diff --git a/CLAUDE.html b/CLAUDE.html index 1362cfb50..3ba5d84c0 100644 --- a/CLAUDE.html +++ b/CLAUDE.html @@ -73,7 +73,7 @@ pkgdown::build_site() # Code coverage report -covr::package_coverage() +covr::package_coverage()

From the shell:

# CRAN check from parent directory
 R CMD check AMR
diff --git a/articles/AMR.html b/articles/AMR.html index 66069c5e5..939c109bb 100644 --- a/articles/AMR.html +++ b/articles/AMR.html @@ -91,7 +91,7 @@ website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was -generated on 24 April 2026.

+generated on 25 April 2026.

Introduction

@@ -147,21 +147,21 @@ make the structure of your data generally look like this:

-2026-04-24 +2026-04-25 abcd Escherichia coli S S -2026-04-24 +2026-04-25 abcd Escherichia coli S R -2026-04-24 +2026-04-25 efgh Escherichia coli R @@ -442,27 +442,27 @@ impression, as it comes with support for the new mo and sir classes that we now have in our data set:

 summary(our_data_1st)
-#>   patient_id          hospital              date           
-#>  Length:2724        Length:2724        Min.   :2011-01-01  
-#>  Class :character   Class :character   1st Qu.:2013-04-07  
-#>  Mode  :character   Mode  :character   Median :2015-06-03  
-#>                                        Mean   :2015-06-09  
-#>                                        3rd Qu.:2017-08-11  
-#>                                        Max.   :2019-12-27  
-#>    bacteria               AMX                    AMC                
-#>  Class :mo             Class:sir              Class:sir             
-#>  <NA>  :0              %S   :41.6% (n=1133)   %S   :52.6% (n=1432)  
-#>  Unique:4              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     
-#>  #1    :B_ESCHR_COLI   %I   :16.4% (n=446)    %I   :12.2% (n=333)   
-#>  #2    :B_STPHY_AURS   %R   :42.0% (n=1145)   %R   :35.2% (n=959)   
-#>  #3    :B_STRPT_PNMN   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     
-#>     CIP                    GEN                  first        
-#>  Class:sir              Class:sir              Mode:logical  
-#>  %S   :52.5% (n=1431)   %S   :61.0% (n=1661)   TRUE:2724     
-#>  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)                    
-#>  %I   : 6.5% (n=176)    %I   : 3.0% (n=82)                   
-#>  %R   :41.0% (n=1117)   %R   :36.0% (n=981)                  
-#>  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)
+#>      patient_id        hospital         date              bacteria           
+#>  Length   :2724   Length   :2724   Min.   :2011-01-01   Class :mo            
+#>  N.unique : 260   N.unique :   3   1st Qu.:2013-04-07   <NA>  :0             
+#>  N.blank  :   0   N.blank  :   0   Median :2015-06-03   Unique:4             
+#>  Min.nchar:   2   Min.nchar:   1   Mean   :2015-06-09   #1    :B_ESCHR_COLI  
+#>  Max.nchar:   3   Max.nchar:   1   3rd Qu.:2017-08-11   #2    :B_STPHY_AURS  
+#>                                    Max.   :2019-12-27   #3    :B_STRPT_PNMN  
+#>     AMX                    AMC                    CIP                
+#>  Class:sir              Class:sir              Class:sir             
+#>  %S   :41.6% (n=1133)   %S   :52.6% (n=1432)   %S   :52.5% (n=1431)  
+#>  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     
+#>  %I   :16.4% (n=446)    %I   :12.2% (n=333)    %I   : 6.5% (n=176)   
+#>  %R   :42.0% (n=1145)   %R   :35.2% (n=959)    %R   :41.0% (n=1117)  
+#>  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     
+#>     GEN                  first        
+#>  Class:sir              Mode:logical  
+#>  %S   :61.0% (n=1661)   TRUE:2724     
+#>  %SDD : 0.0% (n=0)                    
+#>  %I   : 3.0% (n=82)                   
+#>  %R   :36.0% (n=981)                  
+#>  %NI  : 0.0% (n=0)
 
 glimpse(our_data_1st)
 #> Rows: 2,724
diff --git a/articles/AMR.md b/articles/AMR.md
index 0d50d64fd..3d89d6df1 100644
--- a/articles/AMR.md
+++ b/articles/AMR.md
@@ -3,7 +3,7 @@
 **Note:** values on this page will change with every website update
 since they are based on randomly created values and the page was written
 in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 24 April 2026.
+methodology remains unchanged. This page was generated on 25 April 2026.
 
