Topic,Homework,URL
Syllabus,,[Syllabus](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html)
Intro. Chapt. 1 & Chap. 2: The reproducibility crisis,"Due to internet outage on campus, we had to change schedule. Read Baker (2016) and prepare for discussing outcome of study",[Chapter 1](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#2_Chapter_1) & [Chapter 2](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#3_Chapter_2)
Chap. 1 - part A: Learning the basics,[Install software](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#213_Install_R_Markdown_software),[Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partA)
"Chap. 1 - Complete part A & overview of part B: Tables, Figures and References",Read Chapt. 1 - part B (Set your R Markdown environment),[Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partA) & [Part B: Set your R Markdown environment](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#233_Set_your_R_Markdown_environment)
"Chap. 1 - part B: Tables, Figures and References",Work on bioinfo. tutorials,"[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References)"
"Chap. 1 - part B: Tables, Figures and References",Work on bioinfo. tutorials,"[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References)"
Chap. 1 - Complete part B and part C: Advanced R Markdown settings,"**1.** Complete material all the way to the end of section 2.3.6; **2.** Read sections 2.3.7 and 2.3.8 and make sure that the bibliography file ""Bibliography_Reproducible_Science_2.bib” is copied in your working directory; **3.** Read section 2.3.9 and make sure that the csl file ""AmJBot.csl” is copied in your working directory; **4.** Read section 2.4 (Chapter 1 - part C) and get accustomed with the concepts presented in this part. I will be giving a presentation on these concepts and you will be implementing the code.","[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References) & [Part C](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#14_PART_C:_Advanced_R_and_R_Markdown_settings)"
Chap. 1 - part D: User Defined Functions in R,**1.** Complete section 2.4.6 of part C and **2.** Read part D until the end of section 2.5.8.,[Part D](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#15_PART_D:_User_Defined_Functions_in_R)
Chap. 1 - part D: User Defined Functions in R,**1.** Complete exercise in section 2.4.7 of part C and **2.** Read part D until the end of section 2.5.8.,[Part D](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#15_PART_D:_User_Defined_Functions_in_R)
Q&A and work on bioinformatic tutorials,"**1.** Sign up for bioinformatics tutorial (see Syllabus sections 5.1, 6 and 11 ) and **2.** Work with your group to organize your bioinformatics tutorial",[Publications and Resources for bioinformatic tutorials](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html#7_Publications__Textbooks)
"Chap. 3: A roadmap to implement reproducible science in Ecology, Evolution & Behavior",Read material presented in Chapter 3,[Chapter 3](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#4_Chapter_3)
Chap. 4: Open science and CARE principles,Read material presented in Chapter 4,[Chapter 4](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#5_Chapter_4)
Chap. 5: Data management,Read material presented in Chapter 5 - Part A,[Chapter 5 - Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partDM)
Complete Chap. 5: Data management and Chap. 5: Reproducible code,Read material presented in Chapter 5 - Part B + Download folder “Project_ID/“ on Google Drive under this path: Reproducible_Science > Exercises > Chapter_5,[Chapter 5 - Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#repcode)
Chap. 6: Getting published,Turn in tutorial for Chap. 7 & start individual reports,[Chapter 6 - Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#getpub)
Chap. 6: Writing papers in R Markdown ([rticles](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#rticlespkg)) and Work on bioinformatic tutorials,Upload tutorial of Chap. 7 on Google Drive,[Chapter 6 - Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#writpub)
Bioinfo. tutorial - Chap. 7,Turn in tutorial for Chap. 8,
Bioinfo. tutorial - Chap. 7,Upload tutorial of Chap. 8 on Google Drive,
Bioinfo. tutorial - Chap. 8,Turn in tutorial for Chap. 9,
Bioinfo. tutorial - Chap. 8,Upload tutorial of Chap. 9 on Google Drive,
Bioinfo. tutorial - Chap. 9,Turn in tutorial for Chap. 10,
Bioinfo. tutorial - Chap. 9,Upload tutorial of Chap. 10 on Google Drive,
Bioinfo. tutorial - Chap. 10,Turn in tutorial for Chap. 11,
Bioinfo. tutorial - Chap. 10,Upload tutorial of Chap. 11 on Google Drive,
Bioinfo. tutorial - Chap. 11,Turn in tutorial for Chap. 12,
Bioinfo. tutorial - Chap. 11,Upload tutorial of Chap. 12 on Google Drive,
Bioinfo. tutorial - Chap. 12,Students work on ind. projects: Review literature (see Syllabus),
Bioinfo. tutorial - Chap. 12,Students work on ind. projects: Data management workflow,
Individual projects - Q&A,Students work on ind. projects: Data management workflow,
Individual projects - Q&A,Turn in ind. projects (on [Google Drive](https://drive.google.com/drive/folders/1MZt5kNKusCv6OeZpjuuPxUiqBaoQVQAc?usp=sharing)),
Oral presentations of individual projects,,
Oral presentations of individual projects,,