diff --git a/DESCRIPTION b/DESCRIPTION index 432d41a5..ed049c34 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.0.0.9006 -Date: 2020-02-21 +Version: 1.0.0.9007 +Date: 2020-02-22 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 274a6524..64d2dcac 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.0.0.9006 -## Last updated: 21-Feb-2020 +# AMR 1.0.0.9007 +## Last updated: 22-Feb-2020 ### Changed * Fixed floating point error for some MIC compa in EUCAST 2020 guideline diff --git a/R/data.R b/R/data.R index 4b4c65de..1e669761 100755 --- a/R/data.R +++ b/R/data.R @@ -163,7 +163,7 @@ catalogue_of_life <- list( #' Data set with unclean data #' -#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice. +#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice. #' @format A [`data.frame`] with 3,000 observations and 8 variables: #' - `patient_id`\cr ID of the patient #' - `date`\cr date of receipt at the laboratory diff --git a/R/filter_ab_class.R b/R/filter_ab_class.R index 27b15781..b9e71622 100644 --- a/R/filter_ab_class.R +++ b/R/filter_ab_class.R @@ -21,7 +21,7 @@ #' Filter isolates on result in antibiotic class #' -#' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside. +#' Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside. #' @inheritSection lifecycle Stable lifecycle #' @param x a data set #' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics] diff --git a/R/first_isolate.R b/R/first_isolate.R index f421aea1..049ffd6b 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -22,6 +22,7 @@ #' Determine first (weighted) isolates #' #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. +#' @inheritSection lifecycle Stable lifecycle #' @param x a [`data.frame`] containing isolates. #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive) diff --git a/docs/404.html b/docs/404.html index 5e85a070..770a4d9d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5240dc81..563d34d0 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 diff --git a/docs/articles/index.html b/docs/articles/index.html index 4a4ab28f..a4dfb7ed 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 diff --git a/docs/authors.html b/docs/authors.html index 99a1974f..996a5f0a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 diff --git a/docs/index.html b/docs/index.html index 01187865..f582a128 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 diff --git a/docs/news/index.html b/docs/news/index.html index c5fc741c..d1e57c00 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9006 + 1.0.0.9007 @@ -219,13 +219,13 @@ -
+

-AMR 1.0.0.9006 Unreleased +AMR 1.0.0.9007 Unreleased

-
+

-Last updated: 21-Feb-2020 +Last updated: 22-Feb-2020

@@ -1474,7 +1474,7 @@

Contents

    -
  • 1.0.0.9006
    • +
  • 1.0.0.9007
  • 1.0.0
  • 0.9.0
  • 0.8.0
    • diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 5c72ac02..a6bdaad5 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -80,7 +80,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.0.0.9005 + 1.0.0.9007
diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index a104e387..3a61a26f 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -45,7 +45,7 @@ - + @@ -79,7 +79,7 @@ AMR (for R) - 1.0.0.9005 + 1.0.0.9007

@@ -222,7 +222,7 @@
-

A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.

+

A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.

example_isolates_unclean
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index 3bbf6782..672f73b5 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -40,18 +40,12 @@ - - - - - - - + @@ -85,7 +79,7 @@ AMR (for R) - 0.9.0.9025 + 1.0.0.9007
@@ -211,12 +205,6 @@ - -
@@ -234,7 +222,7 @@
-

Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.

+

Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.

filter_ab_class(x, ab_class, result = NULL, scope = "any", ...)
@@ -344,7 +332,7 @@ The lifecycle of this function is stable
       

-  
Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner, Stichting Certe Medische Diagnostiek en Advies.

+  
Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.

 

 
 

@@ -355,23 +343,6 @@ The lifecycle of this function is stable
 
   
-
-
-
 
 
   
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 26ddd36f..c73c2ce0 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -79,7 +79,7 @@
       
       
         AMR (for R)
-        1.0.0.9005
+        1.0.0.9007
       
     

 
@@ -377,6 +377,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
 
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds points_threshold, which default to 2, an isolate will be (re)selected as a first weighted isolate.

 
 
+    
Stable lifecycle

+
+    
+
+
 

+The lifecycle of this function is stable. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.

+
If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

     
Read more on our website!

 
     
@@ -446,6 +453,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
       
  • Value
    • 
       
  • Details
    • 
       
  • Key antibiotics
    • 
+      
  • Stable lifecycle
    • 
       
  • Read more on our website!
    • 
       
  • See also
    • 
       
  • Examples
    • 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d1850dc3..fa813b68 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
       
       
         AMR (for R)
-        1.0.0.9006
+        1.0.0.9007
       
     
 
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index 95ac9936..ae2b47c5 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -79,7 +79,7 @@
       
       
         AMR (for R)
-        1.0.0.9005
+        1.0.0.9007
       
     
 
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index 58fef3c2..ea7050f7 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -79,7 +79,7 @@
       
       
         AMR (for R)
-        1.0.0.9005
+        1.0.0.9007
       
     
 
diff --git a/man/example_isolates_unclean.Rd b/man/example_isolates_unclean.Rd
index 67226586..b4724288 100644
--- a/man/example_isolates_unclean.Rd
+++ b/man/example_isolates_unclean.Rd
@@ -16,7 +16,7 @@
 example_isolates_unclean
 }
 \description{
-A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
+A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
 }
 \section{Read more on our website!}{
 
diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd
index 01bebff6..16b7554c 100644
--- a/man/filter_ab_class.Rd
+++ b/man/filter_ab_class.Rd
@@ -54,7 +54,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 \item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
 }
 \description{
-Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
+Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
 }
 \details{
 The \code{group} column in \link{antibiotics} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \link{antibiotics} data set.
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index cd9f51c9..8f07ec63 100755
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -125,6 +125,14 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
 }
 }
 
+\section{Stable lifecycle}{
+
+\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+
+If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+}
+
 \section{Read more on our website!}{
 
 On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.