diff --git a/docs/lang_da.svg b/docs/lang_da.svg new file mode 100644 index 00000000..881430f4 --- /dev/null +++ b/docs/lang_da.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/lang_de.svg b/docs/lang_de.svg new file mode 100644 index 00000000..65e9a01a --- /dev/null +++ b/docs/lang_de.svg @@ -0,0 +1,9 @@ + + + diff --git a/docs/lang_en.svg b/docs/lang_en.svg new file mode 100644 index 00000000..56487b08 --- /dev/null +++ b/docs/lang_en.svg @@ -0,0 +1,16 @@ + + diff --git a/docs/lang_es.svg b/docs/lang_es.svg new file mode 100644 index 00000000..fba167dd --- /dev/null +++ b/docs/lang_es.svg @@ -0,0 +1,406 @@ + + \ No newline at end of file diff --git a/docs/lang_fr.svg b/docs/lang_fr.svg new file mode 100644 index 00000000..a4bded52 --- /dev/null +++ b/docs/lang_fr.svg @@ -0,0 +1,2 @@ + + diff --git a/docs/lang_it.svg b/docs/lang_it.svg new file mode 100644 index 00000000..0855ee39 --- /dev/null +++ b/docs/lang_it.svg @@ -0,0 +1,6 @@ + + diff --git a/docs/lang_nl.svg b/docs/lang_nl.svg new file mode 100644 index 00000000..f19bd004 --- /dev/null +++ b/docs/lang_nl.svg @@ -0,0 +1,5 @@ + \ No newline at end of file diff --git a/docs/lang_pt.svg b/docs/lang_pt.svg new file mode 100644 index 00000000..5c19329c --- /dev/null +++ b/docs/lang_pt.svg @@ -0,0 +1,67 @@ + + \ No newline at end of file diff --git a/docs/lang_ru.svg b/docs/lang_ru.svg new file mode 100644 index 00000000..855b805a --- /dev/null +++ b/docs/lang_ru.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/lang_sv.svg b/docs/lang_sv.svg new file mode 100644 index 00000000..168a29a7 --- /dev/null +++ b/docs/lang_sv.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/news/index.html b/docs/news/index.html index e714e501..f1fcdee3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@
Data sets for download / own use
-11 December 2021
+12 December 2021
Source:vignettes/datasets.Rmd
datasets.RmdIt was last updated on 11 December 2021 14:59:42 UTC. Find more info about the structure of this data set here.
Direct download links:
- Download as R file (78 kB)
diff --git a/docs/articles/index.html b/docs/articles/index.html index fed50e9b..00cc2d29 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@
Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: https://msberends.github.io/AMR/articles/.
AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
+After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+The AMR package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.
This package can be used for:
-
diff --git a/docs/authors.html b/docs/authors.html
index c2a84a9a..9f380a6e 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
diff --git a/docs/extra.js b/docs/extra.js
index c986cdae..b037832e 100644
--- a/docs/extra.js
+++ b/docs/extra.js
@@ -116,8 +116,8 @@ $(document).ready(function() {
}
$(".template-authors").html(doct_tit($(".template-authors").html()));
$(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
- $('.template-citation-authors h1').eq(0).html("How to cite the
- Removed
p_symbol()and allfilter_*()functions (except forfilter_first_isolate()), which were all deprecated in a previous package version - Removed the
key_antibiotics()andkey_antibiotics_equal()functions, which were deprecated and superseded bykey_antimicrobials()andantimicrobials_equal() - Removed all previously implemented
ggplot2::ggplot()generics for classes<mic>,<disk>,<rsi>and<resistance_predict>as they did not follow theggplot2logic. They were replaced withggplot2::autoplot()generics.
+ - Renamed function
get_locale()toget_AMR_locale()to prevent conflicts with other packages Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for
eucast_rules(),mo_intrinsic_resistant()andmdro(). Theintrinsic_resistantdata set was also updated accordingly.
-Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
+Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
-
Function
set_ab_names()to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:@@ -183,7 +184,7 @@
Function
ab_ddd_units()to get units of DDDs (daily defined doses), deprecating the use ofab_ddd(..., units = TRUE)to be more consistent in data types of function output-Changed
+Changed
- Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year
- The
antibioticsdata set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:- Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5) @@ -229,7 +230,7 @@
- The right input types for
random_mic(),random_disk()andrandom_rsi()are now enforced -
-
as.rsi()has an improved algorithm and can now also correct for textual input (such as “Susceptible”, “Resistant”) in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish
+ -
as.mic()has an improved algorithm - When warnings are thrown because of too few isolates in any
count_*(),proportion_*()function (orresistant()orsusceptible()), thedplyrgroup will be shown, if available
@@ -252,7 +253,7 @@
as.rsi()has an improved algorithm and can now also correct for textual input (such as “Susceptible”, “Resistant”) in all supported languagesget_episode()andis_new_episode()can now cope withNAs-Other
+Other
- This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
- Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using
mo_*functions likemo_name()on microoganism IDs. - Added argument
ignore_patterntoas.mo()which can also be given tomo_*functions likemo_name(), to exclude known non-relevant input from analysing. This can also be set with the optionAMR_ignore_pattern.
- get_locale()now uses at defaultSys.getenv("LANG")or, ifLANGis not set,Sys.getlocale(). This can be overwritten by setting the optionAMR_locale.
+get_locale()now uses at defaultSys.getenv("LANG")or, ifLANGis not set,Sys.getlocale(). This can be overwritten by setting the optionAMR_locale.Big speed improvement for
eucast_rules()Overall speed improvement by tweaking joining functions
Function
mo_shortname()now returns the genus for input where the species is unknown
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 4cd210a0..35281c55 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-12-06T10:09Z
+last_built: 2021-12-12T08:37Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index fced647f..43a6139a 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -17,7 +17,7 @@
- x
any (vector of) text that can be coerced to a valid antibiotic code with
as.ab()- language -
language of the returned text, defaults to system language (see
get_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.- tolower
a 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".
- ... diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 57a9aceb..6b23f8f1 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -17,7 +17,7 @@
- ignore_pattern
a regular expression (case-insensitive) of which all matches in
xmust returnNA. This can be convenient to exclude known non-relevant input and can also be set with the optionAMR_ignore_pattern, e.g.options(AMR_ignore_pattern = "(not reported|contaminated flora)").- language -
language to translate text like "no growth", which defaults to the system language (see
get_locale())
+language to translate text like "no growth", which defaults to the system language (see
get_AMR_locale())- info
a logical to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to
TRUEonly in interactive mode- ... diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 3255efc1..d33e7333 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -17,7 +17,7 @@ @@ -254,7 +254,7 @@
For interpreting disk diffusion diameters according to EUCAST or CLSI. You must clean your disk zones first using
as.disk(), that also gives your columns the new data classdisk. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using themoargument.Using
dplyr, R/SI interpretation can be done very easily with either:
-For interpreting a complete data set, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running
as.rsi(data).
