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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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22
R/ab_property.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Property of an antibiotic
@ -27,6 +30,7 @@
#' @export
#' @importFrom dplyr %>% left_join pull
#' @seealso \code{\link{antibiotics}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' ab_atc("amcl") # J01CR02
#' ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor

22
R/abname.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Name of an antibiotic
@ -28,6 +31,7 @@
#' @source \code{\link{antibiotics}}
#' @export
#' @importFrom dplyr %>% pull
#' @inheritSection AMR Read more on our website!
#' @examples
#' abname("AMCL")
#' # "Amoxicillin and beta-lactamase inhibitor"

23
R/age.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Age in years of individuals
@ -24,6 +27,7 @@
#' @return Integer (no decimals)
#' @seealso \code{\link{age_groups}} to splits age into groups
#' @importFrom dplyr if_else
#' @inheritSection AMR Read more on our website!
#' @export
age <- function(x, reference = Sys.Date()) {
if (length(x) != length(reference)) {
@ -70,6 +74,7 @@ age <- function(x, reference = Sys.Date()) {
#' @return Ordered \code{\link{factor}}
#' @seealso \code{\link{age}} to determine ages based on one or more reference dates
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
#'

23
R/atc.R
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@ -2,21 +2,23 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Transform to ATC code
#'
#' Use this function to determine the ATC code of one or more antibiotics. The data set \code{\link{antibiotics}} will be searched for abbreviations, official names and trade names.
@ -32,6 +34,7 @@
#' Source: \url{https://www.whocc.no/atc/structure_and_principles/}
#' @return Character (vector) with class \code{"act"}. Unknown values will return \code{NA}.
#' @seealso \code{\link{antibiotics}} for the dataframe that is being used to determine ATCs.
#' @inheritSection AMR Read more on our website!
#' @examples
#' # These examples all return "J01FA01", the ATC code of Erythromycin:
#' as.atc("J01FA01")

22
R/count.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Count isolates
@ -35,6 +38,7 @@
#' @rdname count
#' @name count
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a data set available in the AMR package. It is true, genuine data.
#' ?septic_patients

71
R/data.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Data set with 423 antibiotics
@ -41,6 +44,7 @@
#' \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}
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{microorganisms}}
# use this later to further fill AMR::antibiotics
# drug <- "Ciprofloxacin"
@ -123,7 +127,7 @@
#' Data set with taxonomic data from ITIS
#'
#' 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}}.
#' @inheritSection as.mo ITIS
#' @inheritSection itis ITIS
#' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
@ -143,6 +147,7 @@
#' \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}.
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
"microorganisms"
@ -158,6 +163,7 @@
#' \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}.
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old"
@ -169,6 +175,7 @@
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
"microorganisms.umcg"
@ -180,12 +187,13 @@
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.certe"
#' Data set with 2000 blood culture isolates of septic patients
#'
#' 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}.
#' @format A \code{\link{data.frame}} with 2,000 observations and 49 variables:
#' \describe{
#' \item{\code{date}}{date of receipt at the laboratory}
@ -199,45 +207,7 @@
#' \item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
#' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
#' }
#' @examples
#' # ----------- #
#' # PREPARATION #
#' # ----------- #
#'
#' # 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))
#' @inheritSection AMR Read more on our website!
"septic_patients"
#' Supplementary Data
@ -245,6 +215,7 @@
#' 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.
#' @rdname supplementary_data
#' @name supplementary_data
#' @inheritSection AMR Read more on our website!
# # Renew data:
# microorganismsDT <- data.table::as.data.table(AMR::microorganisms)
# # sort on (1) bacteria, (2) fungi, (3) protozoa and then human pathogenic prevalence and then TSN:

22
R/deprecated.R
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@ -2,23 +2,27 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Deprecated functions
#'
#' 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.
#' @inheritSection AMR Read more on our website!
#' @export
#' @keywords internal
#' @name AMR-deprecated

22
R/eucast_rules.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' EUCAST rules
@ -115,6 +118,7 @@
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
#' }
#' }
#' @inheritSection AMR Read more on our website!
#' @examples
#' a <- eucast_rules(septic_patients)
#'

