From b9f01d686eaf664fefcf6f416bc4c10bad38a67d Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 25 Sep 2019 22:37:40 +0200 Subject: [PATCH] (v0.7.1.9089) eucast file update --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/bug_drug_combinations.R | 1 + data-raw/eucast_rules.tsv | 6 +++--- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 8 ++++---- docs/reference/bug_drug_combinations.html | 2 +- docs/reference/index.html | 2 +- 12 files changed, 17 insertions(+), 16 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2a0ae261..e0224063 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.7.1.9088 +Version: 0.7.1.9089 Date: 2019-09-25 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 1ad0fad6..5a548dc6 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9088 +# AMR 0.7.1.9089 Last updated: 25-Sep-2019 ### Breaking diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 73f438ef..326380d9 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -75,6 +75,7 @@ bug_drug_combinations <- function(x, } x <- x %>% + as.data.frame(stringsAsFactors = FALSE) %>% mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>% filter(mo %in% (freq(mo) %>% filter(count >= minimum) %>% diff --git a/data-raw/eucast_rules.tsv b/data-raw/eucast_rules.tsv index c80f122c..8904dc1d 100644 --- a/data-raw/eucast_rules.tsv +++ b/data-raw/eucast_rules.tsv @@ -1,13 +1,13 @@ -# --------------------------------------------------------------------------------------------------- +# ------------------------------------------------------------------------------------------------------------------------------- # For editing this EUCAST reference file, these values can all be used for target antibiotics: # 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_without_CAZ', # 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins' # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. # The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain". -# The like.is.one_of column must contain one of: like, is, one_of ('like' will read the first column as regular expression) +# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression) # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180). # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<< -# --------------------------------------------------------------------------------------------------- +# ------------------------------------------------------------------------------------------------------------------------------- if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints diff --git a/docs/404.html b/docs/404.html index 3531b3d3..643eb395 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 37b3f4de..a5f17d54 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 diff --git a/docs/articles/index.html b/docs/articles/index.html index 04b58646..044539eb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 diff --git a/docs/authors.html b/docs/authors.html index dfc85ca9..4a08074e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 diff --git a/docs/index.html b/docs/index.html index a6bb3d86..01aa8f26 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 diff --git a/docs/news/index.html b/docs/news/index.html index ef73822f..434be9e1 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089 @@ -231,9 +231,9 @@ -
+

-AMR 0.7.1.9088 Unreleased +AMR 0.7.1.9089 Unreleased

Last updated: 25-Sep-2019

@@ -1286,7 +1286,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.7.1.9088
    • +
  • 0.7.1.9089
  • 0.7.1
  • 0.7.0
  • 0.6.1
    • diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index 7bee72e3..85e3a75e 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -85,7 +85,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089
diff --git a/docs/reference/index.html b/docs/reference/index.html index f2d43d27..932128c0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9088 + 0.7.1.9089