+For interpreting a complete data set, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running
as.rsi(your_data).- translate_ab
a character of length 1 containing column names of the antibiotics data set
- language -
language of the returned text, defaults to system language (see
get_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.- minimum
the minimum allowed number of available (tested) isolates. Any isolate count lower than
minimumwill returnNAwith a warning. The default number of30isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.- combine_SI diff --git a/docs/reference/count.html b/docs/reference/count.html index 9c71a208..97273578 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( @@ -184,7 +184,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( count_df( data, translate_ab = "name", - language = get_locale(), + language = get_AMR_locale(), combine_SI = TRUE, combine_IR = FALSE ) @@ -200,7 +200,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
- translate_ab
a column name of the antibiotics data set to translate the antibiotic abbreviations to, using
ab_property()- language -
language of the returned text, defaults to system language (see
get_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.- combine_SI
a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument
combine_IR, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default isTRUE.- combine_IR diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index e2f1132b..1985c765 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index dcc7fccc..22e8fe36 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -17,7 +17,7 @@ @@ -173,7 +173,7 @@ combine_SI = TRUE, combine_IR = FALSE, minimum = 30, - language = get_locale(), + language = get_AMR_locale(), nrow = NULL, colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R = "#ED553B"), @@ -194,7 +194,7 @@ fill = "interpretation", translate_ab = "name", minimum = 30, - language = get_locale(), + language = get_AMR_locale(), combine_SI = TRUE, combine_IR = FALSE, ... @@ -213,7 +213,7 @@ x = "antibiotic", translate_ab = "name", minimum = 30, - language = get_locale(), + language = get_AMR_locale(), combine_SI = TRUE, combine_IR = FALSE, datalabels.size = 3, @@ -245,7 +245,7 @@
- minimum
the minimum allowed number of available (tested) isolates. Any isolate count lower than
minimumwill returnNAwith a warning. The default number of30isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.- language -
language of the returned text, defaults to system language (see
get_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.- nrow
(when using
facet) number of rows- colours diff --git a/docs/reference/index.html b/docs/reference/index.html index 7a2fc584..6c2c78b9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ @@ -348,7 +348,7 @@
- x
any character (vector) that can be coerced to a valid microorganism code with
as.mo(). Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see Examples.- language -
language of the returned text, defaults to system language (see
get_locale()) and can be overwritten by setting the optionAMR_locale, e.g.options(AMR_locale = "de"), see translate. Also used to translate text like "no growth". Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can be overwritten by setting the optionAMR_locale, e.g.options(AMR_locale = "de"), see translate. Also used to translate text like "no growth". Uselanguage = NULLorlanguage = ""to prevent translation.- ...
other arguments passed on to
as.mo(), such as 'allow_uncertain' and 'ignore_pattern'- ab diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 775bab00..b1fb14e0 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -17,7 +17,7 @@
- colours_RSI
colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
- language -
language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see
get_locale()) and can be overwritten by setting the optionAMR_locale, e.g.options(AMR_locale = "de"), see translate. Uselanguage = NULLorlanguage = ""to prevent translation.
+language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see
get_AMR_locale()) and can be overwritten by setting the optionAMR_locale, e.g.options(AMR_locale = "de"), see translate. Uselanguage = NULLorlanguage = ""to prevent translation.- expand
a logical to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
- ... diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index a0bb6590..155b0f4d 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be @@ -180,7 +180,7 @@ resistance() should be used to calculate resistance, susceptibility() should be proportion_df( data, translate_ab = "name", - language = get_locale(), + language = get_AMR_locale(), minimum = 30, as_percent = FALSE, combine_SI = TRUE, @@ -190,7 +190,7 @@ resistance() should be used to calculate resistance, susceptibility() should be rsi_df( data, translate_ab = "name", - language = get_locale(), + language = get_AMR_locale(), minimum = 30, as_percent = FALSE, combine_SI = TRUE, @@ -216,7 +216,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
- translate_ab
a column name of the antibiotics data set to translate the antibiotic abbreviations to, using
ab_property()- language -
language of the returned text, defaults to system language (see
get_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
+language of the returned text, defaults to system language (see
get_AMR_locale()) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.- combine_SI
a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument
combine_IR, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default isTRUE.- combine_IR diff --git a/docs/reference/translate.html b/docs/reference/translate.html index a14b4b1e..c9ddf5e8 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -17,7 +17,7 @@ @@ -161,19 +161,19 @@
Setting the R option
AMR_locale, e.g. by runningoptions(AMR_locale = "de")Setting the system variable
LANGUAGEorLANG, e.g. by addingLANGUAGE="de_DE.utf8"to your.Renvironfile in your home directory
-
AMR package");
- $('.template-citation-authors h1').eq(1).html("All contributors of the AMR package");
+ $('.template-citation-authors h1').eq(0).html("All contributors of the AMR package");
+ $('.template-citation-authors h1').eq(1).html("How to cite the AMR package");
$(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors...");
});
diff --git a/docs/index.html b/docs/index.html
index f03ee645..4ee72b30 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -47,7 +47,7 @@
@@ -195,13 +195,15 @@
AMR (for R) 
-Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021). A new version will be released after the EUCAST guideline for clinical breakpoints (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.
+Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).
+A new version will be released after the EUCAST guideline for clinical breakpoints (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.
What is AMR (for R)?
AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
+After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+The AMR package is available in 
Danish, 
Dutch, 
English, 
French, 
German, 
Italian, 
Portuguese, 
Russian, 
Spanish and 
Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375) but is actively and durably maintained by two public healthcare organisations in the Netherlands.
-
-
+
+
-
-AMR 1.7.1.9066
+
+AMR 1.7.1.9067
-
@@ -161,7 +161,7 @@
Last updated: 11 December 2021
+Last updated: 12 December 2021
-
Breaking changes
+Breaking changes
-
@@ -623,7 +624,7 @@
New
+New
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().
Usage,
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index a658df36..e3e51d3d 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -17,7 +17,7 @@
@@ -168,7 +168,7 @@
allow_uncertain = TRUE,
reference_df = get_mo_source(),
ignore_pattern = getOption("AMR_ignore_pattern"),
- language = get_locale(),
+ language = get_AMR_locale(),
info = interactive(),
...
)
@@ -198,7 +198,7 @@
ab_name(x, language = get_locale(), tolower = FALSE, ...)
+ Usage,ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
ab_cid(x, ...)
@@ -169,13 +169,13 @@
ab_tradenames(x, ...)
-ab_group(x, language = get_locale(), ...)
+ab_group(x, language = get_AMR_locale(), ...)
ab_atc(x, only_first = FALSE, ...)
-ab_atc_group1(x, language = get_locale(), ...)
+ab_atc_group1(x, language = get_AMR_locale(), ...)
-ab_atc_group2(x, language = get_locale(), ...)
+ab_atc_group2(x, language = get_AMR_locale(), ...)
ab_loinc(x, ...)
@@ -183,17 +183,17 @@
ab_ddd_units(x, administration = "oral", ...)
-ab_info(x, language = get_locale(), ...)
+ab_info(x, language = get_AMR_locale(), ...)
ab_url(x, open = FALSE, ...)
-ab_property(x, property = "name", language = get_locale(), ...)
+ab_property(x, property = "name", language = get_AMR_locale(), ...)
set_ab_names(
data,
...,
property = "name",
- language = get_locale(),
+ language = get_AMR_locale(),
snake_case = NULL
)
@@ -202,7 +202,7 @@
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index 70a97de0..d2f393ce 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -17,7 +17,7 @@
@@ -167,7 +167,7 @@
format(
x,
translate_ab = "name (ab, atc)",
- language = get_locale(),
+ language = get_AMR_locale(),
minimum = 30,
combine_SI = TRUE,
combine_IR = FALSE,
@@ -195,7 +195,7 @@
Check Availability of Columns
Translate Strings from AMR Package
Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples.
Usage,
mo_name(x, language = get_locale(), ...)
+ Usage,mo_name(x, language = get_AMR_locale(), ...)
-mo_fullname(x, language = get_locale(), ...)
+mo_fullname(x, language = get_AMR_locale(), ...)
-mo_shortname(x, language = get_locale(), ...)
+mo_shortname(x, language = get_AMR_locale(), ...)
-mo_subspecies(x, language = get_locale(), ...)
+mo_subspecies(x, language = get_AMR_locale(), ...)
-mo_species(x, language = get_locale(), ...)
+mo_species(x, language = get_AMR_locale(), ...)
-mo_genus(x, language = get_locale(), ...)
+mo_genus(x, language = get_AMR_locale(), ...)
-mo_family(x, language = get_locale(), ...)
+mo_family(x, language = get_AMR_locale(), ...)
-mo_order(x, language = get_locale(), ...)
+mo_order(x, language = get_AMR_locale(), ...)