29
R/first_isolate.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Determine first (weighted) isolates
@ -71,6 +74,7 @@
#' @importFrom crayon blue bold silver
#' @return Logical vector
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a dataset available in the AMR package. It is true, genuine data.
#' ?septic_patients
@ -419,12 +423,7 @@ first_isolate <- function(tbl,
& genus == lag(genus)
& species == lag(species),
FALSE,
TRUE)) %>% #,
# days_diff = 0) %>%
# mutate(days_diff = if_else(other_pat_or_mo == FALSE,
# as.integer((date_lab - lag(date_lab)) + lag(days_diff)),
# as.integer(0))) %>%
# mutate(r = days_diff) %>%
TRUE)) %>%
group_by_at(vars(patient_id,
genus,
species)) %>%

31
R/freq.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Frequency table
@ -73,6 +76,7 @@
#' @name freq
#' @return A \code{data.frame} (with an additional class \code{"frequency_tbl"}) with five columns: \code{item}, \code{count}, \code{percent}, \code{cum_count} and \code{cum_percent}.
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' library(dplyr)
#'
@ -812,7 +816,7 @@ print.frequency_tbl <- function(x,
if (opt$tbl_format == "pandoc") {
title <- bold(title)
} else if (opt$tbl_format == "markdown") {
title <- paste0("\n**", title, "**")
title <- paste0("\n**", title, "** ") # two space for newline
}
if (opt$header == TRUE) {
@ -825,7 +829,7 @@ print.frequency_tbl <- function(x,
}
} else if (opt$tbl_format == "markdown") {
# do print title as caption in markdown
cat("\n", title, " ", sep = "") # two trailing spaces for markdown
cat("\n", title, sep = "") # two trailing spaces for markdown
}
if (NROW(x) == 0) {
@ -838,6 +842,11 @@ print.frequency_tbl <- function(x,
if (is.null(opt$na)) {
opt$na <- "<NA>"
}
if (opt$tbl_format == "markdown") {
# no HTML tags
opt$na <- gsub("<", "(", opt$na, fixed = TRUE)
opt$na <- gsub(">", ")", opt$na, fixed = TRUE)
}
options(knitr.kable.NA = opt$na)
x.rows <- nrow(x)

24
R/g.test.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' \emph{G}-test for Count Data
@ -69,6 +72,7 @@
#' }
#' @export
#' @importFrom stats pchisq complete.cases
#' @inheritSection AMR Read more on our website!
#' @examples
#' # = EXAMPLE 1 =
#' # Shivrain et al. (2006) crossed clearfield rice (which are resistant
@ -79,7 +83,7 @@
#' # 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.
#'

22
R/get_locale.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Get language for AMR
@ -22,6 +25,7 @@
#' @details The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
#' @section Supported languages:
#' 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).
#' @inheritSection AMR Read more on our website!
#' @export
get_locale <- function() {
if (!is.null(getOption("AMR_locale"))) {

25
R/ggplot_rsi.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' AMR bar plots with \code{ggplot}
@ -52,6 +55,7 @@
#' @rdname ggplot_rsi
#' @importFrom utils installed.packages
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' library(dplyr)
#' library(ggplot2)
@ -298,6 +302,9 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
#' @rdname ggplot_rsi
#' @export
scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
if (all(breaks[breaks != 0] > 1)) {
breaks <- breaks / 100
}
ggplot2::scale_y_continuous(breaks = breaks,
labels = percent(breaks),
limits = limits)

23
R/globals.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
globalVariables(c(".",
@ -30,7 +33,6 @@ globalVariables(c(".",
"cum_count",
"cum_percent",
"date_lab",
"days_diff",
"diff.percent",
"fctlvl",
"first_isolate_row_index",
@ -58,6 +60,7 @@ globalVariables(c(".",
"microorganisms.umcg",
"mo",
"mo.old",
"more_than_episode_ago",
"n",
"name",
"observations",

62
R/itis.R Normal file
View File

@ -0,0 +1,62 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' ITIS: Integrated Taxonomic Information System
#'
#' 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].
#' @inheritSection AMR Read more on our website!
#' @name itis
#' @rdname itis
#' @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
NULL

22
R/join_microorganisms.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Join a table with \code{microorganisms}
@ -27,6 +30,7 @@
#' @param suffix if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
#' @param ... other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.
#' @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.
#' @inheritSection AMR Read more on our website!
#' @export
#' @examples
#' left_join_microorganisms(as.mo("K. pneumoniae"))

22
R/key_antibiotics.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Key antibiotics for first \emph{weighted} isolates
@ -43,6 +46,7 @@
#' @importFrom dplyr %>% mutate if_else
#' @importFrom crayon blue bold
#' @seealso \code{\link{first_isolate}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a dataset available in the AMR package
#' ?septic_patients

