From 593d740b84553855d25c3183c2ac3508b1da88f7 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Thu, 19 Jan 2023 12:54:53 +0100 Subject: [PATCH] documentation, file permissions --- DESCRIPTION | 4 +-- NEWS.md | 2 +- R/aa_helper_pm_functions.R | 0 R/ab_from_text.R | 0 R/ab_property.R | 0 R/ab_selectors.R | 0 R/amr.R | 0 R/atc_online.R | 0 R/av_from_text.R | 0 R/av_property.R | 0 R/availability.R | 0 R/bug_drug_combinations.R | 0 R/custom_antimicrobials.R | 0 R/custom_eucast_rules.R | 0 R/custom_microorganisms.R | 24 +++++++++--------- R/disk.R | 0 R/episode.R | 0 R/italicise_taxonomy.R | 0 R/mean_amr_distance.R | 0 R/mo_property.R | 4 ++- R/mo_source.R | 0 R/options.R | 39 ++++++++++++++++++++++++++++++ R/plot.R | 0 R/random.R | 0 R/rsi_df.R | 0 R/sysdata.rda | Bin R/vctrs.R | 0 man/AMR-deprecated.Rd | 0 man/AMR-options.Rd | 17 +++++++++++++ man/AMR.Rd | 0 man/WHOCC.Rd | 0 man/WHONET.Rd | 0 man/ab_from_text.Rd | 0 man/ab_property.Rd | 0 man/add_custom_antimicrobials.Rd | 0 man/add_custom_microorganisms.Rd | 20 +++++++-------- man/age.Rd | 0 man/age_groups.Rd | 0 man/antibiotic_class_selectors.Rd | 0 man/antibiotics.Rd | 0 man/as.ab.Rd | 0 man/as.av.Rd | 0 man/as.disk.Rd | 0 man/as.mo.Rd | 0 man/atc_online.Rd | 0 man/av_from_text.Rd | 0 man/av_property.Rd | 0 man/availability.Rd | 0 man/bug_drug_combinations.Rd | 0 man/count.Rd | 0 man/custom_eucast_rules.Rd | 0 man/dosage.Rd | 0 man/eucast_rules.Rd | 0 man/example_isolates.Rd | 0 man/example_isolates_unclean.Rd | 0 man/g.test.Rd | 0 man/get_episode.Rd | 0 man/ggplot_pca.Rd | 0 man/ggplot_rsi.Rd | 0 man/guess_ab_col.Rd | 0 man/intrinsic_resistant.Rd | 0 man/italicise_taxonomy.Rd | 0 man/key_antimicrobials.Rd | 0 man/kurtosis.Rd | 0 man/mdro.Rd | 0 man/mean_amr_distance.Rd | 0 man/microorganisms.codes.Rd | 0 man/mo_matching_score.Rd | 0 man/mo_property.Rd | 0 man/mo_source.Rd | 0 man/pca.Rd | 0 man/plot.Rd | 0 man/proportion.Rd | 0 man/random.Rd | 0 man/resistance_predict.Rd | 0 man/rsi_translation.Rd | 0 man/skewness.Rd | 0 man/translate.Rd | 0 78 files changed, 85 insertions(+), 25 deletions(-) mode change 100644 => 100755 R/aa_helper_pm_functions.R mode change 100644 => 100755 R/ab_from_text.R mode change 100644 => 100755 R/ab_property.R mode change 100644 => 100755 R/ab_selectors.R mode change 100644 => 100755 R/amr.R mode change 100644 => 100755 R/atc_online.R mode change 100644 => 100755 R/av_from_text.R mode change 100644 => 100755 R/av_property.R mode change 100644 => 100755 R/availability.R mode change 100644 => 100755 R/bug_drug_combinations.R mode change 100644 => 100755 R/custom_antimicrobials.R mode change 100644 => 100755 R/custom_eucast_rules.R mode change 100644 => 100755 R/custom_microorganisms.R mode change 100644 => 100755 R/disk.R mode change 100644 => 100755 R/episode.R mode change 100644 => 100755 R/italicise_taxonomy.R mode change 100644 => 100755 R/mean_amr_distance.R mode change 100644 => 100755 R/mo_source.R create mode 100755 R/options.R mode change 100644 => 100755 R/plot.R mode change 100644 => 100755 R/random.R mode change 100644 => 100755 R/rsi_df.R mode change 100644 => 100755 R/sysdata.rda mode change 100644 => 100755 R/vctrs.R mode change 100644 => 100755 man/AMR-deprecated.Rd create mode 100644 man/AMR-options.Rd mode change 100644 => 100755 man/AMR.Rd mode change 100644 => 100755 man/WHOCC.Rd mode change 100644 => 100755 man/WHONET.Rd mode change 100644 => 100755 man/ab_from_text.Rd mode change 100644 => 100755 man/ab_property.Rd mode change 100644 => 100755 man/add_custom_antimicrobials.Rd mode change 100644 => 100755 man/add_custom_microorganisms.Rd mode change 100644 => 100755 man/age.Rd mode change 100644 => 100755 man/age_groups.Rd mode change 100644 => 100755 man/antibiotic_class_selectors.Rd mode change 100644 => 100755 man/antibiotics.Rd mode change 100644 => 100755 man/as.ab.Rd mode change 100644 => 100755 man/as.av.Rd mode change 100644 => 100755 man/as.disk.Rd mode change 100644 => 100755 man/as.mo.Rd mode change 100644 => 100755 man/atc_online.Rd mode change 100644 => 100755 man/av_from_text.Rd mode