurtosis}}
}

6
man/supplementary_data.Rd
View File

@@ -21,4 +21,10 @@ microorganisms.oldDT
\description{
These \code{\link{data.table}s} are transformed from the \code{\link{microorganisms}} and \code{\link{microorganisms}} data sets to improve speed of \code{\link{as.mo}}. They are meant for internal use only, and are only mentioned here for reference.
}
\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.
}
\keyword{datasets}