diff --git a/tests/testthat/test-autoplot.pop_data.R b/tests/testthat/test-autoplot.pop_data.R index 299e951a..1c3c649a 100644 --- a/tests/testthat/test-autoplot.pop_data.R +++ b/tests/testthat/test-autoplot.pop_data.R @@ -26,7 +26,8 @@ test_that("`autoplot.pop_data()` raise autoplot(strata = "strat1", type = "density")) }) -test_that("`autoplot.pop_data()` produces stable results for `type = 'density'`", +test_that("`autoplot.pop_data()` produces + stable results for `type = 'density'`", { skip_if(getRversion() < "4.4.1") # 4.3.3 had issues xs_data <- load_pop_data( diff --git a/vignettes/articles/scrubTyphus_example.Rmd b/vignettes/articles/scrubTyphus_example.Rmd index 35327491..b7696a88 100644 --- a/vignettes/articles/scrubTyphus_example.Rmd +++ b/vignettes/articles/scrubTyphus_example.Rmd @@ -43,7 +43,7 @@ knitr::opts_chunk$set( ```{r setup, message=FALSE} install.packages("devtools") -devtools::install_github("ucd-serg/serocalculator", eval=FALSE) +devtools::install_github("ucd-serg/serocalculator", eval = FALSE) ``` @@ -53,9 +53,9 @@ The first step in conducting this analysis is to load our necessary packages. If ```{r load_packages} library(serocalculator) library(devtools) -install.packages("tidyverse", eval=FALSE) +install.packages("tidyverse", eval = FALSE) library(tidyverse) -install.packages("mixtools", eval=FALSE) +install.packages("mixtools", eval = FALSE) library(mixtools) ``` @@ -151,7 +151,7 @@ Column Name | Description ```{r message=FALSE, warning=FALSE} # biologic noise -b.noise <- xs_data %>% +b_noise <- xs_data %>% group_by(antigen_iso) %>% filter(!is.na(value)) %>% filter(age < 40) %>% # restrict to young ages to capture recent exposures @@ -181,7 +181,7 @@ b.noise <- xs_data %>% # define conditional parameters noise <- data.frame( antigen_iso = c("OT56kda_IgG", "OT56kda_IgM"), - nu = as.numeric(c(b.noise[2, 2], b.noise[1, 2])), # Biologic noise (nu) + nu = as.numeric(c(b_noise[2, 2], b_noise[1, 2])), # Biologic noise (nu) eps = c(0.2, 0.2), # M noise (eps) y.low = c(0.2, 0.2), # low cutoff (llod) y.high = c(200, 200)