So only 61.2% is suitable for resistance analysis! We can now filter +
So only 61.5% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
filter()
dplyr
@@ -644,11 +644,11 @@ on it with the data_1st <- data %>% filter_first_isolate()
data_1st <- data %>% filter_first_isolate()
So we end up with 12 241 isolates for analysis. Now our data looks +
So we end up with 12 299 isolates for analysis. Now our data looks like:
head(data_1st)
data_1st %>% freq(genus, species)
Frequency table
Class: character -Length: 12,241 -Available: 12,241 (100%, NA: 0 = 0%) +Length: 12,299 +Available: 12,299 (100%, NA: 0 = 0%) Unique: 4
Shortest: 16 Longest: 24
proportion_SI()
data_1st %>% resistance(AMX) -# [1] 0.5836941
Or can be used in conjunction with group_by() and summarise(), both from the dplyr package:
group_by()
summarise()
@@ -1169,19 +1169,19 @@ own: Hospital A -0.5864297 +0.5791485 Hospital B -0.5778776 +0.5819352 Hospital C -0.5783004 +0.6098081 Hospital D -0.5938144 +0.5905316 @@ -1206,23 +1206,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital A -0.5864297 -3714 +0.5791485 +3664 Hospital B -0.5778776 -4231 +0.5819352 +4351 Hospital C -0.5783004 -1871 +0.6098081 +1876 Hospital D -0.5938144 -2425 +0.5905316 +2408 @@ -1247,27 +1247,27 @@ therapies very easily: Escherichia -0.6667810 -0.6520322 -0.8814955 +0.6709314 +0.6560901 +0.8901399 Klebsiella -0.6349085 -0.6692073 -0.8833841 +0.6475410 +0.6542474 +0.8792846 Staphylococcus -0.6599815 -0.6497994 -0.8707189 +0.6601671 +0.6576911 +0.8895079 Streptococcus -0.4787291 +0.4812232 0.0000000 -0.4787291 +0.4812232 @@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as Hospital A -58.6% -36.7% +57.9% +35.8% Hospital B -57.8% -36.4% +58.2% +36.2% Hospital C -57.8% -37.7% +61.0% +36.7% Hospital D -59.4% -36.5% +59.1% +36.9% @@ -1427,18 +1427,18 @@ classes) <mic> and <disk>: mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 0.01 >=256 <=0.001 8 0.005 0.005 0.01 1 4 -# [10] >=256 0.0625 4 16 0.01 32 0.01 >=256 32 -# [19] 4 0.0625 0.005 64 128 8 <=0.001 0.25 0.005 -# [28] 0.0625 <=0.001 0.125 0.0625 0.025 0.01 2 32 4 -# [37] 4 128 0.002 <=0.001 0.025 >=256 0.125 0.5 2 -# [46] 0.025 0.005 >=256 16 0.5 2 0.25 0.25 0.25 -# [55] 64 8 <=0.001 8 4 0.0625 <=0.001 0.0625 1 -# [64] 0.0625 0.01 1 0.002 16 <=0.001 0.125 0.005 0.0625 -# [73] 16 0.125 128 0.005 16 64 8 16 <=0.001 -# [82] 16 4 2 0.002 64 8 64 0.5 0.025 -# [91] 1 0.025 1 32 0.002 16 0.125 0.125 16 -# [100] 0.01
<mic>
<disk>
mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 0.01 >=256 <=0.001 8 0.005 0.005 0.01 1 4 -# [10] >=256 0.0625 4 16 0.01 32 0.01 >=256 32 -# [19] 4 0.0625 0.005 64 128 8 <=0.001 0.25 0.005 -# [28] 0.0625 <=0.001 0.125 0.0625 0.025 0.01 2 32 4 -# [37] 4 128 0.002 <=0.001 0.025 >=256 0.125 0.5 2 -# [46] 0.025 0.005 >=256 16 0.5 2 0.25 0.25 0.25 -# [55] 64 8 <=0.001 8 4 0.0625 <=0.001 0.0625 1 -# [64] 0.0625 0.01 1 0.002 16 <=0.001 0.125 0.005 0.0625 -# [73] 16 0.125 128 0.005 16 64 8 16 <=0.001 -# [82] 16 4 2 0.002 64 8 64 0.5 0.025 -# [91] 1 0.025 1 32 0.002 16 0.125 0.125 16 -# [100] 0.01
# base R: plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro") disk_values # Class 'disk' -# [1] 20 19 27 26 31 31 29 20 28 29 17 25 20 20 26 30 21 26 28 26 29 28 25 17 19 -# [26] 18 25 25 24 21 21 17 25 17 31 18 21 18 21 30 18 29 20 27 29 29 19 25 21 22 -# [51] 30 25 30 21 22 23 25 22 27 19 17 30 28 25 17 19 21 26 18 22 31 27 21 26 20 -# [76] 21 30 24 26 17 31 23 23 23 19 25 31 17 21 23 24 22 29 23 24 21 22 27 27 23
# base R: plot(disk_values, mo = "E. coli", ab = "cipro")
head(my_TB_data) # rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -# 1 S I S R I S -# 2 S R I I R I -# 3 S S S S R R -# 4 S R S I I R -# 5 S I R S R I -# 6 S R I R R S +# 1 I R S S R I +# 2 S S I S S I +# 3 R S S S I R +# 4 S I R I S R +# 5 R I S S S S +# 6 R R R S R I # kanamycin -# 1 I +# 1 R # 2 S # 3 S -# 4 R -# 5 I -# 6 S
We can now add the interpretation of MDR-TB to our data set. You can use:
