From 7d9a95e94a377743eb2acb5fa142eefbad6e650e Mon Sep 17 00:00:00 2001 From: Andree Valle Campos Date: Fri, 14 Nov 2025 13:16:47 +0000 Subject: [PATCH 1/3] fix install chunk --- episodes/severity-static.Rmd | 7 ++----- episodes/superspreading-estimate.Rmd | 8 ++------ 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/episodes/severity-static.Rmd b/episodes/severity-static.Rmd index 0ce2edad..253b3854 100644 --- a/episodes/severity-static.Rmd +++ b/episodes/severity-static.Rmd @@ -43,11 +43,8 @@ This episode requires you to be familiar with: Install packages if their are not already installed ```{r, eval = FALSE} -# if {pak} is not installed, run: install.packages("pak") -pak::pak("cfr") -pak::pak("epiparameter") -pak::pak("tidyverse") -pak::pak("outbreaks") +if(!require("pak")) install.packages("pak") +pak::pak(c("cfr", "epiparameter", "tidyverse", "outbreaks")) ``` If you have any error message, diff --git a/episodes/superspreading-estimate.Rmd b/episodes/superspreading-estimate.Rmd index 9c8f1e35..79422d70 100644 --- a/episodes/superspreading-estimate.Rmd +++ b/episodes/superspreading-estimate.Rmd @@ -42,12 +42,8 @@ Learners should familiarise themselves with following concept dependencies befor Install packages if their are not already installed ```{r, eval = FALSE} -# if {pak} is not installed, run: install.packages("pak") -pak::pak("epicontacts") -pak::pak("fitdistrplus") -pak::pak("superspreading") -pak::pak("outbreaks") -pak::pak("tidyverse") +if(!require("pak")) install.packages("pak") +pak::pak(c("epicontacts", "fitdistrplus", "superspreading", "outbreaks", "tidyverse")) ``` If you have any error message, From 88c84dbbb1a224d8b04efe7eceaf28a693b39691 Mon Sep 17 00:00:00 2001 From: Andree Valle Campos Date: Fri, 14 Nov 2025 15:19:15 +0000 Subject: [PATCH 2/3] fix install chunk --- episodes/superspreading-estimate.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/episodes/superspreading-estimate.Rmd b/episodes/superspreading-estimate.Rmd index 79422d70..ba57e548 100644 --- a/episodes/superspreading-estimate.Rmd +++ b/episodes/superspreading-estimate.Rmd @@ -41,7 +41,7 @@ Learners should familiarise themselves with following concept dependencies befor Install packages if their are not already installed -```{r, eval = FALSE} +```r if(!require("pak")) install.packages("pak") pak::pak(c("epicontacts", "fitdistrplus", "superspreading", "outbreaks", "tidyverse")) ``` From 2657d417d59c8e3adb0f12b7149719ae3e6b675e Mon Sep 17 00:00:00 2001 From: Andree Valle Campos Date: Fri, 14 Nov 2025 15:39:07 +0000 Subject: [PATCH 3/3] fix all files with prereq chunk --- episodes/severity-static.Rmd | 4 ++-- episodes/superspreading-estimate.Rmd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/episodes/severity-static.Rmd b/episodes/severity-static.Rmd index 253b3854..6fad7fc9 100644 --- a/episodes/severity-static.Rmd +++ b/episodes/severity-static.Rmd @@ -42,8 +42,8 @@ This episode requires you to be familiar with: Install packages if their are not already installed -```{r, eval = FALSE} -if(!require("pak")) install.packages("pak") +```r +if (!base::require("pak")) install.packages("pak") pak::pak(c("cfr", "epiparameter", "tidyverse", "outbreaks")) ``` diff --git a/episodes/superspreading-estimate.Rmd b/episodes/superspreading-estimate.Rmd index ba57e548..a89a6b74 100644 --- a/episodes/superspreading-estimate.Rmd +++ b/episodes/superspreading-estimate.Rmd @@ -42,7 +42,7 @@ Learners should familiarise themselves with following concept dependencies befor Install packages if their are not already installed ```r -if(!require("pak")) install.packages("pak") +if (!base::require("pak")) install.packages("pak") pak::pak(c("epicontacts", "fitdistrplus", "superspreading", "outbreaks", "tidyverse")) ```