website

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9133
+Version: 1.8.2.9134
-Date: 2023-02-17
+Date: 2023-02-18
 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

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9133
+# AMR 1.8.2.9134
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_helper_functions.R

@@ -1139,7 +1139,7 @@ try_colour <- function(..., before, after, collapse = " ") {
 }
 is_dark <- function() {
   if (is.null(AMR_env$is_dark_theme)) {
-    AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
+    !has_colour() || AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }

R/antibiogram.R

@@ -477,7 +477,9 @@ antibiogram <- function(x,
     colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N min-max)")
   }
 
-  structure(as_original_data_class(new_df, class(x), extra_class = "antibiogram"),
+  out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
+  rownames(out) <- NULL
+  structure(out,
     long = long,
     combine_SI = combine_SI
   )

R/bug_drug_combinations.R

@@ -164,9 +164,9 @@ bug_drug_combinations <- function(x,
   } else {
     out <- run_it(x)
   }
-  rownames(out) <- NULL
   out <- out %pm>% pm_arrange(mo, ab)
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
+  rownames(out) <- NULL
   structure(out, class = c("bug_drug_combinations", ifelse(data_has_groups, "grouped", character(0)), class(out)))
 }
 

index.md

@@ -7,7 +7,7 @@
 * 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**
 
-<div style="display: flex;">
+<div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
 <p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03">https://doi.org/10.18637/jss.v104.i03</a></small></p>
 </div>

pkgdown/extra.css

@@ -36,7 +36,10 @@
   }
 }
 @media (max-width: 575.98px) {
-  footer .pkgdown-footer-right {
+  footer .pkgdown-footer-left {
+    text-align: center;
+  }
+    footer .pkgdown-footer-right {
     text-align: center;
   }
 }

vignettes/AMR.Rmd

@@ -1,7 +1,5 @@
 ---
 title: "How to conduct AMR data analysis"
-author: "Dr. Matthijs Berends"
-date: '`r format(Sys.Date(), "%d %B %Y")`'
 output: 
   rmarkdown::html_vignette:
     toc: true
@@ -18,7 +16,7 @@ editor_options:
 knitr::opts_chunk$set(
   warning = FALSE,
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 5
 )
@@ -586,13 +584,13 @@ autoplot(
 
 The next example uses the `example_isolates` data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practise AMR data analysis.
 
-We will compare the resistance to amoxicillin/clavulanic acid (column `FOS`) between an ICU and other clinical wards. The input for the `fisher.test()` can be retrieved with a transformation like this:
+We will compare the resistance to amoxicillin/clavulanic acid (column `AMC`) between an ICU and other clinical wards. The input for the `fisher.test()` can be retrieved with a transformation like this:
 
 ```{r, results = 'markup'}
 # use package 'tidyr' to pivot data:
 library(tidyr)
 
-check_FOS <- example_isolates %>%
+check_AMC <- example_isolates %>%
   filter(ward %in% c("ICU", "Clinical")) %>% # filter on only these wards
   select(ward, AMC) %>% # select the wards and amoxi/clav
   group_by(ward) %>% # group on the wards
@@ -604,14 +602,18 @@ check_FOS <- example_isolates %>%
   select(ICU, Clinical) %>% # and only select these columns
   as.matrix() # transform to a good old matrix for fisher.test()
 
-check_FOS
+check_AMC
 ```
 
 We can apply the test now with:
 
 ```{r}
 # do Fisher's Exact Test
-fisher.test(check_FOS)
+fisher.test(check_AMC)
 ```
 
-As can be seen, the p value is practically zero (`r format(fisher.test(check_FOS)$p.value, scientific = FALSE)`), which means that the amoxicillin/clavulanic acid resistance found in isolates between patients in ICUs and other clinical wards are really different.
+As can be seen, the p value is practically zero (`r format(fisher.test(check_AMC)$p.value, scientific = FALSE)`), which means that the amoxicillin/clavulanic acid resistance found in isolates between patients in ICUs and other clinical wards are really different.
+
+----
+
+*Author: Dr. Matthijs Berends*

vignettes/EUCAST.Rmd

@@ -15,7 +15,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 4.5
 )

vignettes/MDR.Rmd

@@ -14,7 +14,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#"
+  comment = "#>"
 )
 library(AMR)
 ```

vignettes/PCA.Rmd

@@ -15,7 +15,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 4.5,
   dpi = 100

vignettes/SPSS.Rmd

@@ -16,7 +16,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#"
+  comment = "#>"
 )
 # set to original language (English)
 Sys.setlocale(locale = "C")

vignettes/WHONET.Rmd

@@ -15,7 +15,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 4.5
 )

vignettes/resistance_predict.Rmd

@@ -14,7 +14,7 @@ editor_options:
 ```{r setup, include = FALSE, results = 'markup'}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 4.75
 )

vignettes/welcome_to_AMR.Rmd

@@ -16,7 +16,7 @@ editor_options:
 knitr::opts_chunk$set(
   warning = FALSE,
   collapse = TRUE,
-  comment = "#",
+  comment = "#>",
   fig.width = 7.5,
   fig.height = 5
 )