diff --git a/DESCRIPTION b/DESCRIPTION index ad9c6049e..042566dbb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.8.1 -Date: 2022-03-14 +Version: 1.8.0.9010 +Date: 2022-03-15 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 18f36e42d..02c8e64c2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.8.1 - +# `AMR` 1.8.0.9010 +## Last updated: 15 March 2022 All functions in this package are 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. @@ -14,6 +14,7 @@ All functions in this package are considered to be stable. Updates to the AMR in * More informative warning messages * Added 192 as valid MIC * Updated MIC printing in tibbles +* Increased speed for loading the package ### Other * Fix for unit testing on R 3.3 diff --git a/R/mic.R b/R/mic.R index adf73c8d8..431ff46b3 100755 --- a/R/mic.R +++ b/R/mic.R @@ -243,7 +243,7 @@ droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, pillar_shaft.mic <- function(x, ...) { crude_numbers <- as.double(x) operators <- gsub("[^<=>]+", "", as.character(x)) - operators[operators != ""] <- font_silver(operators[operators != ""], collapse = NULL) + operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL) out <- trimws(paste0(operators, trimws(format(crude_numbers)))) out[is.na(x)] <- font_na(NA) # maketrailing zeroes almost invisible diff --git a/R/mo.R b/R/mo.R index 62f291f32..dea905c91 100755 --- a/R/mo.R +++ b/R/mo.R @@ -1003,6 +1003,35 @@ exec_as.mo <- function(x, } } + # try splitting of characters in the middle and then find ID based on old names ---- + # only when text length is 6 or lower + # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus + if (nchar(g.x_backup_without_spp) <= 6) { + x_length <- nchar(g.x_backup_without_spp) + x_split <- paste0("^", + g.x_backup_without_spp %pm>% substr(1, x_length / 2), + ".* ", + g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length)) + found <- lookup(fullname_lower %like_case% x_split, + haystack = MO.old_lookup, + column = NULL) + if (!all(is.na(found))) { + # it's an old name, so return it + if (property == "ref") { + x[i] <- found["ref"] + } else { + x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup) + } + pkg_env$mo_renamed_last_run <- found["fullname"] + was_renamed(name_old = found["fullname"], + name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup), + ref_old = found["ref"], + ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup), + mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup)) + return(x[i]) + } + } + # try fullname without start and without nchar limit of >= 6 ---- # like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only, diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 94158329d..4deae43b8 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 280769efb..3e4fea67a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,7 +43,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d3d3defe9..358e25152 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 92c297eb3..bc954f2f7 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010 @@ -190,7 +190,7 @@

Data sets for download / own use

-

14 March 2022

+

15 March 2022

Source: vignettes/datasets.Rmd diff --git a/docs/authors.html b/docs/authors.html index e8774d3f9..f9feeed13 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010
diff --git a/docs/index.html b/docs/index.html index f9d0fde29..7ccf02436 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010 diff --git a/docs/news/index.html b/docs/news/index.html index 1bccdd4c6..fb0666b8d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1 + 1.8.0.9010 @@ -157,14 +157,16 @@
-

-AMR 1.8.1

+

+AMR 1.8.0.9010

+
+

Last updated: 15 March 2022

All functions in this package are 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.

-

Changed

+

Changed

  • Fix for using as.rsi() on values containing capped values (such as >=), sometimes leading to NA

    • @@ -182,12 +184,14 @@ ignoring non-taxonomic text, such as:

  • More informative warning messages

  • Added 192 as valid MIC

  • Updated MIC printing in tibbles

    • +

  • Increased speed for loading the package

-

Other

+

Other

  • Fix for unit testing on R 3.3
  • Fix for size of some image elements, as requested by CRAN
+

@@ -368,7 +372,7 @@ guideline
  • Improved plot legends for MICs and disk diffusion values
  • Improved speed of as.ab() and all ab_*() functions
    • -
  • Added fortify() extensions for plotting methods
    • +
  • Added fortify() extensions for plotting methods
  • NA values of the classes <mic>, <disk> and <rsi> are now exported @@ -484,7 +488,7 @@ rewritten.
    • 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 +
  • A ggplot() method for resistance_predict()

    • @@ -628,7 +632,7 @@ function) to select/filter on e.g. linezolid and tedizolid

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

    • -

  • ggplot() generics for classes +

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

  • Function mo_is_yeast(), which determines whether a @@ -697,7 +701,7 @@ printing)

    • 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 +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 @@ -740,7 +744,7 @@ per hour)
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • -
  • Functions print() and summary() on a +
  • 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() @@ -1266,10 +1270,10 @@ 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:

    -