change 100644 => 100755 man/av_property.Rd mode change 100644 => 100755 man/availability.Rd mode change 100644 => 100755 man/bug_drug_combinations.Rd mode change 100644 => 100755 man/count.Rd mode change 100644 => 100755 man/custom_eucast_rules.Rd mode change 100644 => 100755 man/dosage.Rd mode change 100644 => 100755 man/eucast_rules.Rd mode change 100644 => 100755 man/example_isolates.Rd mode change 100644 => 100755 man/example_isolates_unclean.Rd mode change 100644 => 100755 man/g.test.Rd mode change 100644 => 100755 man/get_episode.Rd mode change 100644 => 100755 man/ggplot_pca.Rd mode change 100644 => 100755 man/ggplot_rsi.Rd mode change 100644 => 100755 man/guess_ab_col.Rd mode change 100644 => 100755 man/intrinsic_resistant.Rd mode change 100644 => 100755 man/italicise_taxonomy.Rd mode change 100644 => 100755 man/key_antimicrobials.Rd mode change 100644 => 100755 man/kurtosis.Rd mode change 100644 => 100755 man/mdro.Rd mode change 100644 => 100755 man/mean_amr_distance.Rd mode change 100644 => 100755 man/microorganisms.codes.Rd mode change 100644 => 100755 man/mo_matching_score.Rd mode change 100644 => 100755 man/mo_property.Rd mode change 100644 => 100755 man/mo_source.Rd mode change 100644 => 100755 man/pca.Rd mode change 100644 => 100755 man/plot.Rd mode change 100644 => 100755 man/proportion.Rd mode change 100644 => 100755 man/random.Rd mode change 100644 => 100755 man/resistance_predict.Rd mode change 100644 => 100755 man/rsi_translation.Rd mode change 100644 => 100755 man/skewness.Rd mode change 100644 => 100755 man/translate.Rd diff --git a/DESCRIPTION b/DESCRIPTION index a05f1a74..bab8c9b2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.8.2.9093 -Date: 2023-01-14 +Version: 1.8.2.9094 +Date: 2023-01-19 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index af3ee629..4dc865ed 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9093 +# AMR 1.8.2.9094 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R old mode 100644 new mode 100755 diff --git a/R/ab_from_text.R b/R/ab_from_text.R old mode 100644 new mode 100755 diff --git a/R/ab_property.R b/R/ab_property.R old mode 100644 new mode 100755 diff --git a/R/ab_selectors.R b/R/ab_selectors.R old mode 100644 new mode 100755 diff --git a/R/amr.R b/R/amr.R old mode 100644 new mode 100755 diff --git a/R/atc_online.R b/R/atc_online.R old mode 100644 new mode 100755 diff --git a/R/av_from_text.R b/R/av_from_text.R old mode 100644 new mode 100755 diff --git a/R/av_property.R b/R/av_property.R old mode 100644 new mode 100755 diff --git a/R/availability.R b/R/availability.R old mode 100644 new mode 100755 diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R old mode 100644 new mode 100755 diff --git a/R/custom_antimicrobials.R b/R/custom_antimicrobials.R old mode 100644 new mode 100755 diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R old mode 100644 new mode 100755 diff --git a/R/custom_microorganisms.R b/R/custom_microorganisms.R old mode 100644 new mode 100755 index 3323c7b1..281014d0 --- a/R/custom_microorganisms.R +++ b/R/custom_microorganisms.R @@ -37,11 +37,11 @@ #' #' There are two ways to automate this process: #' -#' **Method 1:** Save the microorganisms to a local or remote file (can even be the internet). To use this method: +#' **Method 1:** Using the [option `AMR_custom_mo`][AMR-options], which is the preferred method. To use this method: #' #' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location. #' -#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file: +#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file: #' #' ```r #' # Add custom microorganism codes: @@ -50,7 +50,7 @@ #' #' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function. #' -#' **Method 2:** Save the microorganism directly to your `.Rprofile` file. An important downside is that this requires to load the `AMR` package at every start-up. To use this method: +#' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method: #' #' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`. #' @@ -58,8 +58,7 @@ #' #' ```r #' # Add