-mo_class(x, language = get_locale(), ...)
+mo_class(x, language = get_AMR_locale(), ...)
-mo_phylum(x, language = get_locale(), ...)
+mo_phylum(x, language = get_AMR_locale(), ...)
-mo_kingdom(x, language = get_locale(), ...)
+mo_kingdom(x, language = get_AMR_locale(), ...)
-mo_domain(x, language = get_locale(), ...)
+mo_domain(x, language = get_AMR_locale(), ...)
-mo_type(x, language = get_locale(), ...)
+mo_type(x, language = get_AMR_locale(), ...)
-mo_gramstain(x, language = get_locale(), ...)
+mo_gramstain(x, language = get_AMR_locale(), ...)
-mo_is_gram_negative(x, language = get_locale(), ...)
+mo_is_gram_negative(x, language = get_AMR_locale(), ...)
-mo_is_gram_positive(x, language = get_locale(), ...)
+mo_is_gram_positive(x, language = get_AMR_locale(), ...)
-mo_is_yeast(x, language = get_locale(), ...)
+mo_is_yeast(x, language = get_AMR_locale(), ...)
-mo_is_intrinsic_resistant(x, ab, language = get_locale(), ...)
+mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(), ...)
-mo_snomed(x, language = get_locale(), ...)
+mo_snomed(x, language = get_AMR_locale(), ...)
-mo_ref(x, language = get_locale(), ...)
+mo_ref(x, language = get_AMR_locale(), ...)
-mo_authors(x, language = get_locale(), ...)
+mo_authors(x, language = get_AMR_locale(), ...)
-mo_year(x, language = get_locale(), ...)
+mo_year(x, language = get_AMR_locale(), ...)
-mo_lpsn(x, language = get_locale(), ...)
+mo_lpsn(x, language = get_AMR_locale(), ...)
-mo_rank(x, language = get_locale(), ...)
+mo_rank(x, language = get_AMR_locale(), ...)
-mo_taxonomy(x, language = get_locale(), ...)
+mo_taxonomy(x, language = get_AMR_locale(), ...)
-mo_synonyms(x, language = get_locale(), ...)
+mo_synonyms(x, language = get_AMR_locale(), ...)
-mo_info(x, language = get_locale(), ...)
+mo_info(x, language = get_AMR_locale(), ...)
-mo_url(x, open = FALSE, language = get_locale(), ...)
+mo_url(x, open = FALSE, language = get_AMR_locale(), ...)
-mo_property(x, property = "fullname", language = get_locale(), ...)
+mo_property(x, property = "fullname", language = get_AMR_locale(), ...)Arguments
For language-dependent output of AMR functions, like mo_name(), mo_gramstain(), mo_type() and ab_name().
Usage,
+ get_locale()Usage,
get_AMR_locale()Details
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv. This file will be read by all functions where a translated output can be desired, like all mo_* functions (such as mo_name(), mo_gramstain(), mo_type(), etc.) and ab_* functions (such as ab_name(), ab_group(), etc.).
Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
+Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
Please suggest your own translations by creating a new issue on our repository.
Changing the Default Language
The system language will be used at default (as returned by Sys.getenv("LANG") or, if LANG is not set, Sys.getlocale()), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
So if the R option AMR_locale is set, the system variables LANGUAGE and LANG will be ignored.
Thus, if the R option AMR_locale is set, the system variables LANGUAGE and LANG will be ignored.
