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(v0.9.0.9008) Happy new year! Add lifecycles

new-mo-algorithm
parent
commit
ced1a7b7fa
  1. 8
      .gitlab-ci.R
  2. 8
      .gitlab-ci.yml
  3. 4
      DESCRIPTION
  4. 5
      NEWS.md
  5. 9
      R/ab.R
  6. 9
      R/ab_property.R
  7. 10
      R/age.R
  8. 8
      R/amr.R
  9. 9
      R/atc_online.R
  10. 11
      R/availability.R
  11. 9
      R/bug_drug_combinations.R
  12. 8
      R/catalogue_of_life.R
  13. 9
      R/count.R
  14. 8
      R/data.R
  15. 9
      R/deprecated.R
  16. 9
      R/disk.R
  17. 9
      R/eucast_rules.R
  18. 9
      R/extended.R
  19. 9
      R/filter_ab_class.R
  20. 8
      R/first_isolate.R
  21. 8
      R/freq.R
  22. 9
      R/g.test.R
  23. 9
      R/ggplot_rsi.R
  24. 8
      R/globals.R
  25. 9
      R/guess_ab_col.R
  26. 9
      R/join_microorganisms.R
  27. 9
      R/key_antibiotics.R
  28. 9
      R/kurtosis.R
  29. 56
      R/lifecycle.R
  30. 11
      R/like.R
  31. 9
      R/mdro.R
  32. 9
      R/mic.R
  33. 8
      R/misc.R
  34. 9
      R/mo.R
  35. 9
      R/mo_history.R
  36. 8
      R/mo_property.R
  37. 9
      R/mo_source.R
  38. 9
      R/p_symbol.R
  39. 9
      R/proportion.R
  40. 9
      R/read.4d.R
  41. 9
      R/resistance_predict.R
  42. 9
      R/rsi.R
  43. 8
      R/rsi_calc.R
  44. 8
      R/rsi_df.R
  45. 9
      R/skewness.R
  46. 9
      R/translate.R
  47. 8
      R/whocc.R
  48. 8
      R/zzz.R
  49. 8
      _pkgdown.yml
  50. 8
      appveyor.yml
  51. 21
      codecov.yml
  52. 164
      data-raw/country_analysis.R
  53. 24
      data-raw/internals.R
  54. 8
      data-raw/reproduction_of_antibiotics.R
  55. 8
      data-raw/reproduction_of_antivirals.R
  56. 21
      data-raw/reproduction_of_microorganisms.R
  57. 21
      data-raw/reproduction_of_microorganisms_new.R
  58. 2
      docs/404.html
  59. 2
      docs/LICENSE-text.html
  60. 2
      docs/articles/index.html
  61. 7
      docs/authors.html
  62. BIN
      docs/countries.png
  63. BIN
      docs/countries_large.png
  64. 8
      docs/extra.css
  65. 8
      docs/extra.js
  66. 10
      docs/index.html
  67. 1
      docs/lifecycle_archived.svg
  68. 1
      docs/lifecycle_dormant.svg
  69. 1
      docs/lifecycle_experimental.svg
  70. 1
      docs/lifecycle_maturing.svg
  71. 1
      docs/lifecycle_questioning.svg
  72. 1
      docs/lifecycle_retired.svg
  73. 1
      docs/lifecycle_stable.svg
  74. 88
      docs/lifecycle_tidyverse.svg
  75. 14
      docs/news/index.html
  76. 11
      docs/reference/AMR-deprecated.html
  77. 11
      docs/reference/ab_property.html
  78. 12
      docs/reference/age.html
  79. 12
      docs/reference/age_groups.html
  80. 11
      docs/reference/as.ab.html
  81. 10
      docs/reference/as.disk.html
  82. 12
      docs/reference/as.mic.html
  83. 12
      docs/reference/as.mo.html
  84. 12
      docs/reference/as.rsi.html
  85. 11
      docs/reference/atc_online.html
  86. 16
      docs/reference/availability.html
  87. 12
      docs/reference/bug_drug_combinations.html
  88. 12
      docs/reference/count.html
  89. 11
      docs/reference/eucast_rules.html
  90. 12
      docs/reference/extended-functions.html
  91. 1
      docs/reference/figures/lifecycle_archived.svg
  92. 1
      docs/reference/figures/lifecycle_dormant.svg
  93. 1
      docs/reference/figures/lifecycle_experimental.svg
  94. 1
      docs/reference/figures/lifecycle_maturing.svg
  95. 1
      docs/reference/figures/lifecycle_questioning.svg
  96. 1
      docs/reference/figures/lifecycle_retired.svg
  97. 1
      docs/reference/figures/lifecycle_stable.svg
  98. 88
      docs/reference/figures/lifecycle_tidyverse.svg
  99. 12
      docs/reference/filter_ab_class.html
  100. 11
      docs/reference/g.test.html
  101. Some files were not shown because too many files have changed in this diff Show More

8
.gitlab-ci.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

8
.gitlab-ci.yml

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 0.9.0.9007
Date: 2019-12-27
Version: 0.9.0.9008
Date: 2020-01-05
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