custom antibiotic drug codes: -#' library(AMR) -#' add_custom_microorganisms( +#' AMR::add_custom_microorganisms( #' data.frame(genus = "Enterobacter", #' species = "asburiae/cloacae") #' ) @@ -71,7 +70,6 @@ #' @export #' @examples #' \donttest{ -#' #' # a combination of species is not formal taxonomy, so #' # this will result in only "Enterobacter asburiae": #' mo_name("Enterobacter asburiae/cloacae") @@ -102,13 +100,15 @@ #' #' # the function tries to be forgiving: #' add_custom_microorganisms( -#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE", +#' data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE", #' SPECIES = "SPECIES") #' ) -#' mo_name("ESCHERICHIA / KLEBSIELLA") -#' mo_rank("ESCHERICHIA / KLEBSIELLA") +#' mo_name("BACTEROIDES / PARABACTEROIDES") +#' mo_rank("BACTEROIDES / PARABACTEROIDES") +#' #' # taxonomy still works, although a slashline genus was given as input: -#' mo_family("Escherichia/Klebsiella") +#' mo_family("Bacteroides/Parabacteroides") +#' #' #' # for groups and complexes, set them as species or subspecies: #' add_custom_microorganisms( @@ -208,8 +208,10 @@ add_custom_microorganisms <- function(x) { x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)] # fill in other columns that are used in internal algorithms + x$prevalence <- NA_real_ + x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)] + x$prevalence[is.na(x$prevalence)] <- 1.25 x$status <- "accepted" - x$prevalence <- 1 x$ref <- paste("Self-added,", format(Sys.Date(), "%Y")) x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)] # complete missing kingdom index, so mo_matching_score() will not return NA diff --git a/R/disk.R b/R/disk.R old mode 100644 new mode 100755 diff --git a/R/episode.R b/R/episode.R old mode 100644 new mode 100755 diff --git a/R/italicise_taxonomy.R b/R/italicise_taxonomy.R old mode 100644 new mode 100755 diff --git a/R/mean_amr_distance.R b/R/mean_amr_distance.R old mode 100644 new mode 100755 diff --git a/R/mo_property.R b/R/mo_property.R index e79f413e..3d5572d6 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -777,7 +777,7 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A info <- lapply(x, function(y) { c( - list(identifier = x), + list(mo = as.character(x)), mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms), list( status = mo_status(y, language = language, keep_synonyms = keep_synonyms), @@ -894,6 +894,8 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, .. return(set_clean_class(x, new_class = c("mo", "character"))) } else if (property == "snomed") { return(sort(as.character(eval(parse(text = x))))) + } else if (property == "prevalence") { + return(as.double(x)) } else { # everything else as character return(as.character(x)) diff --git a/R/mo_source.R b/R/mo_source.R old mode 100644 new mode 100755 diff --git a/R/options.R b/R/options.R new file mode 100755 index 00000000..c73e05f3 --- /dev/null +++ b/R/options.R @@ -0,0 +1,39 @@ +# ==================================================================== # +# TITLE # +# AMR: An R Package for Working with Antimicrobial Resistance Data # +# # +# SOURCE # +# https://github.com/msberends/AMR # +# # +# CITE AS # +# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # +# (2022). AMR: An R Package for Working with Antimicrobial Resistance # +# Data. Journal of Statistical Software, 104(3), 1-31. # +# doi:10.18637/jss.v104.i03 # +# # +# Developed at the University of Groningen and the University Medical # +# Center Groningen in The Netherlands, in collaboration with many # +# colleagues from around the world, see our website. # +# # +# 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. # +# We created this package for both routine data analysis and academic # +# research and it was publicly released in the hope that it will be # +# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # +# # +# Visit our website for the full manual and a complete tutorial about # +# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # +# ==================================================================== # + +#' Options