diff --git a/config.yaml b/config.yaml index 97381f8f..6ccf34c5 100644 --- a/config.yaml +++ b/config.yaml @@ -11,7 +11,7 @@ carpentry: 'incubator' # Overall title for pages. -title: 'Accessing and using delays to Quantify transmission' +title: 'Accessing and using delays to quantify transmission' # Date the lesson was created (YYYY-MM-DD, this is empty by default) created: diff --git a/md5sum.txt b/md5sum.txt index 500387cd..d2336f25 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,7 +1,7 @@ "file" "checksum" "built" "date" "CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2024-03-28" "LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2024-03-28" -"config.yaml" "60bcd408d5c52c87dcde88475d3f1748" "site/built/config.yaml" "2024-04-08" +"config.yaml" "4dea249856f65ec77bd9087f7741cea2" "site/built/config.yaml" "2024-04-18" "index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2024-03-28" "links.md" "fe82d0a436c46f4b07b82684ed2cceaf" "site/built/links.md" "2024-03-28" "episodes/delays-reuse.Rmd" "99c8549fdb699dea71a19f6022ddbeff" "site/built/delays-reuse.md" "2024-04-08" @@ -9,6 +9,6 @@ "episodes/delays-functions.Rmd" "53216ab4c9d20d5e157bf4a06429f7a9" "site/built/delays-functions.md" "2024-04-08" "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-03-28" "learners/reference.md" "e030f09656b2233a643e7aa2727e4fab" "site/built/reference.md" "2024-03-28" -"learners/setup.md" "64f432f4e2d4e1986341fd106f85b23d" "site/built/setup.md" "2024-04-08" +"learners/setup.md" "3e64f735ad0024b64b6f263d42f222f6" "site/built/setup.md" "2024-04-18" "profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2024-03-28" "renv/profiles/lesson-requirements/renv.lock" "66cc4d60718393932c53d9e114e5af9f" "site/built/renv.lock" "2024-03-28" diff --git a/setup.md b/setup.md index 8d3613f0..3abc3901 100644 --- a/setup.md +++ b/setup.md @@ -18,8 +18,8 @@ Each task has its tutorial website. Each tutorial website consists of a set of e | [Early task tutorials ➠](https://epiverse-trace.github.io/tutorials-early/) | [Middle task tutorials ➠](https://epiverse-trace.github.io/tutorials-middle) | [Late task tutorials ➠](https://epiverse-trace.github.io/tutorials-late/) | |---|---|---| -| Reading and cleaning case data | Real-time analysis and forecasting | Scenario modelling | -| Read and clean linelist data, Access delay distributions, and Estimate transmission metrics. | Forecast cases, Estimate severity, and Estimate superspreading. | Simulate disease spread and Investigate interventions. | +| Reading, cleaning, and validating case data | Real-time analysis and forecasting | Scenario modelling | +| Access delay distributions, and estimate transmission metrics. | Forecast cases, estimate severity, and estimate superspreading. | Simulate disease spread and investigate impact of interventions. | Each episode contains: @@ -33,17 +33,18 @@ Also check out the [glossary](../reference.md) for any terms you may be unfamili ### Epiverse-TRACE R packages -Our strategy is to gradually incorporate specialised **R packages** into our traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks. +Our strategy is to gradually incorporate specialised **R packages** into traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks. -![In **R**, the fundamental unit of shareable code is the **package**. A package bundles together code, data, documentation, and tests and is easy to share with others ([Wickham and Bryan, 2023](https://r-pkgs.org/introduction.html))](episodes/fig/pkgs-hexlogos-2.png) +![In **R**, the fundamental unit of shareable code is the **package**. A package bundles together code, data, documentation, and tests and is easy to share with others ([Wickham and Bryan, 2023](https://r-pkgs.org/introduction.html))](episodes/fig/pkgs-hexlogos-2.png). :::::::::::::::::::::::::::: prereq This course assumes intermediate R knowledge. This workshop is for you if: -- You can use the magrittr pipe `%>%` and/or native pipe `|>` -- You are familiar with functions from `{dplyr}`, `{tidyr}`, and `{ggplot2}` - You can read data into R, transform and reshape data, and make a wide variety of graphs +- You are familiar with functions from `{dplyr}`, `{tidyr}`, and `{ggplot2}` +- You can use the magrittr pipe `%>%` and/or native pipe `|>`. + We expect participants to have some exposure to basic Statistical, Mathematical and Epidemic theory concepts, but NOT intermediate or expert familiarity with modeling. @@ -74,7 +75,7 @@ This tutorial requires **R version 4.0.0 or later**. To check if your R version is up to date: -- In RStudio your R version will be printed in [the console window](https://docs.posit.co/ide/user/ide/guide/code/console.html). Or run `sessionInfo()` there. +- In RStudio your R version will be printed in [the console window](https://docs.posit.co/ide/user/ide/guide/code/console.html). Or run `sessionInfo()`. - **To update R**, download and install the latest version from the [R project website](https://cran.rstudio.com/) for your operating system. @@ -117,7 +118,8 @@ pak::pak(new_packages) These installation steps could ask you `? Do you want to continue (Y/n)` write `Y` and press Enter. -You should update **all of the packages** required for the tutorial, even if you installed them relatively recently. New versions bring improvements and important bug fixes. +You should update **all of the packages** required for the tutorial, even if you installed them relatively recently. +New versions bring improvements and fix bugs. When the installation has finished, you can try to load the packages by pasting the following code into the console: