diff --git a/DESCRIPTION b/DESCRIPTION index 893113e9..93bb0c94 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9074 +Version: 1.7.1.9075 Date: 2021-12-14 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index a48f2ccc..4cac5722 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9074 +# `AMR` 1.7.1.9075 ## Last updated: 14 December 2021 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. diff --git a/R/mo.R b/R/mo.R index fe928f2f..1a18fb8c 100755 --- a/R/mo.R +++ b/R/mo.R @@ -613,8 +613,6 @@ exec_as.mo <- function(x, on.exit(close(progress)) } - xx <<- x_backup[!already_known] - for (i in which(!already_known)) { if (initial_search == TRUE) { diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index d60b2a50..b5fa4af6 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 9f08b067..4cc1e5e5 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9073 + 1.7.1.9075 @@ -788,7 +788,7 @@ If you are reading this page from within R, please

Intrinsic bacterial resistance

-

A data set with 134,956 rows and 2 columns, containing the following column names:
microorganism and antibiotic.

+

A data set with 134,956 rows and 2 columns, containing the following column names:
mo and ab.

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

It was last updated on 14 December 2021 17:16:54 UTC. Find more info about the structure of this data set here.

Direct download links:

@@ -808,7 +808,7 @@ If you are reading this page from within R, please

Source

-

This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2 (2020).

+

This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3 (2021).

Example content @@ -826,14 +826,6 @@ If you are reading this page from within R, please Enterobacter cloacae -Acetylspiramycin - - -Enterobacter cloacae -Amoxicillin - - -Enterobacter cloacae Amoxicillin/clavulanic acid @@ -842,19 +834,19 @@ If you are reading this page from within R, please Enterobacter cloacae -Ampicillin/sulbactam +Amoxicillin Enterobacter cloacae -Avoparcin +Acetylspiramycin Enterobacter cloacae -Azithromycin +Avoparcin Enterobacter cloacae -Benzylpenicillin +Azithromycin Enterobacter cloacae @@ -862,27 +854,11 @@ If you are reading this page from within R, please Enterobacter cloacae -Cefadroxil - - -Enterobacter cloacae -Cefazolin - - -Enterobacter cloacae -Cefoxitin - - -Enterobacter cloacae -Cephalexin - - -Enterobacter cloacae Cephalothin Enterobacter cloacae -Clarithromycin +Cefadroxil Enterobacter cloacae @@ -890,8 +866,16 @@ If you are reading this page from within R, please Enterobacter cloacae +Clarithromycin + + +Enterobacter cloacae Cycloserine + +Enterobacter cloacae +Cefazolin + Enterobacter cloacae Dalbavancin @@ -910,19 +894,27 @@ If you are reading this page from within R, please Enterobacter cloacae -Fusidic acid +Cefoxitin Enterobacter cloacae -Gamithromycin +Fusidic acid Enterobacter cloacae -Josamycin +Gamithromycin Enterobacter cloacae -Kitasamycin (Leucomycin) +Josamycin + + +Enterobacter cloacae +Kitasamycin + + +Enterobacter cloacae +Cephalexin Enterobacter cloacae @@ -934,39 +926,31 @@ If you are reading this page from within R, please Enterobacter cloacae -Meleumycin - - -Enterobacter cloacae -Midecamycin - - -Enterobacter cloacae Miocamycin Enterobacter cloacae -Nafithromycin +Meleumycin Enterobacter cloacae +Midecamycin + + +Enterobacter cloacae Norvancomycin - + Enterobacter cloacae Oleandomycin - + Enterobacter cloacae Oritavancin - -Enterobacter cloacae -Pirlimycin - Enterobacter cloacae -Primycin +Benzylpenicillin Enterobacter cloacae @@ -974,6 +958,14 @@ If you are reading this page from within R, please Enterobacter cloacae +Pirlimycin + + +Enterobacter cloacae +Primycin + + +Enterobacter cloacae Quinupristin/dalfopristin @@ -994,15 +986,15 @@ If you are reading this page from within R, please Enterobacter cloacae -Solithromycin +Ampicillin/sulbactam Enterobacter cloacae -Spiramycin +Solithromycin Enterobacter cloacae -Tedizolid +Spiramycin Enterobacter cloacae @@ -1010,7 +1002,15 @@ If you are reading this page from within R, please Enterobacter cloacae -Telavancin +Thiacetazone + + +Enterobacter cloacae +Tilmicosin + + +Enterobacter cloacae +Tildipirosin Enterobacter cloacae @@ -1018,15 +1018,7 @@ If you are reading this page from within R, please Enterobacter cloacae -Thiacetazone - - -Enterobacter cloacae -Tildipirosin - - -Enterobacter cloacae -Tilmicosin +Telavancin Enterobacter cloacae @@ -1046,8 +1038,16 @@ If you are reading this page from within R, please Enterobacter cloacae +Tedizolid + + +Enterobacter cloacae Vancomycin + +Enterobacter cloacae +Nafithromycin +