@@ -438,40 +438,40 @@ Unique: 5 1 Mono-resistant -3144 -62.88% -3144 -62.88% +3179 +63.58% +3179 +63.58% 2 Negative -1032 -20.64% -4176 -83.52% +1012 +20.24% +4191 +83.82% 3 Multi-drug-resistant -465 -9.30% -4641 -92.82% +455 +9.10% +4646 +92.92% 4 Poly-resistant -263 -5.26% -4904 -98.08% +247 +4.94% +4893 +97.86% 5 Extensively drug-resistant -96 -1.92% +107 +2.14% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index 52262515..176daaa8 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -290,7 +290,7 @@ function: # [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" # Importance of components: # PC1 PC2 PC3 PC4 PC5 PC6 PC7 -# Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 +# Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 # Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 # Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
# Groups (n=4, named as 'order'): diff --git a/articles/SPSS.html b/articles/SPSS.html index 3cd7089a..6e5157a4 100644 --- a/articles/SPSS.html +++ b/articles/SPSS.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed R has a huge community. Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 480 015 +online community for programmers. At the time of writing, 480 788 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 753be116..9330995e 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/datasets.html b/articles/datasets.html index 59a6256f..8a5d9b06 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/index.html b/articles/index.html index e5d4ecd9..a1231a30 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index ce8ddbba..92e726d9 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 03ef291c..021e2603 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/authors.html b/authors.html index 610cf2b0..b9695dae 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/extra.css b/extra.css index 0995fd15..a84fbe85 100644 --- a/extra.css +++ b/extra.css @@ -62,6 +62,7 @@ pre code { /* never wrap code on smaller screens */ word-wrap: normal !important; white-space: pre !important; + font-size: 0.8em !important; } .ot, .dv, .fl, .cn, .at, .op a { diff --git a/index.html b/index.html index b2c92695..04cdfaaf 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/news/index.html b/news/index.html index caf93d3b..945d439a 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -142,7 +142,7 @@ -AMR 1.8.2.9119 +AMR 1.8.2.9120 (this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!) This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below. TL;DR @@ -156,31 +156,32 @@ Now available in 20 languages Many small bug fixes -New +New -SIR vs. RSI +SIR vs. RSI For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR. While existing functions such as as.rsi(), rsi_df() and ggplot_rsi() still work, their replacements as.sir(), sir_df(), ggplot_sir() are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set rsi_translation is now called clinical_breakpoints to better reflect its content. The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024. -New antibiogram function +New antibiogram function With the new antibiogram() function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker et al. (2021, DOI 10.1177/20499361211011373) and Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2). The help page for antibiogram() extensively elaborates on use cases, and antibiogram() also supports printing in R Markdown and Quarto, with support for 20 languages. Furthermore, different plotting methods were implemented to allow for graphical visualisations as well. -Interpretation of MIC and disk diffusion values +Interpretation of MIC and disk diffusion values The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for as.sir(). EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for eucast_rules() to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new AMR_guideline option, such as: options(AMR_guideline = "CLSI 2020"). +With the new arguments include_PKPD (default: TRUE) and include_screening (default: FALSE), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in our new manual. Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013. -Supported languages +Supported languages We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language. We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 20 languages in total, and according to download stats used in almost all countries in the world! -Microbiological taxonomy +Microbiological taxonomy The microorganisms data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022. We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett et al. (2022, DOI 10.1099/mic.0.001269) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See mo_matching_score() on how their work was incorporated into the prevalence column of the microorganisms data set. Using their results, the as.mo() and all mo_*() functions are now much better capable of converting user input to valid taxonomic records. The new function add_custom_microorganisms() allows users to add custom microorganisms to the AMR package. @@ -204,7 +205,7 @@ The microorganisms.old data set was removed, and all previously accepted names are now included in the microorganisms data set. A new column status contains "accepted" for currently accepted names and "synonym" for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier. -Antibiotic agents and selectors +Antibiotic agents and selectors The new function add_custom_antimicrobials() allows users to add custom antimicrobial codes and names to the AMR package. The antibiotics data set was greatly updated: The following 20 antibiotics have been added (also includes the new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT) @@ -216,14 +217,14 @@ Also, we added support for using antibiotic selectors in scoped dplyr verbs (with or without using vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() for examples. -Antiviral agents +Antiviral agents We now added extensive support for antiviral agents! For the first time, the AMR package has extensive support for antiviral drugs and to work with their names, codes and other data in any way. The antivirals data set has been extended with 18 new drugs (also from the new J05AJ ATC group) and now also contains antiviral identifiers and LOINC codes A new data type av (antivirals) has been added, which is functionally similar to ab for antibiotics Functions as.av(), av_name(), av_atc(), av_synonyms(), av_from_text() have all been added as siblings to their ab_*() equivalents -Other new functions +Other new functions Function sir_confidence_interval() to add confidence intervals in AMR calculation. This is now also included in sir_df() and proportion_df(). Function mean_amr_distance() to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. Function sir_interpretation_history() to view the history of previous runs of as.sir() (previously as.rsi()). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which as.sir() was run. @@ -232,7 +233,7 @@ -Changes +Changes Argument combine_IR has been removed from this package (affecting functions count_df(), proportion_df(), and sir_df() and some plotting functions), since it was replaced with combine_SI three years ago Using units in ab_ddd(..., units = "...") had been deprecated for some time and is now not supported anymore. Use ab_ddd_units() instead. Support for data.frame-enhancing R packages, more specifically: data.table::data.table, janitor::tabyl, tibble::tibble, and tsibble::tsibble. AMR package functions that have a data set as output (such as sir_df() and bug_drug_combinations()), will now return the same data type as the input. @@ -270,9 +271,11 @@ Fix for mo_shortname() in case of higher taxonomic ranks (order, class, phylum) Cleaning columns with as.sir(), as.mic(), or as.disk() will now show the column name in the warning for invalid results Fix for using