5
NEWS.md

@ -1,9 +1,10 @@ @@ -1,9 +1,10 @@
# AMR 0.9.0.9007
## <small>Last updated: 27-Dec-2019</small>
# AMR 0.9.0.9008
## <small>Last updated: 05-Jan-2020</small>
### Changes
* Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
* Input values for `as.disk()` limited to a maximum of 50 millimeters
* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle)
### Other
* Add a `CITATION` file

9
R/ab.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Transform to antibiotic ID
#'
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @inheritSection lifecycle Maturing lifecycle
#' @param x character vector to determine to antibiotic ID
#' @param ... arguments passed on to internal functions
#' @rdname as.ab

9
R/ab_property.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Property of an antibiotic
#'
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
#' @inheritSection lifecycle Maturing lifecycle
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.ab()]
#' @param tolower logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
#' @param property one of the column names of one of the [antibiotics] data set

10
R/age.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Age in years of individuals
#'
#' Calculates age in years based on a reference date, which is the sytem date at default.
#' @inheritSection lifecycle Stable lifecycle
#' @param x date(s), will be coerced with [as.POSIXlt()]
#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()] and cannot be lower than `x`
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
@ -91,6 +92,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) { @@ -91,6 +92,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
#' Split ages into age groups
#'
#' Split ages into age groups defined by the `split` parameter. This allows for easier demographic (antimicrobial resistance) analysis.
#' @inheritSection lifecycle Stable lifecycle
#' @param x age, e.g. calculated with [age()]
#' @param split_at values to split `x` at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.
#' @param na.rm a logical to indicate whether missing values should be removed

8
R/amr.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/atc_online.R

@ -6,21 +6,22 @@ @@ -6,21 +6,22 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Get ATC properties from WHOCC website
#'
#' @inheritSection lifecycle Questioning lifecycle
#' @description Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
#'
#' **This function requires an internet connection.**

11
R/availability.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Check availability of columns
#'
#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. [resistance()].
#' Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. [susceptibility()] and [resistance()].
#' @inheritSection lifecycle Stable lifecycle
#' @param tbl a [`data.frame`] or [`list`]
#' @param width number of characters to present the visual availability, defaults to filling the width of the console
#' @details The function returns a [`data.frame`] with columns `"resistant"` and `"visual_resistance"`. The values in that columns are calculated with [resistance()].

9
R/bug_drug_combinations.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Determine bug-drug combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see Examples.
#' @inheritSection lifecycle Stable lifecycle
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column

8
R/catalogue_of_life.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/count.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
@ -24,6 +24,7 @@ @@ -24,6 +24,7 @@
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in [summarise()] and support grouped variables, see *Examples*.
#'
#' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
#' @inheritSection lifecycle Stable lifecycle
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed.
#' @inheritParams proportion
#' @inheritSection as.rsi Interpretation of R and S/I

8
R/data.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/deprecated.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Deprecated functions
#'
#' These functions are so-called '[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 (if there is one).
#' @inheritSection lifecycle Retired lifecycle
#' @inheritSection AMR Read more on our website!
#' @export
#' @keywords internal

9
R/disk.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Class 'disk'
#'
#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname as.disk
#' @param x vector
#' @param na.rm a logical indicating whether missing values should be removed

9
R/eucast_rules.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
@ -29,6 +29,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" @@ -29,6 +29,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
#'
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
#' @inheritSection lifecycle Maturing lifecycle
#' @param x data with antibiotic columns, like e.g. `AMX` and `AMC`
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of `c("breakpoints", "expert", "other", "all")`

9
R/extended.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Extended functions
#'
#' These functions are extensions of functions in other packages.
#' @inheritSection lifecycle Stable lifecycle
#' @inheritSection AMR Read more on our website!
#' @export
#' @keywords internal

9
R/filter_ab_class.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Filter isolates on result in antibiotic class
#'
#' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a data set
#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`AMR::antibiotics$group`][antibiotics]
#' @param result an antibiotic result: S, I or R (or a combination of more of them)

8
R/first_isolate.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

8
R/freq.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/g.test.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' *G*-test for Count Data
#'
#' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable (1). A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**).
#' @inheritSection lifecycle Questioning lifecycle
#' @inherit stats::chisq.test params return
#' @details If `x` is a matrix with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given.
#'

9
R/ggplot_rsi.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' AMR plots with `ggplot2`
#'
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal [ggplot2][ggplot2::ggplot()] functions.
#' @inheritSection lifecycle Maturing lifecycle
#' @param data a [`data.frame`] with column(s) of class [`rsi`] (see [as.rsi()])
#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
#' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable

8
R/globals.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/guess_ab_col.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Guess antibiotic column
#'
#' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
#' @inheritSection lifecycle Maturing lifecycle
#' @param x a [`data.frame`]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed

9
R/join_microorganisms.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Join a table with [microorganisms]
#'
#' Join the data set [microorganisms] easily to an existing table or character vector.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname join
#' @name join
#' @aliases join inner_join

