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(v2.1.1.9236) documentation

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dr. M.S. (Matthijs) Berends
2025-04-12 11:46:42 +02:00
parent 36fd99e1f4
commit 40d7a971c3
141 changed files with 181 additions and 172 deletions
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2
R/aa_amr-package.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' The `AMR` Package

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R/aa_globals.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints

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R/aa_helper_functions.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# faster implementation of left_join than using merge() by poorman - we use match():

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R/aa_helper_pm_functions.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# ------------------------------------------------

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R/aa_options.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Options for the AMR package

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R/ab.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to an Antibiotic ID

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R/ab_from_text.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Retrieve Antimicrobial Drug Names and Doses from Clinical Text

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R/ab_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of an Antibiotic

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R/age.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Age in Years of Individuals

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R/amr_selectors.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Antimicrobial Selectors

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R/antibiogram.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Generate Traditional, Combination, Syndromic, or WISCA Antibiograms

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R/atc_online.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get ATC Properties from WHOCC Website

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R/av.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to an Antiviral Drug ID

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R/av_from_text.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Retrieve Antiviral Drug Names and Doses from Clinical Text

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R/av_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of an Antiviral Drug

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R/availability.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Check Availability of Columns

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R/bug_drug_combinations.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Bug-Drug Combinations

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R/count.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Count Available Isolates

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R/custom_antimicrobials.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Add Custom Antimicrobials

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R/custom_eucast_rules.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Define Custom EUCAST Rules

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R/custom_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Add Custom Microorganisms

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R/data.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs

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R/disk.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to Disk Diffusion Diameters

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R/eucast_rules.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# ====================================================== #
@ -219,7 +219,7 @@ eucast_rules <- function(x,
if (interactive() && isTRUE(verbose) && isTRUE(info)) {
txt <- paste0(
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.",
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?"
)

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R/export_biosample.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Export Data Set as NCBI BioSample Antibiogram

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R/first_isolate.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine First Isolates

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R/g.test.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' *G*-test for Count Data

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R/get_episode.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Clinical or Epidemic Episodes

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R/ggplot_pca.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' PCA Biplot with `ggplot2`

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R/ggplot_sir.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' AMR Plots with `ggplot2`

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R/guess_ab_col.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Guess Antibiotic Column

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R/italicise_taxonomy.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Italicise Taxonomic Families, Genera, Species, Subspecies

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R/join_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Join [microorganisms] to a Data Set

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R/key_antimicrobials.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' (Key) Antimicrobials for First Weighted Isolates

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R/kurtosis.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Kurtosis of the Sample

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R/like.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Vectorised Pattern Matching with Keyboard Shortcut

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R/mdro.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Multidrug-Resistant Organisms (MDRO)

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R/mean_amr_distance.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate the Mean AMR Distance

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R/mic.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# these are allowed MIC values and will become factor levels

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R/mo.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Arbitrary Input to Valid Microbial Taxonomy

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R/mo_matching_score.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate the Matching Score for Microorganisms

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R/mo_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of a Microorganism

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R/mo_source.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' User-Defined Reference Data Set for Microorganisms

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R/pca.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Principal Component Analysis (for AMR)

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R/plotting.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Plotting Helpers for AMR Data Analysis

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R/proportion.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate Antimicrobial Resistance

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R/random.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Random MIC Values/Disk Zones/SIR Generation

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R/resistance_predict.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Predict Antimicrobial Resistance

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R/sir.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data

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R/sir_calc.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
dots2vars <- function(...) {
@ -217,7 +217,7 @@ sir_calc <- function(...,
}
if (as_percent == TRUE) {
percentage(fraction, digits = 1)
trimws(percentage(fraction, digits = 1))
} else {
fraction
}

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R/sir_df.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' @rdname proportion

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R/skewness.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Skewness of the Sample

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R/top_n_microorganisms.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Filter Top *n* Microorganisms

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R/translate.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Translate Strings from the AMR Package

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R/vctrs.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# These are all S3 implementations for the vctrs package,

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R/whocc.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

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R/zz_deprecated.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Deprecated Functions

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R/zzz.R
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@ -24,7 +24,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# set up package environment, used by numerous AMR functions