22
R/kurtosis.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Kurtosis of the sample
@ -25,6 +28,7 @@
#' @exportMethod kurtosis
#' @seealso \code{\link{skewness}}
#' @rdname kurtosis
#' @inheritSection AMR Read more on our website!
#' @export
kurtosis <- function(x, na.rm = FALSE) {
UseMethod("kurtosis")

22
R/like.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Pattern Matching
@ -27,6 +30,7 @@
#' @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...).
#' @source Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default and let it support multiple patterns.
#' @seealso \code{\link[base]{grep}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' # simple test
#' a <- "This is a test"

22
R/mdro.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Determine multidrug-resistant organisms (MDRO)
@ -32,6 +35,7 @@
#' @importFrom dplyr %>%
#' @importFrom crayon red blue bold
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' library(dplyr)
#'

22
R/mic.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Class 'mic'
@ -27,6 +30,7 @@
#' @export
#' @importFrom dplyr %>%
#' @seealso \code{\link{as.rsi}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
#' is.mic(mic_data)

21
R/misc.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
# No export, no Rd

31
R/mo.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Transform to microorganism ID
@ -74,14 +77,7 @@
#' }
#'
#' \code{guess_mo} is an alias of \code{as.mo}.
#' @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].
#'
#' @inheritSection itis ITIS
# (source as a section, so it can be inherited by other man pages)
#' @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}
@ -93,6 +89,7 @@
#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
#' @seealso \code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
#' The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
#' @inheritSection AMR Read more on our website!
#' @examples
#' # These examples all return "B_STPHY_AUR", the ID of S. aureus:
#' as.mo("stau")

24
R/mo_property.R
View File

@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Property of a microorganism
@ -30,7 +33,7 @@
#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
#' }
#' @inheritSection get_locale Supported languages
#' @inheritSection as.mo ITIS
#' @inheritSection itis ITIS
#' @inheritSection as.mo Source
#' @rdname mo_property
#' @name mo_property
@ -41,6 +44,7 @@
#' }
#' @export
#' @seealso \code{\link{microorganisms}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' # All properties of Escherichia coli
#' ## taxonomic properties

22
R/p.symbol.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Symbol of a p value
@ -22,6 +25,7 @@
#' @param p p value
#' @param emptychar text to show when \code{p > 0.1}
#' @return Text
#' @inheritSection AMR Read more on our website!
#' @export
p.symbol <- function(p, emptychar = " ") {
setting.bak <- options()$scipen

22
R/portion.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Calculate resistance of isolates
@ -58,6 +61,7 @@
#' @rdname portion
#' @name portion
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a data set available in the AMR package. It is true, genuine data.
#' ?septic_patients

22
R/read.4d.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Read data from 4D database
@ -22,6 +25,7 @@
#' @inheritParams utils::read.table
#' @param info a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions
#' @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.
#' @inheritSection AMR Read more on our website!
#' @export
read.4D <- function(file,
info = interactive(),

25
R/resistance_predict.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Predict antimicrobial resistance
@ -45,7 +48,7 @@
#' @export
#' @importFrom stats predict glm lm
#' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when
# @importFrom tidyr spread
#' @inheritSection AMR Read more on our website!
#' @examples
#' \dontrun{
#' # use it with base R:
@ -137,7 +140,7 @@ resistance_predict <- function(tbl,
tbl[, col_ab] <- gsub('I', 'R', tbl %>% pull(col_ab))
}
tbl <- tbl %>%
tbl <- tbl %>%
mutate_at(col_ab, as.rsi) %>%
filter_at(col_ab, all_vars(!is.na(.)))
tbl[, col_ab] <- droplevels(tbl[, col_ab])

22
R/rsi.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Class 'rsi'
@ -27,6 +30,7 @@
#' @export
#' @importFrom dplyr %>%
#' @seealso \code{\link{as.mic}}
#' @inheritSection AMR Read more on our website!
#' @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"))

21
R/rsi_calc.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all

22
R/skewness.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Skewness of the sample
@ -26,6 +29,7 @@
#' @exportMethod skewness
#' @seealso \code{\link{kurtosis}}
#' @rdname skewness
#' @inheritSection AMR Read more on our website!
#' @export
skewness <- function(x, na.rm = FALSE) {
UseMethod("skewness")

26
R/zzz.R
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@ -2,18 +2,21 @@
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' The \code{AMR} Package
@ -23,8 +26,11 @@
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.
#'
#' 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}