diff --git a/DESCRIPTION b/DESCRIPTION index 3459d9c8..b70d1ffd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.5.0.9041 -Date: 2021-03-11 +Version: 1.6.0 +Date: 2021-03-14 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 4ac14376..b1a879fe 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.5.0.9041 -## Last updated: 11 March 2021 +# AMR 1.6.0 + ### New * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package. @@ -407,7 +407,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag * Speed improvements, especially for the *G. species* format (G for genus), like *E. coli* and *K pneumoniae* * Support for more common codes used in laboratory information systems * 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) +* Added a lifecycle state to every function, following the lifecycle circle of the `tidyverse` * For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey) * Changes to the `antibiotics` data set (thanks to Peter Dutey): * Added more synonyms to colistin, imipenem and piperacillin/tazobactam diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R index 4df43510..61be46ff 100644 --- a/R/ab_class_selectors.R +++ b/R/ab_class_selectors.R @@ -27,7 +27,7 @@ #' #' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} #' @inheritSection lifecycle Stable Lifecycle -#' @param only_rsi_columns a logical to indicate whether only columns of class [``]([rsi]) must be selected (defaults to `FALSE`) +#' @param only_rsi_columns a logical to indicate whether only columns of class `` must be selected (defaults to `FALSE`), see [as.rsi()] #' @inheritParams filter_ab_class #' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} #' diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index f20ac6ac..9170048b 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -57,7 +57,7 @@ #' 4. Added total amount of explained variance as a caption in the plot #' 5. Cleaned all syntax based on the `lintr` package, fixed grammatical errors and added integrity checks #' 6. Updated documentation -#' @details The colours for labels and points can be changed by adding another scale layer for colour, like `scale_colour_viridis_d()` or `scale_colour_brewer()`. +#' @details The colours for labels and points can be changed by adding another scale layer for colour, such as `scale_colour_viridis_d()` and `scale_colour_brewer()`. #' @rdname ggplot_pca #' @export #' @examples diff --git a/README.md b/README.md index 3dd3d815..86da63ad 100755 --- a/README.md +++ b/README.md @@ -10,13 +10,13 @@ -The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](data-raw). +The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/master/data-raw). -`AMR` is a free, open-source and independent R package 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. +`AMR` is a free, open-source and independent R package 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. It is currently being used in over 150 countries. -After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. +After installing this package, R knows ~70,000 distinct microbial species and all ~550 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. -This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (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 and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. +This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (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 is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package. diff --git a/cran-comments.md b/cran-comments.md index d4177285..cf5b1db7 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1 +1 @@ -* Ever since one of the first CRAN releases, CHECK returns a NOTE for having a data and R directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. +* This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible. diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index bf03f305..b1e77944 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 324973e8..4cec1e55 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f85aa3b5..9a11931d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 79d6e273..8fb9a0a8 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 @@ -211,7 +211,7 @@ If you are reading this page from within R, please Microorganisms (currently accepted names)

A data set with 70,026 rows and 16 columns, containing the following column names:
mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence and snomed.

This data set is in R available as microorganisms, after you load the AMR package.

-

It was last updated on 11 March 2021 09:32:27 UTC. Find more info about the structure of this data set here.

+

It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set here.

Direct download links:

Changed

    -
  • -

    Updated the bacterial taxonomy to 3 March 2021 (using LSPN)

    +
  • Updated the bacterial taxonomy to 3 March 2021 (using LSPN)
    • Added 3,372 new species and 1,523 existing species became synomyms
    • The URL of a bacterial species (mo_url()) will now lead to https://lpsn.dsmz.de
    • -
  • -

    Big update for plotting classes rsi, <mic>, and <disk>:

    +
  • Big update for plotting classes rsi, <mic>, and <disk>:
    • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
      • -
    • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
      • +
    • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • -

  • is.rsi() and is.rsi.eligible() now return a vector of TRUE/FALSE when the input is a data set, by iterating over all columns

    • -

  • Using functions without setting a data set (e.g., mo_is_gram_negative(), mo_is_gram_positive(), mo_is_intrinsic_resistant(), first_isolate(), mdro()) now work with dplyrs group_by() again

    • -

  • first_isolate() can be used with group_by() (also when using a dot . as input for the data) and now returns the names of the groups

    • +
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
  • -

    MIC values (see as.mic()) can now be used in any mathematical processing, such as usage inside functions min(), max(), range(), and with binary operators (+, -, etc.). This allows easy distribution analysis and fast filtering on MIC values:

