| Agenda | Day 1. Synthesis & Unix | Day 2. Communication and Version Control | Day 3. Advanced Unix and Data tools | Day 4. Open Data and R | Day 5. People and Data Wrangling |
|---|---|---|---|---|---|
| 8:15-8:30 | Welcome (Jones, Budden) | Feedback, questions, and discussion | Feedback, questions, and discussion | Feedback, questions, and discussion | Feedback, questions, and discussion |
| 8:30-9:00 | Participant intros; brief bio, project interests, goals for course (all) | Activity: Version control, Git, Github, Git in RStudio (Brun) | Advanced unix tools (awk, sed, iconv, etc.) (Jones) | Ecological Metadata in R (Mecum) | Social aspects of collaboration, high-performing groups, data policies (Budden and Jones) |
| 9:00-9:30 | Course overview, discussion of expectations (Jones, Budden) | Activity: Version control, Git, Github, Git in RStudio (Brun) | Advanced unix tools (awk, sed, iconv, etc.) (Jones) | Open data in R and ROpenSci (Mecum & Jones) | Facilitating group discussions (Budden) |
| 9:30-9:45 | Break | Break | Break | Break | Break |
| 9:45-11:00 | Intro to servers, networks, and the unix command line (Jones) | Activity: Version control, Git, Github, Git in RStudio (Brun) | Bash shell scripts (Jones) | Data liberation (scraping, text mining) (Brun) | Introduction to tidyverse wrangling (Lortie) |
| 11:00-12:00 | Thinking preferences activity (Budden) | Activity: Version control, Git, Github, Git in RStudio (Brun) | R Review/ Assessment (Mecum) | Data liberation (scraping, text mining) (Brun) | Tutorial and exercises wrangling to filter, sort, and merge (Lortie) |
| Noon-1:00 | Lunch | Lunch | Lunch | Lunch | Lunch |
| 1:00-1:30 | R Markdown & Rstudio setup (Mecum) | Communications: The message box (Budden) | Data Management & Scientific data repositories (Budden) | Regular expressions (Mecum) | Data munging, QA/QC, cleaning (Mecum) |
| 1:30-2:00 | R Markdown & Rstudio setup (Mecum) | Group work on message box (Budden) | Publishing Data in R (Jones) | Message box 2: Group exchange and feedback (Budden) | Data munging, QA/QC, cleaning (Mecum) |
| 2:00-2:15 | Break | Break | Break | Break | Break |
| 2:15-5:00 | Pre-Assessment (Budden) and Synthesis Groups (Jones) | Synthesis Groups | Synthesis Groups | Synthesis Groups | Synthesis Groups |
| 5:00-5:15 | Peanut Gallery | Peanut Gallery | Peanut Gallery | Peanut Gallery | Peanut Gallery |
| Agenda | Day 6. Open Meta-analysis | Day 7. Tabular Data | Day 8. Programming and Workflows | Day 9. Reproducible research | Day 10. Metagenomics |
|---|---|---|---|---|---|
| 8:15-8:30 | Feedback, questions, and discussion | Feedback, questions, and discussion | Mid-term assessment | Feedback, questions, and discussion | Feedback, questions, and discussion |
| 8:30-9:00 | Metas and systematic reviews (Lortie) | Overview of tabular data modeling (Jones) | Lecture: Workflows and software modeling (Jones) | LECTURE: Science in the open: Provenance and Reproducibility (Jones) | Introduction to metagenomic data (Teal) |
| 9:00-9:30 | Metas steps 1-3 (Lortie) | Data Modeling Exercise with Group projects (Jones) | Wrangling followup: tidyr’s separate, gather, and spread | Activity: Asserting provenance in R (Jones) | Metagenomics (Teal) |
| 9:30-9:45 | Break | Break | Break | Break | Break |
| 9:45-11:00 | Metas step 4 (Lortie) | Activity: SQL and PostgreSQL (Jones) | Activity: Functions and modular code in R (Jones) | Practical provenance (Lowndes) | Metagenomics (Teal) |
| 11:00-12:00 | Metas step 5 (Lortie) | Activity: SQL and PostgreSQL (Jones) | Activity: Creating R Packages (Jones) | Activity: Recording provenance with recordr (Jones) | Metagenomics (Teal) |
| Noon-1:00 | Lunch (starts 11:45) | Lunch | Lunch | Lunch | Lunch |
| 1:00-1:30 | LAB: complete group metas (Lortie) | SQL and database access in R (Mecum) | Testing R code and analysis (Mecum) | Activity: Reproducible papers with Rmd (Mecum and Jones) | Advanced Metagenomics (Teal) |
| 1:30-2:00 | Presentations by groups of meta-analyses | SQL and database access in R (Mecum) | Workflow design activity (Group projects) (Jones) | Activity: Reproducible papers with Rmd | Hands-on exercise and workflow (Teal) |
| 2:00-2:15 | Break | Break | Break | Break | Break |
| 2:15-5:00 | Synthesis Groups | Synthesis Groups | Synthesis Groups | Synthesis Groups | Synthesis Groups |
| 5:00-5:15 | Peanut Gallery | Peanut Gallery | Peanut Gallery | Peanut Gallery | Peanut Gallery |
| Agenda | Day 11. Geospatial Data | Day 12. Geospatial analysis and Algorithmic Approaches | Day 13. Data Viz | Day 14. Scaling up analysis | Day 15. Group projects! Publications. Group reports |
|---|---|---|---|---|---|
| 8:15-8:30 | Feedback, questions, and discussion | Feedback, questions, and discussion | Feedback, questions, and discussion | Feedback, questions, and discussion | Feedback, questions, and discussion |
| 8:30-9:00 | Intro to GIS - geospatial data concepts (Wasser) | LAB: geospatial analysis (Wasser) | Data Viz and interactive tools (Mecum) | Parallel processing (in R)(Jones) | Group 1 presentation and discussion |
| 9:00-9:30 | Go from an Excel-like set of data to QGIS (Brun) | LAB: geospatial analysis (Wasser) | Data Viz and interactive tools (Mecum) | Parallel processing (in R)(Jones) | Group 1 presentation and discussion |
| 9:30-9:45 | Break | Break | Break | Break | Break |
| 9:45-11:00 | Intro to GIS in R (Wasser & Mecum) | LAB: geospatial analysis (Wasser) | Data Viz and interactive tools (Mecum) | Open Science (Lortie) (10-10:30) Synthesis Groups |
Group 2 presentation and discussion |
| 11:00-12:00 | Intro to GIS in R (Wasser & Mecum) | LAB: geospatial analysis (Wasser) | Perfunctory Python (Brun) (30 mins) | Synthesis Groups | Group 3 presentation and discussion |
| Noon-1:00 | Lunch | Lunch | Lunch | Lunch | Lunch |
| 1:00-1:30 | Publishing maps to the web in R (Mecum) | LAB: NetCDF and HDF5 (Wasser & Mecum) | Synthesis Groups | Synthesis Groups | Post-course assessment |
| 1:30-2:00 | Publication ready maps in R (Mecum) | LAB: NetCDF and HDF5 (Wasser & Mecum) | Synthesis Groups | Synthesis Groups | Discussion: open science for synthesis and course feedback |
| 2:00-2:15 | Break | Break | Break | Break | Break |
| 2:15-5:00 | Synthesis Groups | Synthesis Groups | Synthesis Groups | Synthesis Groups | Adjourn |
| 5:00-5:15 | Peanut Gallery | Peanut Gallery | Peanut Gallery | Peanut Gallery | Celebration |