new logo

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9009
+Version: 2.1.1.9010
-Date: 2024-02-24
+Date: 2024-02-25
 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

NEWS.md

@@ -1,23 +1,24 @@
-# AMR 2.1.1.9009
+# AMR 2.1.1.9010
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
 
-## A New Milestone: One Health Support (= Human + Veterinary + Environmental)
+#### A New Milestone: One Health Support (= Human + Veterinary + Environmental)
 This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-* `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
-* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
-* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
-* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
-* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
 
 ## Breaking
 * Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
 
-## New functions
+## New
-* The group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
+* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
-* `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
+* Function `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
+* One Health implementation
+  * Function `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
+  * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
+  * The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
+  * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
+  * `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
 
-### Changed
+## Changed
 * For MICs:
   * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
   * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `limit_mic_range()` and `scale_*_mic()` functions.
@@ -26,6 +27,9 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Updated all ATC codes from WHOCC
 * Updated all antibiotic DDDs from WHOCC
 
+## Other
+* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
+
 
 # AMR 2.1.1
 

_pkgdown.yml

@@ -35,7 +35,11 @@ template:
   bootswatch: "flatly"
   assets: "pkgdown/logos" # use logos in this folder
   bslib:
+    base_font: {google: "Lato"}
+    heading_font: {google: " Lato"}
     code_font: {google: "Fira Code"}
+    navbar-bg: "#a8d5ef"
+    nav-link-color: "#212529"
     # body-text-align: "justify"
     line-height-base: 1.75
     # the green "success" colour of this bootstrap theme should be the same as the green in our logo

data-raw/AMR new logo.txt

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+green grass #a7dbc3
+green bacteria #128F76
+blue sky #a8d5ef

index.md

@@ -1,8 +1,9 @@
 # The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
 
+* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
 * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
 * Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
-* Applies all recent **CLSI and EUCAST clinical breakpoints** for MICs and disk zones
+* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for  MICs and disk zones
 * Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
 * Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC** and **SNOMED CT**
 * Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is completely **dependency-free**, highly suitable for places with **limited resources**

pkgdown/favicon/browserconfig.xml

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+            <square310x310logo src="/mstile-310x310.png?v=newlogo"/>
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+            <TileColor>#128f76</TileColor>
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pkgdown/favicon/site.webmanifest

@@ -1,20 +1,19 @@
 {
-    "name": "AMR (for R)",
+    "name": "AMR for R",
-    "short_name": "AMR (for R)",
+    "short_name": "AMR for R",
     "icons": [
         {
-            "src": "/android-chrome-192x192.png?v=2",
+            "src": "/android-chrome-192x192.png?v=newlogo",
             "sizes": "192x192",
             "type": "image/png"
         },
         {
-            "src": "/android-chrome-512x512.png?v=2",
+            "src": "/android-chrome-512x512.png?v=newlogo",
             "sizes": "512x512",
             "type": "image/png"
         }
     ],
-    "theme_color": "#ffffff",
+    "theme_color": "#128f76",
-    "background_color": "#ffffff",
+    "background_color": "#128f76",
-    "start_url": "https://msberends.github.io/AMR/",
     "display": "standalone"
 }