    -
    -
-x <- random_mic(10)
-x
-#> Class <mic>
-#>  [1] 0.5    64     64     128    0.125  4      0.5    0.0625 0.0625 0.125 
-x[x > 4]
-#> Class <mic>
-#> [1] 64  64  128
    +is.rsi() and is.rsi.eligible() now return a vector of TRUE/FALSE when the input is a data set, by iterating over all columns
    • +
  • Using functions without setting a data set (e.g., mo_is_gram_negative(), mo_is_gram_positive(), mo_is_intrinsic_resistant(), first_isolate(), mdro()) now work with dplyrs group_by() again
    • +
  • +first_isolate() can be used with group_by() (also when using a dot . as input for the data) and now returns the names of the groups
    • +
  • Updated the data set microorganisms.codes (which contains popular LIS and WHONET codes for microorganisms) for some species of Mycobacterium that previously incorrectly returned M. africanum
    • -

  • Updated the data set microorganisms.codes (which contains popular LIS and WHONET codes for microorganisms) for some species of Mycobacterium that previously incorrectly returned M. africanum

    • -

  • WHONET code "PNV" will now correctly be interpreted as PHN, the antibiotic code for phenoxymethylpenicillin (‘peni V’)

    • -

  • Fix for verbose output of mdro(..., verbose = TRUE) for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only P. aeruginosa)

    • -

  • is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.

    • -

  • Functions get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)

    • -

  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)

    • -

  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()

    • -

  • Improved speed and reliability of guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.

    • -

  • Fix for mo_name() when used in other languages than English

    • -

  • The like() function (and its fast alias %like%) now always use Perl compatibility, improving speed for many functions in this package (e.g., as.mo() is now up to 4 times faster)

    • -

  • Staphylococcus cornubiensis is now correctly categorised as coagulase-positive

    • -

  • random_disk() and random_mic() now have an expanded range in their randomisation

    • -

  • Support for GISA (glycopeptide-intermediate S. aureus), so e.g. mo_genus("GISA") will return "Staphylococcus"

    • -

  • Added translations of German and Spanish for more than 200 antimicrobial drugs

    • -

  • Speed improvement for as.ab() when the input is an official name or ATC code

    • -

  • Added argument include_untested_rsi to the first_isolate() functions (defaults to TRUE to keep existing behaviour), to be able to exclude rows where all R/SI values (class <rsi>, see as.rsi()) are empty

    • +
  • WHONET code "PNV" will now correctly be interpreted as PHN, the antibiotic code for phenoxymethylpenicillin (‘peni V’)
    • +
  • Fix for verbose output of mdro(..., verbose = TRUE) for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only P. aeruginosa)
    • +
  • +is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
    • +
  • Functions get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)
    • +
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • +
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by() +
    • +
  • Improved speed and reliability of guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.
    • +
  • Fix for mo_name() when used in other languages than English
    • +
  • The like() function (and its fast alias %like%) now always use Perl compatibility, improving speed for many functions in this package (e.g., as.mo() is now up to 4 times faster)
    • +
  • +Staphylococcus cornubiensis is now correctly categorised as coagulase-positive
    • +
  • +random_disk() and random_mic() now have an expanded range in their randomisation
    • +
  • Support for GISA (glycopeptide-intermediate S. aureus), so e.g. mo_genus("GISA") will return "Staphylococcus" +
    • +
  • Added translations of German and Spanish for more than 200 antimicrobial drugs
    • +
  • Speed improvement for as.ab() when the input is an official name or ATC code
    • +
  • Added argument include_untested_rsi to the first_isolate() functions (defaults to TRUE to keep existing behaviour), to be able to exclude rows where all R/SI values (class <rsi>, see as.rsi()) are empty
@@ -366,7 +373,6 @@
  • Loading the package (i.e., library(AMR)) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
    • -

    @@ -857,7 +863,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • 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 +
  • Added a lifecycle state to every function, following the lifecycle circle of the tidyverse
  • For in as.ab(): support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
  • Changes to the antibiotics data set (thanks to Peter Dutey): diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index fd82b2f7..a0dd91a1 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: 2021-03-11T20:23Z +last_built: 2021-03-14T08:55Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 76e806ee..8a7ab5d9 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -83,7 +83,7 @@ AMR (for R) - 1.5.0.9021 + 1.6.0

    • @@ -283,7 +283,7 @@ only_rsi_columns -

    a logical to indicate whether only columns of class <rsi> must be selected (defaults to FALSE)

    +

    a logical to indicate whether only columns of class <rsi> must be selected (defaults to FALSE), see as.rsi()

    diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index abe9e7ec..4d14a013 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 2174ff38..a14a50f7 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index 0b4093d1..99b1f3bd 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index d17b104b..bc333ca5 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9040 + 1.6.0 @@ -383,7 +383,7 @@

    Details

    -

    The colours for labels and points can be changed by adding another scale layer for colour, like scale_colour_viridis_d() or scale_colour_brewer().

    +

    The colours for labels and points can be changed by adding another scale layer for colour, such as scale_colour_viridis_d() and scale_colour_brewer().

    Stable Lifecycle

    diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index d9ad79b6..f814f368 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 929e4e40..35cdd7b0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index eb42359d..6f8738ed 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index f043ccbd..b76eab58 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index c837636d..6097226d 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index 2d73a1fd..5afbfd73 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 6f494b1f..43e82601 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/docs/survey.html b/docs/survey.html index 31ba1dd1..29b47f81 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9041 + 1.6.0 diff --git a/git_premaster.sh b/git_premaster.sh index 1e4bfd3c..8bb72753 100755 --- a/git_premaster.sh +++ b/git_premaster.sh @@ -124,7 +124,8 @@ echo "••••••••••••••••••••" echo "• Building package •" echo "••••••••••••••••••••" echo "• Building 'data-raw/AMR_latest.tar.gz'..." -Rscript -e "x <- devtools::build(path = 'data-raw/AMR_latest.tar.gz', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)" +Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)" +mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz echo "• Installing..." Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)" echo diff --git a/index.md b/index.md index 532045cf..bc25b4b8 100644 --- a/index.md +++ b/index.md @@ -13,15 +13,15 @@ `AMR` is a free, open-source and independent [R package](https://www.r-project.org) 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 [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. +After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) 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. -This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (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](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)). +This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (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](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).

    - Used in 148 countries
    - Since its first public release in early 2018, this package has been downloaded from 148 countries. Click the map to enlarge and to see the country names.

    + Used in 155 countries
    + Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.

    ##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side! @@ -75,7 +75,7 @@ The development of this package is part of, related to, or made possible by:
    - +
    @@ -98,7 +98,7 @@ This package can be used for: * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html)) * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html)) - * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](./articles/datasets.html)) + * Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI ([link](./articles/datasets.html)) * Principal component analysis for AMR ([tutorial](./articles/PCA.html)) ### Get this package diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 55732a63..349cc5e5 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -52,7 +52,7 @@ tetracyclines(only_rsi_columns = FALSE) \arguments{ \item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} -\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{}} must be selected (defaults to \code{FALSE})} +\item{only_rsi_columns}{a logical to indicate whether only columns of class \verb{} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}} } \description{ These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} diff --git a/man/ggplot_pca.Rd b/man/ggplot_pca.Rd index dde88f82..c4de268a 100644 --- a/man/ggplot_pca.Rd +++ b/man/ggplot_pca.Rd @@ -106,7 +106,7 @@ ggplot_pca( Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function. } \details{ -The colours for labels and points can be changed by adding another scale layer for colour, like \code{scale_colour_viridis_d()} or \code{scale_colour_brewer()}. +The colours for labels and points can be changed by adding another scale layer for colour, such as \code{scale_colour_viridis_d()} and \code{scale_colour_brewer()}. } \section{Stable Lifecycle}{ diff --git a/pkgdown/extra.js b/pkgdown/extra.js index 199f8f0a..0c4f1b4c 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -66,7 +66,7 @@ $(document).ready(function() { // edit footer $('footer').html( '
    ' + - '

    AMR (for R). Developed at the University of Groningen in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen.

    ' + + '

    AMR (for R). Developed at the University of Groningen in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.

    ' + '' + '
    '); // all links should open in new tab/window diff --git a/pkgdown/logos/countries.png b/pkgdown/logos/countries.png index f9136554..ba6bf274 100644 Binary files a/pkgdown/logos/countries.png and b/pkgdown/logos/countries.png differ diff --git a/pkgdown/logos/countries_large.png b/pkgdown/logos/countries_large.png index 2e02aa32..aa101866 100644 Binary files a/pkgdown/logos/countries_large.png and b/pkgdown/logos/countries_large.png differ diff --git a/tests/testthat.R b/tests/testthat.R index 124e838c..d9acb765 100755 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -24,8 +24,8 @@ # ==================================================================== # # the testthat package is in Suggests, but very old R versions will not be -# able to install it. Yet, we want checks in those R versions as well, so -# only run unit tests in later R versions: +# able to install it. Yet, we want basic R CMD CHECK's in those R versions +# as well, so only run unit tests in later R versions: if (require("testthat")) { library(testthat, warn.conflicts = FALSE) library(AMR)