 ## Introduction
 
@@ -51,9 +51,9 @@ structure of your data generally look like this:
 
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-04-24 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-04-24 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-04-24 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-04-25 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-04-25 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-04-25 |    efgh    | Escherichia coli |  R  |  S  |
 
 ### Needed R packages
 
@@ -367,27 +367,27 @@ and `sir` classes that we now have in our data set:
 
 ``` r
 summary(our_data_1st)
-#>   patient_id          hospital              date           
-#>  Length:2724        Length:2724        Min.   :2011-01-01  
-#>  Class :character   Class :character   1st Qu.:2013-04-07  
-#>  Mode  :character   Mode  :character   Median :2015-06-03  
-#>                                        Mean   :2015-06-09  
-#>                                        3rd Qu.:2017-08-11  
-#>                                        Max.   :2019-12-27  
-#>    bacteria               AMX                    AMC                
-#>  Class :mo             Class:sir              Class:sir             
-#>    :0              %S   :41.6% (n=1133)   %S   :52.6% (n=1432)  
-#>  Unique:4              %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     
-#>  #1    :B_ESCHR_COLI   %I   :16.4% (n=446)    %I   :12.2% (n=333)   
-#>  #2    :B_STPHY_AURS   %R   :42.0% (n=1145)   %R   :35.2% (n=959)   
-#>  #3    :B_STRPT_PNMN   %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     
-#>     CIP                    GEN                  first        
-#>  Class:sir              Class:sir              Mode:logical  
-#>  %S   :52.5% (n=1431)   %S   :61.0% (n=1661)   TRUE:2724     
-#>  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)                    
-#>  %I   : 6.5% (n=176)    %I   : 3.0% (n=82)                   
-#>  %R   :41.0% (n=1117)   %R   :36.0% (n=981)                  
-#>  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)
+#>      patient_id        hospital         date              bacteria           
+#>  Length   :2724   Length   :2724   Min.   :2011-01-01   Class :mo            
+#>  N.unique : 260   N.unique :   3   1st Qu.:2013-04-07     :0             
+#>  N.blank  :   0   N.blank  :   0   Median :2015-06-03   Unique:4             
+#>  Min.nchar:   2   Min.nchar:   1   Mean   :2015-06-09   #1    :B_ESCHR_COLI  
+#>  Max.nchar:   3   Max.nchar:   1   3rd Qu.:2017-08-11   #2    :B_STPHY_AURS  
+#>                                    Max.   :2019-12-27   #3    :B_STRPT_PNMN  
+#>     AMX                    AMC                    CIP                
+#>  Class:sir              Class:sir              Class:sir             
+#>  %S   :41.6% (n=1133)   %S   :52.6% (n=1432)   %S   :52.5% (n=1431)  
+#>  %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)      %SDD : 0.0% (n=0)     
+#>  %I   :16.4% (n=446)    %I   :12.2% (n=333)    %I   : 6.5% (n=176)   
+#>  %R   :42.0% (n=1145)   %R   :35.2% (n=959)    %R   :41.0% (n=1117)  
+#>  %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)      %NI  : 0.0% (n=0)     
+#>     GEN                  first        
+#>  Class:sir              Mode:logical  
+#>  %S   :61.0% (n=1661)   TRUE:2724     
+#>  %SDD : 0.0% (n=0)                    
+#>  %I   : 3.0% (n=82)                   
+#>  %R   :36.0% (n=981)                  
+#>  %NI  : 0.0% (n=0)
 
 glimpse(our_data_1st)
 #> Rows: 2,724
diff --git a/articles/datasets.html b/articles/datasets.html
index da1b7a971..c5cde755f 100644
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -80,7 +80,7 @@
   

       
Download data sets for download / own use

             
-            
24 April 2026

+            
25 April 2026

       
       Source: vignettes/datasets.Rmd
       
datasets.Rmd

diff --git a/news/index.html b/news/index.html
index 29c928897..6a9804e35 100644
--- a/news/index.html
+++ b/news/index.html
@@ -87,7 +87,9 @@
 

 

 
Fixes

-