g.test() with zeroes in a 2x2 table + +get_episode() now returns class integer instead of numeric since they are always whole numbers -Other +Other Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions All R and Rmd files in this project are now styled using the styler package diff --git a/pkgdown.yml b/pkgdown.yml index d671b203..b078e48d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2023-02-12T10:25Z +last_built: 2023-02-12T14:14Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 4d222e8a..9bfad609 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 1da517b8..794b8503 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -157,6 +157,7 @@ AMR_guideline Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default is "EUCAST 2022". Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022). AMR_ignore_pattern A regular expression to define input that must be ignored in as.mo() and all mo_* functions. AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to TRUE. +AMR_include_screening A logical to use in as.sir(), to indicate that clinical breakpoints for screening are allowed, defaults to FALSE. AMR_keep_synonyms A logical to use in as.mo() and all mo_* functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. AMR_locale A language to use for the AMR package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). AMR_mo_source A file location for a manual code list to be used in as.mo() and all mo_* functions. This is explained in set_mo_source(). @@ -167,7 +168,10 @@ Settings in R are not saved globally and are thus lost when R is exited. You can save your options to your own .Rprofile file, which is a user-specific file. You can edit it using: utils::file.edit("~/.Rprofile") -In this file, you can set options such as options(AMR_locale = "pt") for Portuguese language support of antibiotics. +In this file, you can set options such as: + options(AMR_locale = "pt") + options(AMR_include_PKPD = TRUE) +to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with as.sir(). Share Options Within Team diff --git a/reference/AMR.html b/reference/AMR.html index 4e99fa68..d22aa878 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German, AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/Rplot005.png b/reference/Rplot005.png index c51e4d0a..49984b20 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 1edabe08..99b1bc71 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index 429f6772..f18882ab 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index cec26e02..cfc95a61 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index a2b9b7e6..da7558bd 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/WHONET.html b/reference/WHONET.html index a69155b9..ef9c8442 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index a523bad1..77641e5c 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/ab_property.html b/reference/ab_property.html index 0b967d45..8db4d5a5 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index af84ab56..45a334c2 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 89f59569..b18096a7 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/age.html b/reference/age.html index e5cb028b..25bcd20f 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -205,16 +205,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1973-02-10 50 50.00548 26 -#> 2 1996-11-25 26 26.21644 3 -#> 3 1944-11-18 78 78.23562 55 -#> 4 1953-05-17 69 69.74247 46 -#> 5 1947-10-24 75 75.30411 52 -#> 6 1946-10-16 76 76.32603 53 -#> 7 1990-07-02 32 32.61644 9 -#> 8 1967-10-18 55 55.32055 32 -#> 9 1974-09-23 48 48.38904 25 -#> 10 1978-11-08 44 44.26301 21 +#> 1 1992-02-02 31 31.02740 7 +#> 2 1946-11-05 76 76.27123 53 +#> 3 1941-11-26 81 81.21370 58 +#> 4 1935-11-05 87 87.27123 64 +#> 5 1976-09-09 46 46.42740 23 +#> 6 1957-04-07 65 65.85205 42 +#> 7 1981-12-01 41 41.20000 18 +#> 8 1956-12-07 66 66.18356 43 +#> 9 1932-02-10 91 91.00548 67 +#> 10 1991-09-13 31 31.41644 8
R has a huge community.
Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 480 015 +online community for programmers. At the time of writing, 480 788 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 753be116..9330995e 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/datasets.html b/articles/datasets.html index 59a6256f..8a5d9b06 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/index.html b/articles/index.html index e5d4ecd9..a1231a30 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index ce8ddbba..92e726d9 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 03ef291c..021e2603 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/authors.html b/authors.html index 610cf2b0..b9695dae 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/extra.css b/extra.css index 0995fd15..a84fbe85 100644 --- a/extra.css +++ b/extra.css @@ -62,6 +62,7 @@ pre code { /* never wrap code on smaller screens */ word-wrap: normal !important; white-space: pre !important; + font-size: 0.8em !important; } .ot, .dv, .fl, .cn, .at, .op a { diff --git a/index.html b/index.html index b2c92695..04cdfaaf 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/news/index.html b/news/index.html index caf93d3b..945d439a 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -142,7 +142,7 @@ -AMR 1.8.2.9119 +AMR 1.8.2.9120 (this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!) This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below. TL;DR @@ -156,31 +156,32 @@ Now available in 20 languages Many small bug fixes -New +New -SIR vs. RSI +SIR vs. RSI For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR. While existing functions such as as.rsi(), rsi_df() and ggplot_rsi() still work, their replacements as.sir(), sir_df(), ggplot_sir() are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set rsi_translation is now called clinical_breakpoints to better reflect its content. The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024. -New antibiogram function +New antibiogram function With the new antibiogram() function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker et al. (2021, DOI 10.1177/20499361211011373) and Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2). The help page for antibiogram() extensively elaborates on use cases, and antibiogram() also supports printing in R Markdown and Quarto, with support for 20 languages. Furthermore, different plotting methods were implemented to allow for graphical visualisations as well. -Interpretation of MIC and disk diffusion values +Interpretation of MIC and disk diffusion values The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for as.sir(). EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for eucast_rules() to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new AMR_guideline option, such as: options(AMR_guideline = "CLSI 2020"). +With the new arguments include_PKPD (default: TRUE) and include_screening (default: FALSE), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in our new manual. Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013. -Supported languages +Supported languages We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language. We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 20 languages in total, and according to download stats used in almost all countries in the world! -Microbiological taxonomy +Microbiological taxonomy The microorganisms data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022. We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett et al. (2022, DOI 10.1099/mic.0.001269) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See mo_matching_score() on how their work was incorporated into the prevalence column of the microorganisms data set. Using their results, the as.mo() and all mo_*() functions are now much better capable of converting user input to valid taxonomic records. The new function add_custom_microorganisms() allows users to add custom microorganisms to the AMR package. @@ -204,7 +205,7 @@ The microorganisms.old data set was removed, and all previously accepted names are now included in the microorganisms data set. A new column status contains "accepted" for currently accepted names and "synonym" for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier. -Antibiotic agents and selectors +Antibiotic agents and selectors The new function add_custom_antimicrobials() allows users to add custom antimicrobial codes and names to the AMR package. The antibiotics data set was greatly updated: The following 20 antibiotics have been added (also includes the new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT) @@ -216,14 +217,14 @@ Also, we added support for using antibiotic selectors in scoped dplyr verbs (with or without using vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() for examples. -Antiviral agents +Antiviral agents We now added extensive support for antiviral agents! For the first time, the AMR package has extensive support for antiviral drugs and to work with their names, codes and other data in any way. The antivirals data set has been extended with 18 new drugs (also from the new J05AJ ATC group) and now also contains antiviral identifiers and LOINC codes A new data type av (antivirals) has been added, which is functionally similar to ab for antibiotics Functions as.av(), av_name(), av_atc(), av_synonyms(), av_from_text() have all been added as siblings to their ab_*() equivalents -Other new functions +Other new functions Function sir_confidence_interval() to add confidence intervals in AMR calculation. This is now also included in sir_df() and proportion_df(). Function mean_amr_distance() to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. Function sir_interpretation_history() to view the history of previous runs of as.sir() (previously as.rsi()). