differences for PR #164

md5sum.txt

@@ -4,14 +4,15 @@
 "config.yaml" "0f7deb99a9178d8470bd18343974bd37" "site/built/config.yaml" "2024-11-14"
 "index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2024-11-14"
 "links.md" "fe82d0a436c46f4b07b82684ed2cceaf" "site/built/links.md" "2024-11-14"
+"pull_request_template.md" "0dfe2865b93d6343ab4e9a05b87e8f31" "site/built/pull_request_template.md" "2024-11-14"
 "episodes/read-cases.Rmd" "505a3d2556d248ca2a848da35277f02c" "site/built/read-cases.md" "2024-11-14"
 "episodes/clean-data.Rmd" "9de251ead5bff20edfbb87fc0f1569c4" "site/built/clean-data.md" "2024-11-14"
 "episodes/validate.Rmd" "aae4e51ffdc0eb34733066bcde9a733e" "site/built/validate.md" "2024-11-14"
 "episodes/describe-cases.Rmd" "b1e07bd1ddf8868f3ab9087b5e58d185" "site/built/describe-cases.md" "2024-11-14"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-11-14"
 "learners/epikinetics-descriptive.md" "50400941620956b3366fd99d51ed465b" "site/built/epikinetics-descriptive.md" "2024-11-14"
 "learners/epikinetics-statistics.md" "26868caf5a6b4a948ecb8f95c40694ab" "site/built/epikinetics-statistics.md" "2024-11-14"
-"learners/reference.md" "106717912e909a7c8d9e3e8fea48e17d" "site/built/reference.md" "2024-11-14"
-"learners/setup.md" "21a93de6ee19180365e56e32b9fcbb54" "site/built/setup.md" "2024-11-14"
+"learners/reference.md" "307af33a29515c20073092ad2e6452d6" "site/built/reference.md" "2024-11-14"
+"learners/setup.md" "c066675ec13be6509ab8d775bf2c95d1" "site/built/setup.md" "2024-11-14"
 "profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2024-11-14"
-"renv/profiles/lesson-requirements/renv.lock" "a317377094f5ab7ff4acc5259a3e446c" "site/built/renv.lock" "2024-11-14"
+"renv/profiles/lesson-requirements/renv.lock" "80c766a56218d586f6193aaa0b4ef0f9" "site/built/renv.lock" "2024-11-14"

pull_request_template.md

@@ -0,0 +1,15 @@
+* **Please check if the PR fulfills these requirements**
+
+- [ ] I have read the CONTRIBUTING guidelines
+- [ ] I created a new feature branch
+- [ ] I have opened and refer to an issue or I am referring to an existing issue
+- [ ] Lesson builds locally
+
+* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+
+* **What is the issue you are addressing?**
+
+* **If contributing new additional material please explain why you think it is needed**
+
+* **Other information**:

reference.md

@@ -22,7 +22,7 @@ title: 'Glossary of Terms: Epiverse-TRACE'
 : The contact matrix is a square matrix consisting of rows/columns equal to the number age groups. Each element represents the frequency of contacts between age groups. If we believe that transmission of an infection is driven by contact, and that contact rates are very different for different age groups, then specifying a contact matrix allows us to account for age specific rates of transmission. 
 
 [C++]{#cplusplus}
-: C++ is a high-level programming language that can be used within R to speed up sections of code. To learn more about C++ check out these [tutorials](https://cplusplus.com/doc/tutorial/) and learn more about the integration of C++ and R [here](https://www.rcpp.org/).
+: C++ is a high-level programming language that can be used within R to speed up sections of code. To learn more about C++ check out these [tutorials](https://cplusplus.com/doc/tutorial/) and learn more about the integration of C++ and R in the [rcpp documentation](https://www.rcpp.org/).
 [Censoring]{#censoring}
 : 
 Means that we know an event happened, but we do not know exactly when it happened. Most epidemiological data are “doubly censored” because there is uncertainty surrounding both primary and secondary event times. Not accounting for censoring can lead to biased estimates of the delay’s standard deviation ([Park et al., in progress](https://github.com/parksw3/epidist-paper)).

setup.md

@@ -37,13 +37,13 @@ Each episode contains:
 + **Challenges**: complete challenges to test your understanding.
 + **Explainers**: add to your understanding of mathematical and modelling concepts with the explainer boxes.
 
-Also check out the [glossary](../reference.md) for any terms you may be unfamiliar with.
+Also check out the [glossary](./reference.md) for any terms you may be unfamiliar with.
 
 ### Epiverse-TRACE R packages
 
 Our strategy is to gradually incorporate specialised **R packages** into a traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks.
 
-![I](episodes/fig/pkgs-hexlogos-2.png).
+![I](episodes/fig/pkgs-hexlogos-2.png){alt='Outbreak analysis R packages hexagonal logos'}.
 
 <p><figure>
     <img src="episodes/fig/pkgs-hexlogos-2.png"