diff --git a/NEWS.md b/NEWS.md index a6f49dde..86d252a8 100644 --- a/NEWS.md +++ b/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 diff --git a/vignettes/articles/scrubTyphus_example.Rmd b/vignettes/articles/scrubTyphus_example.Rmd index b7696a88..6a76363e 100644 --- a/vignettes/articles/scrubTyphus_example.Rmd +++ b/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.