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_site.yml
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name: "IDEMAcourse"
output_dir: "docs"
exclude: ["auxiliary", "*.csv"]
favicon: idema_logo.png
base_url: https://andreashandel.github.io/IDEMAcourse/
repository_url: https://github.com/andreashandel/IDEMAcourse/
navbar:
title: "IDEMA Course"
logo:
image: IDEMAlogo.png
href: https://andreashandel.github.io/IDEMAcourse/
left:
- text: "General Information"
menu:
- text: "Syllabus"
href: ./Course_Syllabus.html
- text: "Schedule"
href: ./Course_Schedule.html
- text: "Modules"
menu:
- text: "1. Course, Tools and Topic Introduction"
menu:
- text: "1a. Course introduction"
href: ./Course_Introduction.html
- text: "1b. Teaching and Learning thoughts"
href: ./Teaching_and_Learning.html
- text: "1c. R and Rstudio"
href: ./R_and_RStudio.html
- text: "1d. DSAIDE"
href: ./DSAIDE.html
- text: "1e. Further Tools"
href: ./Further_Tools.html
- text: "1f. Topic introduction"
href: ./ID_Dynamics_Introduction.html
- text: "1g. Exercises"
href: ./Course_Introduction_Exercises.html
- text: "1h. Assessments"
href: ./Course_Introduction_Assessments.html
- text: "2. Characterizing infection states"
menu:
- text: "2a. Characteristics of ID"
href: ./Characteristics_of_ID.html
- text: "2b. Exercises"
href: ./Characteristics_of_ID_Exercises.html
- text: "2c. Assessments"
href: ./Characteristics_of_ID_Assessments.html
- text: "3. Patterns of ID"
menu:
- text: "3a. Patterns of ID"
href: ./Patterns_of_ID.html
- text: "3b. Exercises"
href: ./Patterns_of_ID_Exercises.html
- text: "3c. Assessments"
href: ./Patterns_of_ID_Assessments.html
- text: "4. Reproductive Number 1"
menu:
- text: "4a. Reproductive Number 1"
href: ./Reproductive_Number_1.html
- text: "4b. Exercises"
href: ./Reproductive_Number_1_Exercises.html
- text: "4c. Assessments"
href: ./Reproductive_Number_1_Assessments.html
- text: "5. Reproductive Number 2"
menu:
- text: "5a. Reproductive Number 2"
href: ./Reproductive_Number_2.html
- text: "5b. Exercises"
href: ./Reproductive_Number_2_Exercises.html
- text: "5c. Assessments"
href: ./Reproductive_Number_2_Assessments.html
- text: "6. Infectious Disease Control 1"
menu:
- text: "6a. ID Control 1"
href: ./ID_Control_1.html
- text: "6b. Exercises"
href: ./ID_Control_1_Exercises.html
- text: "6c. Assessments"
href: ./ID_Control_1_Assessments.html
- text: "7. Direct Transmission"
menu:
- text: "7a. Direct Transmission"
href: ./Direct_Transmission.html
- text: "7b. Exercises"
href: ./Direct_Transmission_Exercises.html
- text: "7c. Assessments"
href: ./Direct_Transmission_Assessments.html
- text: "8. Environmental Transmission"
menu:
- text: "8a. Environmental Transmission"
href: ./Environmental_Transmission.html
- text: "8b. Exercises"
href: ./Environmental_Transmission_Exercises.html
- text: "8c. Assessments"
href: ./Environmental_Transmission_Assessments.html
- text: "9. Vector-borne infectious diseases"
menu:
- text: "9a. Vector-borne Transmission"
href: ./Vectorborne_Transmission.html
- text: "9b. Exercises"
href: ./Vectorborne_Transmission_Exercises.html
- text: "9c. Assessments"
href: ./Vectorborne_Transmission_Assessments.html
- text: "10. Host heterogeneity"
menu:
- text: "10a. Host heterogeneity"
href: ./Host_Heterogeneity.html
- text: "10b. Exercises"
href: ./Host_Heterogeneity_Exercises.html
- text: "10c. Assessments"
href: ./Host_Heterogeneity_Assessments.html
- text: "11. Infectious Disease Control 2"
menu:
- text: "11a. ID Control 2"
href: ./ID_Control_2.html
- text: "11b. Exercises"
href: ./ID_Control_2_Exercises.html
- text: "11c. Assessments"
href: ./ID_Control_2_Assessments.html
- text: "12. Stochasticity and Extinctions"
menu:
- text: "12a. Stochasticity and Extinctions"
href: ./Stochasticity_and_Extinctions.html
- text: "12b. Exercises"
href: ./Stochasticity_and_Extinctions_Exercises.html
- text: "12c. Assessments"
href: ./Stochasticity_and_Extinctions_Assessments.html
- text: "13. Evolutionary Dynamics"
menu:
- text: "13a. Evolutionary Dynamics"
href: ./Evolutionary_Dynamics.html
- text: "13b. Exercises"
href: ./Evolutionary_Dynamics_Exercises.html
- text: "13c. Assessments"
href: ./Evolutionary_Dynamics_Assessments.html
- text: "Project"
menu:
- text: "Project information"
href: ./Project_Information.html
- text: "Project rubric"
href: ./Project_Rubric.html
- text: "Project review"
href: ./Project_Review.html
- text: "Project examples"
href: ./Project_Examples.html
- text: "Communication"
href: ./Course_Communication.html
- text: "Glossary"
href: ./Course_Glossary.html
- text: "Resources"
menu:
- text: "Course Resources"
href: ./Course_Resources.html
- text: "General Resources"
href: ./General_Resources.html
right:
- icon: fab fa-github
href: https://github.com/andreashandel/IDEMAcourse
output:
html_document:
theme: cerulean
highlight: espresso
toc: true
toc_depth: 2
toc_float:
collapsed: false
includes:
in_header: include_head.html
css: IDEMACourse.css