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which as.sir() was run. @@ -232,7 +233,7 @@ -Changes +Changes Argument combine_IR has been removed from this package (affecting functions count_df(), proportion_df(), and sir_df() and some plotting functions), since it was replaced with combine_SI three years ago Using units in ab_ddd(..., units = "...") had been deprecated for some time and is now not supported anymore. Use ab_ddd_units() instead. Support for data.frame-enhancing R packages, more specifically: data.table::data.table, janitor::tabyl, tibble::tibble, and tsibble::tsibble. AMR package functions that have a data set as output (such as sir_df() and bug_drug_combinations()), will now return the same data type as the input. @@ -270,9 +271,11 @@ Fix for mo_shortname() in case of higher taxonomic ranks (order, class, phylum) Cleaning columns with as.sir(), as.mic(), or as.disk() will now show the column name in the warning for invalid results Fix for using g.test() with zeroes in a 2x2 table + +get_episode() now returns class integer instead of numeric since they are always whole numbers -Other +Other Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions All R and Rmd files in this project are now styled using the styler package diff --git a/pkgdown.yml b/pkgdown.yml index d671b203..b078e48d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2023-02-12T10:25Z +last_built: 2023-02-12T14:14Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 4d222e8a..9bfad609 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 1da517b8..794b8503 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -157,6 +157,7 @@ AMR_guideline Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default is "EUCAST 2022". Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022). AMR_ignore_pattern A regular expression to define input that must be ignored in as.mo() and all mo_* functions. AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to TRUE. +AMR_include_screening A logical to use in as.sir(), to indicate that clinical breakpoints for screening are allowed, defaults to FALSE. AMR_keep_synonyms A logical to use in as.mo() and all mo_* functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. AMR_locale A language to use for the AMR package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). AMR_mo_source A file location for a manual code list to be used in as.mo() and all mo_* functions. This is explained in set_mo_source(). @@ -167,7 +168,10 @@ Settings in R are not saved globally and are thus lost when R is exited. You can save your options to your own .Rprofile file, which is a user-specific file. You can edit it using: utils::file.edit("~/.Rprofile") -In this file, you can set options such as options(AMR_locale = "pt") for Portuguese language support of antibiotics. +In this file, you can set options such as: + options(AMR_locale = "pt") + options(AMR_include_PKPD = TRUE) +to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with as.sir(). Share Options Within Team diff --git a/reference/AMR.html b/reference/AMR.html index 4e99fa68..d22aa878 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German, AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/Rplot005.png b/reference/Rplot005.png index c51e4d0a..49984b20 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 1edabe08..99b1bc71 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index 429f6772..f18882ab 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index cec26e02..cfc95a61 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index a2b9b7e6..da7558bd 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/WHONET.html b/reference/WHONET.html index a69155b9..ef9c8442 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index a523bad1..77641e5c 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/ab_property.html b/reference/ab_property.html index 0b967d45..8db4d5a5 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index af84ab56..45a334c2 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 89f59569..b18096a7 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 diff --git a/reference/age.html b/reference/age.html index e5cb028b..25bcd20f 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9119 + 1.8.2.9120 @@ -205,16 +205,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1973-02-10 50 50.00548 26 -#> 2 1996-11-25 26 26.21644 3 -#> 3 1944-11-18 78 78.23562 55 -#> 4 1953-05-17 69 69.74247 46 -#> 5 1947-10-24 75 75.30411 52 -#> 6 1946-10-16 76 76.32603 53 -#> 7 1990-07-02 32 32.61644 9 -#> 8 1967-10-18 55 55.32055 32 -#> 9 1974-09-23 48 48.38904 25 -#> 10 1978-11-08 44 44.26301 21 +#> 1 1992-02-02 31 31.02740 7 +#> 2 1946-11-05 76 76.27123 53 +#> 3 1941-11-26 81 81.21370 58 +#> 4 1935-11-05 87 87.27123 64 +#> 5 1976-09-09 46 46.42740 23 +#> 6 1957-04-07 65 65.85205 42 +#> 7 1981-12-01 41 41.20000 18 +#> 8 1956-12-07 66 66.18356 43 +#> 9 1932-02-10 91 91.00548 67 +#> 10 1991-09-13 31 31.41644 8
(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)
This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.
TL;DR
For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.
