Merge pull request #305 from UCD-SERG/pr/234/patch-01

polishing edits on pr #234

NEWS.md

@@ -2,6 +2,10 @@
 
 ## New features
 
+* Improved error messaging for `autoplot.pop_data()` (#234).
+
+* Clarified package installation instructions in scrub typhus vignette (#234).
+
 * Updated `simulate_xsectionalData.Rmd()` (linting, removing deprecated functions).
 
 * Added default value for `antigen_isos` argument in `log_likelihood()` (#286)
@@ -18,6 +22,8 @@
 
 ## Developer-facing changes
 
+* Added `test-autoplot.pop_data` test (#234)
+
 * initialized [`lintr`](https://lintr.r-lib.org/) with `lintr::use_lint()` (#278)
 
 * created unit test for `df_to_array()` (#276)
@@ -44,7 +50,6 @@ including:
   - lint changed files (#256)
 
 # serocalculator 1.2.0
-* Added `test-autoplot.pop_data` test
 
 * Added `test-summary.pop_data` test
 

vignettes/articles/scrubTyphus_example.Rmd

@@ -40,26 +40,26 @@ knitr::opts_chunk$set(
 )
 ```
 
-
-```{r setup, message=FALSE}
-install.packages("devtools")
-devtools::install_github("ucd-serg/serocalculator", eval = FALSE)
-```
-
-
 ### Load packages
-The first step in conducting this analysis is to load our necessary packages. If you haven't installed already, you will need to do so before loading.
+The first step in conducting this analysis is to load our necessary packages. 
+If you haven't installed already, you will need to do so before loading.
+We will also need to have the `tidyverse` and `mixtools` packages installed
+for data manipulation and graphics operations we will perform in this vignette.
+Please see the websites for 
+[`serocalculator`](https://ucd-serg.github.io/serocalculator/#installing-the-serocalculator-package),
+[`tidyverse`](https://tidyverse.tidyverse.org/#installation),
+and [`mixtools`](https://github.com/dsy109/mixtools?tab=readme-ov-file#installation)
+for guidance on installing these packages into your R package library.
+
+Once all three of those packages are installed, we can load them into 
+our active R session environment:
 
 ```{r load_packages}
 library(serocalculator)
-library(devtools)
-install.packages("tidyverse", eval = FALSE)
 library(tidyverse)
-install.packages("mixtools", eval = FALSE)
 library(mixtools)
 ```
 
-
 ### Load data
 
 Pathogen-specific sample datasets, noise parameters, and longitudinal antibody dynamics for **serocalculator** are available on the [Serocalculator Repository](https://osf.io/ne8pc/) on Open Science Framework (OSF). We will pull this data directly into our R environment.