@@ -1057,7 +1057,7 @@ If you are reading this page from within R, please here.

+

It was last updated on 14 December 2021 21:17:09 UTC. Find more info about the structure of this data set here.

Direct download links:

Source diff --git a/docs/articles/index.html b/docs/articles/index.html index 5be25900..66781702 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.7.1.9074 + 1.7.1.9075

diff --git a/docs/news/index.html b/docs/news/index.html index e2796c65..d6f09490 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.7.1.9074 + 1.7.1.9075 @@ -157,13 +157,13 @@
-

-AMR 1.7.1.9074

+

+AMR 1.7.1.9075

-

Last updated: 14 December 2021

+

Last updated: 14 December 2021

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.

-

Breaking changes

+

Breaking changes

  • Removed p_symbol() and all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package version
  • Removed the key_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal()
    • @@ -171,7 +171,7 @@
  • Renamed function get_locale() to get_AMR_locale() to prevent conflicts with other packages
-

New

+

New

  • Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the rsi_translation data set. This data set now more strictly follows the WHONET software as well.

  • 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_is_intrinsic_resistant() and mdro(). The intrinsic_resistant data set was also updated accordingly.

  • Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish

    • @@ -186,7 +186,7 @@

  • Function ab_ddd_units() to get units of DDDs (daily defined doses), deprecating the use of ab_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 antibiotics data 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)
      • @@ -258,7 +258,7 @@ get_episode() and is_new_episode() can now cope with NAs
-

Other

+

Other

  • This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.
diff --git a/vignettes/datasets.Rmd b/vignettes/datasets.Rmd index 7e864b4d..1cf9c534 100644 --- a/vignettes/datasets.Rmd +++ b/vignettes/datasets.Rmd @@ -120,10 +120,8 @@ Included (sub)species per taxonomic kingdom: ```{r, echo = FALSE} microorganisms %>% - pull(kingdom) %>% - table() %>% - as.data.frame() %>% - mutate(Freq = format(Freq, big.mark = ",")) %>% + count(kingdom) %>% + mutate(n = format(n, big.mark = ",")) %>% setNames(c("Kingdom", "Number of (sub)species")) %>% print_df() ``` @@ -222,7 +220,7 @@ This data set is in R available as `intrinsic_resistant`, after you load the `AM ### Source -This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on `r AMR:::format_eucast_version_nr("3.2")`. +This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on `r AMR:::format_eucast_version_nr("3.3")`. ### Example content @@ -230,6 +228,8 @@ Example rows when filtering on *Enterobacter cloacae*: ```{r, echo = FALSE} intrinsic_resistant %>% + transmute(microorganism = mo_name(mo), + antibiotic = ab_name(ab)) %>% filter(microorganism == "Enterobacter cloacae") %>% print_df(rows = Inf) ```