for the AMR package +#' +#' This is an overview of the package-specific [options()] you can set in the `AMR` package. +#' @section Options: +#' * `AMR_custom_ab`: allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()]. +#' * `AMR_custom_mo`: allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()]. +#' @keywords internal +#' @name AMR-options +# @export +NULL diff --git a/R/plot.R b/R/plot.R old mode 100644 new mode 100755 diff --git a/R/random.R b/R/random.R old mode 100644 new mode 100755 diff --git a/R/rsi_df.R b/R/rsi_df.R old mode 100644 new mode 100755 diff --git a/R/sysdata.rda b/R/sysdata.rda old mode 100644 new mode 100755 diff --git a/R/vctrs.R b/R/vctrs.R old mode 100644 new mode 100755 diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd old mode 100644 new mode 100755 diff --git a/man/AMR-options.Rd b/man/AMR-options.Rd new file mode 100644 index 00000000..eefba262 --- /dev/null +++ b/man/AMR-options.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/options.R +\name{AMR-options} +\alias{AMR-options} +\title{Options for the AMR package} +\description{ +This is an overview of the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package. +} +\section{Options}{ + +\itemize{ +\item \code{AMR_custom_ab}: allows to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}. +\item \code{AMR_custom_mo}: allows to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}. +} +} + +\keyword{internal} diff --git a/man/AMR.Rd b/man/AMR.Rd old mode 100644 new mode 100755 diff --git a/man/WHOCC.Rd b/man/WHOCC.Rd old mode 100644 new mode 100755 diff --git a/man/WHONET.Rd b/man/WHONET.Rd old mode 100644 new mode 100755 diff --git a/man/ab_from_text.Rd b/man/ab_from_text.Rd old mode 100644 new mode 100755 diff --git a/man/ab_property.Rd b/man/ab_property.Rd old mode 100644 new mode 100755 diff --git a/man/add_custom_antimicrobials.Rd b/man/add_custom_antimicrobials.Rd old mode 100644 new mode 100755 diff --git a/man/add_custom_microorganisms.Rd b/man/add_custom_microorganisms.Rd old mode 100644 new mode 100755 index 6f5eccc4..e0db9432 --- a/man/add_custom_microorganisms.Rd +++ b/man/add_custom_microorganisms.Rd @@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum There are two ways to automate this process: -\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method: +\strong{Method 1:} Using the , which is the preferred method. To use this method: \enumerate{ \item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location. -\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file: +\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file: \if{html}{\out{
}}\preformatted{# Add custom microorganism codes: options(AMR_custom_mo = "~/my_custom_mo.rds") @@ -34,14 +34,13 @@ options(AMR_custom_mo = "~/my_custom_mo.rds") Upon package load, this file will be loaded and run through the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function. } -\strong{Method 2:} Save the microorganism directly to your \code{.Rprofile} file. An important downside is that this requires to load the \code{AMR} package at every start-up. To use this method: +\strong{Method 2:} Loading the microorganism directly from your \code{.Rprofile} file. An important downside is that this requires the \code{AMR} package to be installed or else this method will fail. To use this method: \enumerate{ \item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}. \item Add a text like below and save the file: \if{html}{\out{
