v0.7.0

vignettes/G_test.Rmd

@@ -1,23 +0,0 @@
----
-title: "How to use the *G*-test"
-author: "Matthijs S. Berends"
-date: '`r format(Sys.Date(), "%d %B %Y")`'
-output: 
-  rmarkdown::html_vignette:
-    toc: true
-vignette: >
-  %\VignetteIndexEntry{How to use the G-test}
-  %\VignetteEncoding{UTF-8}
-  %\VignetteEngine{knitr::rmarkdown}
-editor_options: 
-  chunk_output_type: console
----
-
-```{r setup, include = FALSE, results = 'markup'}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#"
-)
-```
-
-*(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./../reference/g.test.html))*

vignettes/WHONET.Rmd

@@ -34,7 +34,7 @@ library(readxl)
 data <- read_excel(path = "path/to/your/file.xlsx")
 ```
 
-This package comes with an [example data set `WHONET`](./reference/WHONET.html). We will use it for this analysis.
+This package comes with an [example data set `WHONET`](https://msberends.gitlab.io/AMR/reference/WHONET.html). We will use it for this analysis.
 
 # Preparation
 
@@ -48,7 +48,7 @@ library(AMR)     # this package
 
 We will have to transform some variables to simplify and automate the analysis:
 
-* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](./reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
+* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](https://msberends.gitlab.io/AMR/reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
 * Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
 
 ```{r}