9
R/key_antibiotics.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Key antibiotics for first *weighted* isolates
#'
#' These function can be used to determine first isolates (see [first_isolate()]). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first *weighted* isolates.
#' @inheritSection lifecycle Stable lifecycle
#' @param x table with antibiotics coloms, like `AMX` or `amox`
#' @param y,z characters to compare
#' @inheritParams first_isolate

9
R/kurtosis.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Kurtosis of the sample
#'
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
#' @inheritSection lifecycle Questioning lifecycle
#' @param x a vector of values, a [`matrix`] or a [`data.frame`]
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
#' @exportMethod kurtosis

56
R/lifecycle.R

@ -0,0 +1,56 @@ @@ -0,0 +1,56 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
###############
# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add another dependency for such an easy job?
###############
#' Lifecycles of functions in the `AMR` package
#' @name lifecycle
#' @rdname lifecycle
#' @description Our functions are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
#'
#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of our functions.
#' @section Experimental lifecycle:
#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN.
#' @section Maturing lifecycle:
#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
#' @section Stable lifecycle:
#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
#'
#' If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
#' @section Retired lifecycle:
#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
#' @section Archived lifecycle:
#' \if{html}{\figure{lifecycle_archived.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **archived**. The development of an archived function has ended, and it is no longer available in future package versions.
#' @section Dormant lifecycle:
#' \if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **dormant**. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
#' @section Questioning lifecycle:
#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our `AMR` package at all.
NULL

11
R/like.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Pattern Matching
#'
#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) to compare items of each index in both vectors, or can both have the same length to iterate over all cases.
#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
#' @param pattern a character string containing a regular expression (or [`character`] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible. If a [`character`] vector of length 2 or more is supplied, the first element is used with a warning.
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.

9
R/mdro.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
#' @inheritSection lifecycle Maturing lifecycle
#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
#' @param info a logical to indicate whether progress should be printed to the console
#' @inheritParams eucast_rules

9
R/mic.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Class 'mic'
#'
#' This transforms a vector to a new class [`mic`], which is an ordered [`factor`] with valid MIC values as levels. Invalid MIC values will be translated as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname as.mic
#' @param x vector
#' @param na.rm a logical indicating whether missing values should be removed

8
R/misc.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/mo.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Transform to microorganism ID
#'
#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (like `"S. aureus"`), an abbreviation known in the field (like `"MRSA"`), or just a genus. Please see *Examples*.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a character vector or a [`data.frame`] with one or two columns
#' @param Becker a logical to indicate whether *Staphylococci* should be categorised into coagulase-negative *Staphylococci* ("CoNS") and coagulase-positive *Staphylococci* ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2). Note that this does not include species that were newly named after these publications, like *S. caeli*.
#'

9
R/mo_history.R

@ -6,20 +6,21 @@ @@ -6,20 +6,21 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# print successful as.mo coercions to a options entry
#' @inheritSection lifecycle Stable lifecycle
#' @importFrom dplyr %>% distinct filter
#' @importFrom utils write.csv
set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {

8
R/mo_property.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/mo_source.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
@ -24,6 +24,7 @@ @@ -24,6 +24,7 @@
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
#'
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
#' @inheritSection lifecycle Stable lifecycle
#' @param path location of your reference file, see Details
#' @rdname mo_source
#' @name mo_source

9
R/p_symbol.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Symbol of a p-value
#'
#' Return the symbol related to the p-value: 0 '`***`' 0.001 '`**`' 0.01 '`*`' 0.05 '`.`' 0.1 ' ' 1. Values above `p = 1` will return `NA`.
#' @inheritSection lifecycle Questioning lifecycle
#' @param p p value
#' @param emptychar text to show when `p > 0.1`
#' @return Text

9
R/proportion.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
@ -24,6 +24,7 @@ @@ -24,6 +24,7 @@
#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in [dplyr::summarise()] and support grouped variables, please see *Examples*.
#'
#' [resistance()] should be used to calculate resistance, [susceptibility()] should be used to calculate susceptibility.\cr
#' @inheritSection lifecycle Stable lifecycle
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of `0.123456` will then be returned as `"12.3%"`.

9
R/read.4d.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#
#' Read data from 4D database
#'
#' This function is only useful for the MMB department of the UMCG. Use this function to **import data by just defining the `file` parameter**. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with [as.mo()] and transform all antimicrobial columns with [as.rsi()].
#' @inheritSection lifecycle Dormant lifecycle
#' @inheritParams utils::read.table
#' @param info a logical to indicate whether info about the import should be printed, defaults to `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.

9
R/resistance_predict.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Predict antimicrobial resistance
#'
#' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#' @inheritSection lifecycle Maturing lifecycle
#' @param col_ab column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`)
#' @param col_date column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class
#' @param year_min lowest year to use in the prediction model, dafaults to the lowest year in `col_date`

9
R/rsi.R

@ -6,22 +6,23 @@ @@ -6,22 +6,23 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Class 'rsi'
#'
#' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimeters)
#' @param mo a microorganism code, generated with [as.mo()]

8
R/rsi_calc.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

8
R/rsi_df.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #

9
R/skewness.R

@ -6,16 +6,16 @@ @@ -6,16 +6,16 @@
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #