diff --git a/DESCRIPTION b/DESCRIPTION index 0d13288e..3fd5df79 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.0.9001 +Version: 1.7.0.9002 Date: 2021-06-01 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index fa4847c2..820f36e3 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.0.9001 +# `AMR` 1.7.0.9002 ## Last updated: 1 June 2021 ### New diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index d22c4bfa..dafcaadc 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/rsi.md5 b/data-raw/rsi.md5 index 63ef7521..ee35a907 100644 --- a/data-raw/rsi.md5 +++ b/data-raw/rsi.md5 @@ -1 +1 @@ -a4388a944969e5961917f72383156d33 +1a7fe52f8185c9bb2c470712863d1887 diff --git a/data-raw/rsi_translation.dta b/data-raw/rsi_translation.dta index 5cc7cc9c..4cc6fa64 100644 Binary files a/data-raw/rsi_translation.dta and b/data-raw/rsi_translation.dta differ diff --git a/data-raw/rsi_translation.rds b/data-raw/rsi_translation.rds index 9cc4e4b5..7c32865d 100644 Binary files a/data-raw/rsi_translation.rds and b/data-raw/rsi_translation.rds differ diff --git a/data-raw/rsi_translation.sas b/data-raw/rsi_translation.sas index 8ab8f026..4df1e081 100644 Binary files a/data-raw/rsi_translation.sas and b/data-raw/rsi_translation.sas differ diff --git a/data-raw/rsi_translation.sav b/data-raw/rsi_translation.sav index 47ba090d..7d7661d6 100644 Binary files a/data-raw/rsi_translation.sav and b/data-raw/rsi_translation.sav differ diff --git a/data-raw/rsi_translation.txt b/data-raw/rsi_translation.txt index 8b3d409d..eed44c58 100644 --- a/data-raw/rsi_translation.txt +++ b/data-raw/rsi_translation.txt @@ -10059,7 +10059,7 @@ "CLSI 2020" "MIC" "Vibrio" "Ampicillin/sulbactam" "M45 Table 20" 8 32 FALSE "CLSI 2020" "DISK" "(unknown name)" "Ampicillin/sulbactam" "Generic CLSI rules" "10-10ug" 15 11 FALSE "CLSI 2020" "MIC" "(unknown name)" "Ampicillin/sulbactam" "Generic CLSI rules" "10-10ug" 8 32 FALSE -"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfamethoxazole" "Table 2A" "200 – 300ug" 17 12 FALSE +"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfamethoxazole" "Table 2A" "200 - 300ug" 17 12 FALSE "CLSI 2020" "MIC" "Enterobacteriaceae" "Sulfamethoxazole" "Table 2A" 256 512 FALSE "CLSI 2020" "DISK" "Neisseria meningitidis" "Sulfamethoxazole" "Table 2I" "200-300ug" FALSE "CLSI 2020" "MIC" "Neisseria meningitidis" "Sulfamethoxazole" "Table 2I" 2 8 FALSE @@ -10068,7 +10068,7 @@ "CLSI 2020" "DISK" "Vibrio" "Sulfamethoxazole" "M45 Table 20" "200ug" 17 12 FALSE "CLSI 2020" "DISK" "(unknown name)" "Sulfamethoxazole" "Generic CLSI rules" "200-300ug" 17 12 FALSE "CLSI 2020" "MIC" "(unknown name)" "Sulfamethoxazole" "Generic CLSI rules" "200-300ug" 256 512 FALSE -"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfisoxazole" "Table 2A" "200 – 300ug" 17 12 FALSE +"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfisoxazole" "Table 2A" "200 - 300ug" 17 12 FALSE "CLSI 2020" "MIC" "Enterobacteriaceae" "Sulfisoxazole" "Table 2A" 256 512 FALSE "CLSI 2020" "DISK" "Neisseria meningitidis" "Sulfisoxazole" "Table 2I" "200-300ug" FALSE "CLSI 2020" "MIC" "Neisseria meningitidis" "Sulfisoxazole" "Table 2I" 2 8 FALSE @@ -10092,7 +10092,7 @@ "CLSI 2020" "MIC" "Streptococcus pneumoniae" "Sparfloxacin" "Table 2G" 0.5 2 FALSE "CLSI 2020" "DISK" "(unknown name)" "Sparfloxacin" "Generic CLSI rules" "5ug" 19 15 FALSE "CLSI 2020" "MIC" "(unknown name)" "Sparfloxacin" "Generic CLSI rules" "5ug" 0.5 2 FALSE -"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfonamide" "Table 2A" "200 – 300ug" 17 12 FALSE +"CLSI 2020" "DISK" "Enterobacteriaceae" "Sulfonamide" "Table 2A" "200 - 300ug" 17 12 FALSE "CLSI 2020" "MIC" "Enterobacteriaceae" "Sulfonamide" "Table 2A" 256 512 FALSE "CLSI 2020" "DISK" "Neisseria meningitidis" "Sulfonamide" "Table 2I" "200-300ug" FALSE "CLSI 2020" "MIC" "Neisseria meningitidis" "Sulfonamide" "Table 2I" 2 8 FALSE diff --git a/data-raw/rsi_translation.xlsx b/data-raw/rsi_translation.xlsx index c2956852..0b25c4ca 100644 Binary files a/data-raw/rsi_translation.xlsx and b/data-raw/rsi_translation.xlsx differ diff --git a/data/rsi_translation.rda b/data/rsi_translation.rda index 1626d84c..01889a76 100644 Binary files a/data/rsi_translation.rda and b/data/rsi_translation.rda differ diff --git a/docs/404.html b/docs/404.html index 9f6c5985..dbf8025b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.0.9001 + 1.7.0.9002 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f1f7cab0..4efddbc9 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.0.9001 + 1.7.0.9002 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 57eac212..57a32e65 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.0.9001 + 1.7.0.9002 @@ -1007,7 +1007,7 @@ If you are reading this page from within R, please Interpretation from MIC values / disk diameters to R/SI

A data set with 21,996 rows and 10 columns, containing the following column names:
guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R and uti.

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

-

It was last updated on 1 June 2021 06:44:05 UTC. Find more info about the structure of this data set here.

+

It was last updated on 1 June 2021 14:31:18 UTC. Find more info about the structure of this data set here.

Direct download links:

  • Function betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
    • -
  • A ggplot() method for resistance_predict() +
  • A ggplot() method for resistance_predict()
    • @@ -407,7 +407,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -464,7 +464,7 @@
 
  • 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
    •
  • 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
    • @@ -481,7 +481,7 @@ 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() +
  • 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
    • @@ -816,7 +816,7 @@

    Making this package independent of especially the tidyverse (e.g. packages dplyr and tidyr) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.

    Negative effects of this change are:

    @@ -1415,7 +1415,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • The age() function gained a new argument exact to determine ages with decimals
  • Removed deprecated functions guess_mo(), guess_atc(), EUCAST_rules(), interpretive_reading(), rsi()
    • -
  • Frequency tables (freq()): +
  • Frequency tables (freq()): @@ -1440,7 +1440,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • Added ceftazidim intrinsic resistance to Streptococci
  • Changed default settings for age_groups(), to let groups of fives and tens end with 100+ instead of 120+
    • -
  • Fix for freq() for when all values are NA +
  • Fix for freq() for when all values are NA
  • Fix for first_isolate() for when dates are missing
  • Improved speed of guess_ab_col() @@ -1679,7 +1679,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    • -
  • Frequency tables (freq() function): +
  • Frequency tables (freq() function):