}}\preformatted{ # Add custom antibiotic drug codes: - library(AMR) - add_custom_microorganisms( + AMR::add_custom_microorganisms( data.frame(genus = "Enterobacter", species = "asburiae/cloacae") ) @@ -52,7 +51,6 @@ Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to } \examples{ \donttest{ - # a combination of species is not formal taxonomy, so # this will result in only "Enterobacter asburiae": mo_name("Enterobacter asburiae/cloacae") @@ -83,13 +81,15 @@ mo_info("Enterobacter asburiae/cloacae") # the function tries to be forgiving: add_custom_microorganisms( - data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE", + data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE", SPECIES = "SPECIES") ) -mo_name("ESCHERICHIA / KLEBSIELLA") -mo_rank("ESCHERICHIA / KLEBSIELLA") +mo_name("BACTEROIDES / PARABACTEROIDES") +mo_rank("BACTEROIDES / PARABACTEROIDES") + # taxonomy still works, although a slashline genus was given as input: -mo_family("Escherichia/Klebsiella") +mo_family("Bacteroides/Parabacteroides") + # for groups and complexes, set them as species or subspecies: add_custom_microorganisms( diff --git a/man/age.Rd b/man/age.Rd old mode 100644 new mode 100755 diff --git a/man/age_groups.Rd b/man/age_groups.Rd old mode 100644 new mode 100755 diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd old mode 100644 new mode 100755 diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd old mode 100644 new mode 100755 diff --git a/man/as.ab.Rd b/man/as.ab.Rd old mode 100644 new mode 100755 diff --git a/man/as.av.Rd b/man/as.av.Rd old mode 100644 new mode 100755 diff --git a/man/as.disk.Rd b/man/as.disk.Rd old mode 100644 new mode 100755 diff --git a/man/as.mo.Rd b/man/as.mo.Rd old mode 100644 new mode 100755 diff --git a/man/atc_online.Rd b/man/atc_online.Rd old mode 100644 new mode 100755 diff --git a/man/av_from_text.Rd b/man/av_from_text.Rd old mode 100644 new mode 100755 diff --git a/man/av_property.Rd b/man/av_property.Rd old mode 100644 new mode 100755 diff --git a/man/availability.Rd b/man/availability.Rd old mode 100644 new mode 100755 diff --git a/man/bug_drug_combinations.Rd b/man/bug_drug_combinations.Rd old mode 100644 new mode 100755 diff --git a/man/count.Rd b/man/count.Rd old mode 100644 new mode 100755 diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd old mode 100644 new mode 100755 diff --git a/man/dosage.Rd b/man/dosage.Rd old mode 100644 new mode 100755 diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd old mode 100644 new mode 100755 diff --git a/man/example_isolates.Rd b/man/example_isolates.Rd old mode 100644 new mode 100755 diff --git a/man/example_isolates_unclean.Rd b/man/example_isolates_unclean.Rd old mode 100644 new mode 100755 diff --git a/man/g.test.Rd b/man/g.test.Rd old mode 100644 new mode 100755 diff --git a/man/get_episode.Rd b/man/get_episode.Rd old mode 100644 new mode 100755 diff --git a/man/ggplot_pca.Rd b/man/ggplot_pca.Rd old mode 100644 new mode 100755 diff --git a/man/ggplot_rsi.Rd b/man/ggplot_rsi.Rd old mode 100644 new mode 100755 diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd old mode 100644 new mode 100755 diff --git a/man/intrinsic_resistant.Rd b/man/intrinsic_resistant.Rd old mode 100644 new mode 100755 diff --git a/man/italicise_taxonomy.Rd b/man/italicise_taxonomy.Rd old mode 100644 new mode 100755 diff --git a/man/key_antimicrobials.Rd b/man/key_antimicrobials.Rd old mode 100644 new mode 100755 diff --git a/man/kurtosis.Rd b/man/kurtosis.Rd old mode 100644 new mode 100755 diff --git a/man/mdro.Rd b/man/mdro.Rd old mode 100644 new mode 100755 diff --git a/man/mean_amr_distance.Rd b/man/mean_amr_distance.Rd old mode 100644 new mode 100755 diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd old mode 100644 new mode 100755 diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd old mode 100644 new mode 100755 diff --git a/man/mo_property.Rd b/man/mo_property.Rd old mode 100644 new mode 100755 diff --git a/man/mo_source.Rd b/man/mo_source.Rd old mode 100644 new mode 100755 diff --git a/man/pca.Rd b/man/pca.Rd old mode 100644 new mode 100755 diff --git a/man/plot.Rd b/man/plot.Rd old mode 100644 new mode 100755 diff --git a/man/proportion.Rd b/man/proportion.Rd old mode 100644 new mode 100755 diff --git a/man/random.Rd b/man/random.Rd old mode 100644 new mode 100755 diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd old mode 100644 new mode 100755 diff --git a/man/rsi_translation.Rd b/man/rsi_translation.Rd old mode 100644 new mode 100755 diff --git a/man/skewness.Rd b/man/skewness.Rd old mode 100644 new mode 100755 diff --git a/man/translate.Rd b/man/translate.Rd old mode 100644 new mode 100755