# The 'language' argument of below functions
# will be set automatically to your system language
-# with get_locale()
+# with get_AMR_locale()
# English
mo_name("CoNS", language = "en")
#> "Coagulase-negative Staphylococcus (CoNS)"
# Danish
-mo_name("CoNS", language = "nl")
-#> "Koagulase-negative stafylokokker (CoNS)"
+mo_name("CoNS", language = "da")
+#> "Koagulase-negative stafylokokker (KNS)"
# Dutch
mo_name("CoNS", language = "nl")
diff --git a/docs/survey.html b/docs/survey.html
index 385c8146..f6a4d68b 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -17,7 +17,7 @@
AMR package");
- $('.template-citation-authors h1').eq(1).html("All contributors of the AMR package");
+ $('.template-citation-authors h1').eq(0).html("All contributors of the AMR package");
+ $('.template-citation-authors h1').eq(1).html("How to cite the AMR package");
$(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors...");
});
diff --git a/pkgdown/logos/lang_da.svg b/pkgdown/logos/lang_da.svg
new file mode 100644
index 00000000..881430f4
--- /dev/null
+++ b/pkgdown/logos/lang_da.svg
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/pkgdown/logos/lang_de.svg b/pkgdown/logos/lang_de.svg
new file mode 100644
index 00000000..65e9a01a
--- /dev/null
+++ b/pkgdown/logos/lang_de.svg
@@ -0,0 +1,9 @@
+
+
+
diff --git a/pkgdown/logos/lang_en.svg b/pkgdown/logos/lang_en.svg
new file mode 100644
index 00000000..56487b08
--- /dev/null
+++ b/pkgdown/logos/lang_en.svg
@@ -0,0 +1,16 @@
+
+
diff --git a/pkgdown/logos/lang_es.svg b/pkgdown/logos/lang_es.svg
new file mode 100644
index 00000000..fba167dd
--- /dev/null
+++ b/pkgdown/logos/lang_es.svg
@@ -0,0 +1,406 @@
+
+
\ No newline at end of file
diff --git a/pkgdown/logos/lang_fr.svg b/pkgdown/logos/lang_fr.svg
new file mode 100644
index 00000000..a4bded52
--- /dev/null
+++ b/pkgdown/logos/lang_fr.svg
@@ -0,0 +1,2 @@
+
+
diff --git a/pkgdown/logos/lang_it.svg b/pkgdown/logos/lang_it.svg
new file mode 100644
index 00000000..0855ee39
--- /dev/null
+++ b/pkgdown/logos/lang_it.svg
@@ -0,0 +1,6 @@
+
+
diff --git a/pkgdown/logos/lang_nl.svg b/pkgdown/logos/lang_nl.svg
new file mode 100644
index 00000000..f19bd004
--- /dev/null
+++ b/pkgdown/logos/lang_nl.svg
@@ -0,0 +1,5 @@
+
\ No newline at end of file
diff --git a/pkgdown/logos/lang_pt.svg b/pkgdown/logos/lang_pt.svg
new file mode 100644
index 00000000..5c19329c
--- /dev/null
+++ b/pkgdown/logos/lang_pt.svg
@@ -0,0 +1,67 @@
+
+
\ No newline at end of file
diff --git a/pkgdown/logos/lang_ru.svg b/pkgdown/logos/lang_ru.svg
new file mode 100644
index 00000000..855b805a
--- /dev/null
+++ b/pkgdown/logos/lang_ru.svg
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/pkgdown/logos/lang_sv.svg b/pkgdown/logos/lang_sv.svg
new file mode 100644
index 00000000..168a29a7
--- /dev/null
+++ b/pkgdown/logos/lang_sv.svg
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/vignettes/welcome_to_AMR.Rmd b/vignettes/welcome_to_AMR.Rmd
index d55edded..81b678e9 100644
--- a/vignettes/welcome_to_AMR.Rmd
+++ b/vignettes/welcome_to_AMR.Rmd
@@ -28,7 +28,9 @@ Note: to keep the package size as small as possible, we only included this vigne
`AMR` is a free, open-source and independent R package (see [Copyright](https://msberends.github.io/AMR/#copyright)) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
-After installing this package, R knows `r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species and all `r AMR:::format_included_data_number(rbind(AMR::antibiotics[, "atc", drop = FALSE], AMR::antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
+After installing this package, R knows `r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species and all `r AMR:::format_included_data_number(rbind(AMR::antibiotics[, "atc", drop = FALSE], AMR::antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+
+The `AMR` package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.