  • Fixed multiple bugs in the parallel = TRUE mode of as.sir() for data frames: (1) PSOCK workers (Windows / R < 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of AMR_env instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (mclapply) where pre-existing sir_interpretation_history rows were included in every worker’s captured log; (4) removed use of non-exported internal functions (%pm>%, pm_pull, as.sir.default) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape \u00a (3 digits) in the “DONE” status message
    • 
+
    • 
+as.sir() with reference_data: custom guideline names now correctly classify values as R using EUCAST convention (> breakpoint_R for MIC, < breakpoint_R for disk); custom breakpoints with host = NA now serve as a host-agnostic fallback when no host-specific row matches (fixes #239)
      • 
+
    • Fixed multiple bugs in the parallel = TRUE mode of as.sir() for data frames: (1) PSOCK workers (Windows / R < 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of AMR_env instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (mclapply) where pre-existing sir_interpretation_history rows were included in every worker’s captured log; (4) removed use of non-exported internal functions (%pm>%, pm_pull, as.sir.default) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape \u00a (3 digits) in the “DONE” status message
      • 
 
    • Fixed a bug in as.sir() where values that were purely numeric (e.g., "1") and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
      • 
 
    • Fixed a bug in as.mic() where MIC values in scientific notation (e.g., "1e-3") were incorrectly handled because the letter e was removed along with other Unicode letters; scientific notation e is now preserved
      • 
 
    • Fixed a bug in as.ab() where certain AB codes containing “PH” or “TH” (such as ETH, MTH, PHE, PHN, STH, THA, THI1) would incorrectly return NA when combined in a vector with any untranslatable value (#245)
      • 
diff --git a/news/index.md b/news/index.md
index 30639f31f..2fe3d2b45 100644
--- a/news/index.md
+++ b/news/index.md
@@ -63,6 +63,12 @@
 
 #### Fixes
 
+- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with
+  `reference_data`: custom guideline names now correctly classify values
+  as R using EUCAST convention (`> breakpoint_R` for MIC,
+  `< breakpoint_R` for disk); custom breakpoints with `host = NA` now
+  serve as a host-agnostic fallback when no host-specific row matches
+  (fixes [\#239](https://github.com/msberends/AMR/issues/239))
 - Fixed multiple bugs in the `parallel = TRUE` mode of
   [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data
   frames: (1) PSOCK workers (Windows / R \< 4.0) now correctly load the
diff --git a/pkgdown.yml b/pkgdown.yml
index 3f3e3ea1a..18c32d330 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   PCA: PCA.html
   WHONET: WHONET.html
   WISCA: WISCA.html
-last_built: 2026-04-24T22:40Z
+last_built: 2026-04-25T12:44Z
 urls:
   reference: https://amr-for-r.org/reference
   article: https://amr-for-r.org/articles
diff --git a/reference/age.html b/reference/age.html
index e35f6f5fa..ff97bd5db 100644
--- a/reference/age.html
+++ b/reference/age.html
@@ -112,16 +112,16 @@
 
 df
 #>    birth_date age age_exact age_at_y2k
-#> 1  1999-06-30  26  26.81644          0
-#> 2  1968-01-29  58  58.23288         31
-#> 3  1965-12-05  60  60.38356         34
-#> 4  1980-03-01  46  46.14795         19
-#> 5  1949-11-01  76  76.47671         50
-#> 6  1947-02-14  79  79.18904         52
-#> 7  1940-02-19  86  86.17534         59
-#> 8  1988-01-10  38  38.28493         11
-#> 9  1997-08-27  28  28.65753          2
-#> 10 1978-01-26  48  48.24110         21
+#> 1  1999-06-30  26  26.81918          0
+#> 2  1968-01-29  58  58.23562         31
+#> 3  1965-12-05  60  60.38630         34
+#> 4  1980-03-01  46  46.15068         19
+#> 5  1949-11-01  76  76.47945         50
+#> 6  1947-02-14  79  79.19178         52
+#> 7  1940-02-19  86  86.17808         59
+#> 8  1988-01-10  38  38.28767         11
+#> 9  1997-08-27  28  28.66027          2
+#> 10 1978-01-26  48  48.24384         21