While existing functions such as as.rsi(), rsi_df() and ggplot_rsi() still work, their replacements as.sir(), sir_df(), ggplot_sir() are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set rsi_translation is now called clinical_breakpoints to better reflect its content.
as.rsi()
rsi_df()
ggplot_rsi()
as.sir()
sir_df()
ggplot_sir()
rsi_translation
clinical_breakpoints
The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.
With the new antibiogram() function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker et al. (2021, DOI 10.1177/20499361211011373) and Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2).
antibiogram()
The help page for antibiogram() extensively elaborates on use cases, and antibiogram() also supports printing in R Markdown and Quarto, with support for 20 languages.
Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.
The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for as.sir(). EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for eucast_rules() to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new AMR_guideline option, such as: options(AMR_guideline = "CLSI 2020").
eucast_rules()
AMR_guideline
options(AMR_guideline = "CLSI 2020")
With the new arguments include_PKPD (default: TRUE) and include_screening (default: FALSE), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in our new manual.
include_PKPD
TRUE
include_screening
FALSE
Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.
We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language.
We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 20 languages in total, and according to download stats used in almost all countries in the world!
AMR
The microorganisms data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.
microorganisms
We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett et al. (2022, DOI 10.1099/mic.0.001269) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See mo_matching_score() on how their work was incorporated into the prevalence column of the microorganisms data set. Using their results, the as.mo() and all mo_*() functions are now much better capable of converting user input to valid taxonomic records.
mo_matching_score()
prevalence
as.mo()
mo_*()
The new function add_custom_microorganisms() allows users to add custom microorganisms to the AMR package.
add_custom_microorganisms()
microorganisms.old
status
"accepted"
"synonym"
The new function add_custom_antimicrobials() allows users to add custom antimicrobial codes and names to the AMR package.
add_custom_antimicrobials()
The antibiotics data set was greatly updated:
antibiotics
Also, we added support for using antibiotic selectors in scoped dplyr verbs (with or without using vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() for examples.
vars()
... %>% summarise_at(aminoglycosides(), resistance)
resistance()
We now added extensive support for antiviral agents! For the first time, the AMR package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.
antivirals
av
ab
as.av()
av_name()
av_atc()
av_synonyms()
av_from_text()
ab_*()
sir_confidence_interval()
proportion_df()
mean_amr_distance()
sir_interpretation_history()
combine_IR
count_df()
combine_SI
units
ab_ddd(..., units = "...")
ab_ddd_units()
data.frame
data.table::data.table
janitor::tabyl
tibble::tibble
tsibble::tsibble
bug_drug_combinations()
mo_shortname()
as.mic()
as.disk()
g.test()
get_episode()
integer
numeric
styler
AMR_guideline Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default is "EUCAST 2022". Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022).
"CLSI"
"CLSI 2019"
"EUCAST 2022"
AMR_ignore_pattern A regular expression to define input that must be ignored in as.mo() and all mo_* functions.
AMR_ignore_pattern
mo_*
AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to TRUE.
AMR_include_PKPD
AMR_include_screening A logical to use in as.sir(), to indicate that clinical breakpoints for screening are allowed, defaults to FALSE.
AMR_include_screening
AMR_keep_synonyms A logical to use in as.mo() and all mo_* functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names.
AMR_keep_synonyms
AMR_locale A language to use for the AMR package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).
AMR_locale
AMR_mo_source A file location for a manual code list to be used in as.mo() and all mo_* functions. This is explained in set_mo_source().
AMR_mo_source
set_mo_source()
Settings in R are not saved globally and are thus lost when R is exited. You can save your options to your own .Rprofile file, which is a user-specific file. You can edit it using:
.Rprofile
utils::file.edit("~/.Rprofile")
In this file, you can set options such as options(AMR_locale = "pt") for Portuguese language support of antibiotics.
options(AMR_locale = "pt")
In this file, you can set options such as:
options(AMR_locale = "pt") + options(AMR_include_PKPD = TRUE)
to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with as.sir().