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‎README.md‎

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Welcome to Advanced Programming in R and HPC! You can find the syllabus
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[here](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/syllabus.md).
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Readings for the week can be found in the GitHub issues associated with
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them.
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Readings for each session can be found in the GitHub issues associated
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with them.
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## Contents
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| Week | Title | Lecture | Lab |
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|:---|:---|:---|:---|
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| 8/20 and 8/22 | Intro to Git + Intro to classes + [quarto](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/quarto.html) ([source](01-git/quarto.qmd)) | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/01-git/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/01-git/lab.qmd)) |
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| 8/27 and 8/29 | R Essentials + [Homework 1](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/01-essentialsSimulations.html) ([source](02-essentials/01-essentialsSimulations.qmd)) | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/02-essentials/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/02-essentials/lab.qmd)) |
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| 9/03 and 9/5 | Debugging and profiling | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/03-debugging-and-profiling/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/03-debugging-and-profiling/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/03-debugging-and-profiling/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/03-debugging-and-profiling/lab.qmd)) |
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| 9/10 and 9/12 | Functions and data.table + [Homework 2](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/homework.html) ([source](04-more-functions-and-datatable/homework.qmd)) | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/04-more-functions-and-datatable/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/04-more-functions-and-datatable/lab.qmd)) |
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| 9/17 and 9/19 | Introduction to C++ | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/05-cpp/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/05-cpp/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/05-cpp/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/05-cpp/lab.qmd)) |
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| 9/24 and 9/26 | C++ in R Deliver a paragraph in abstract mode describing their projects for the midterm. | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/06-rcpp/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/06-rcpp/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/06-rcpp/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/06-rcpp/lab.qmd)) |
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| 10/01 and 10/03 | Parallel Computing | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/07-parallel-computing/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/07-parallel-computing/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/07-parallel-computing/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/07-parallel-computing/lab.qmd)) |
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| 10/08 and 10/10 | Fall Break | | |
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| 10/15 and 10/17 (presentations) | Midterm project [+ Homework 3 (vectorization and Rcpp)](https://UofUEpiBio.github.io/PHS7045-advanced-programming/09-midterm/homework.html) ([source](09-midterm/homework.qmd)) | | |
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| 10/22 and 10/24 | UofU’s CHPC ([CHPC overview slides](10-chpc-week/chpc_overview.pdf), [Linux slides](10-chpc-week/IntroLinux-RClass.pdf), [using R slides](10-chpc-week/using_r_at_chpc.pdf), [Slurm slides](10-chpc-week/RClass-Slurm.pdf)) | | |
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| 10/29 and 10/31 | Slurm + Homework 4 (Slurm) | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/11-slurm-week1/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/11-slurm-week1/slides.qmd)) | |
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| 11/05 and 11/07 | More practice with slurm + [Homework 4](https://UofUEpiBio.github.io/PHS7045-advanced-programming/12-slurm-week2/12-slurm-hw.html) ([source](12-slurm-week2/12-slurm-hw.qmd)) | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/12-slurm-week2/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/12-slurm-week2/slides.qmd)) | |
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| 11/12 and 11/14 | R packages I | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/13-rpkgs-i/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/13-rpkgs-i/slides.qmd)) | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/13-rpkgs-i/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/13-rpkgs-i/lab.qmd)) |
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| 11/19 and 11/21 | R packages II | | |
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| 11/26 and 11/28 (off) | Automatic Reports with GitHub Actions | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/15-autoreport/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/15-autoreport/slides.qmd)) | |
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| 12/03 and 12/05 (hybrid) | Final Prep (Hackathon) | | |
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| 12/10 (pkg) and 12/12 (talk) | Final ([Requirements](https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/02-final.html)) | | |
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| Week | Date | Session | Title | Materials |
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|---:|:---|:---|:---|:---|
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| 1 | 8/25/26 | Lecture | Intro to Git | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/01-git/slides.qmd)) |
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| 1 | 8/27/26 | Lab | Intro to classes | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/01-git/lab.qmd))<br>+ [quarto](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/quarto.html) ([source](01-git/quarto.qmd)) |
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| 2 | 9/1/26 | Lecture | R Essentials | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/02-essentials/slides.qmd)) |
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| 2 | 9/3/26 | Lab | R Essentials | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/02-essentials/lab.qmd))<br>+ [Homework 1](https://UofUEpiBio.github.io/PHS7045-advanced-programming/02-essentials/01-essentialsSimulations.html) ([source](02-essentials/01-essentialsSimulations.qmd)) |
18+
| 3 | 9/8/26 | Lecture | Debugging and profiling | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/03-debugging-and-profiling/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/03-debugging-and-profiling/slides.qmd)) |
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| 3 | 9/10/26 | Lab | Debugging and profiling | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/03-debugging-and-profiling/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/03-debugging-and-profiling/lab.qmd)) |
20+
| 4 | 9/15/26 | Lecture | Functions and data.table | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/04-more-functions-and-datatable/slides.qmd)) |
21+
| 4 | 9/17/26 | Lab | Functions and data.table | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/04-more-functions-and-datatable/lab.qmd))<br>+ [Homework 2](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/homework.html) ([source](04-more-functions-and-datatable/homework.qmd)) |
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| 5 | 9/22/26 | Lecture | Introduction to C++ | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/05-cpp/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/05-cpp/slides.qmd)) |
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| 5 | 9/24/26 | Lab | Introduction to C++ | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/05-cpp/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/05-cpp/lab.qmd)) |
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| 6 | 9/29/26 | Lecture | C++ in R | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/06-rcpp/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/06-rcpp/slides.qmd)) |
25+
| 6 | 10/1/26 | Lab | C++ in R | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/06-rcpp/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/06-rcpp/lab.qmd))<br>Deliver a paragraph in abstract mode describing their projects for the midterm. |
26+
| 7 | 10/6/26 | Break | Fall Break | |
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| 7 | 10/8/26 | Break | Fall Break | |
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| 8 | 10/13/26 | Lecture | Parallel Computing | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/07-parallel-computing/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/07-parallel-computing/slides.qmd)) |
29+
| 8 | 10/15/26 | Lab | Parallel Computing | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/07-parallel-computing/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/07-parallel-computing/lab.qmd)) |
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| 9 | 10/20/26 | Lecture | Midterm project | |
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| 9 | 10/22/26 | Presentations | Midterm project | [Homework 3](https://UofUEpiBio.github.io/PHS7045-advanced-programming/09-midterm/homework.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/09-midterm/homework.qmd)) |
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| 10 | 10/27/26 | Lecture | UofU’s CHPC | [CHPC overview](https://UofUEpiBio.github.io/PHS7045-advanced-programming/10-chpc-week/chpc_overview.pdf)<br>[Linux slides](10-chpc-week/IntroLinux-RClass.pdf), [using R slides](10-chpc-week/using_r_at_chpc.pdf), [Slurm slides](10-chpc-week/RClass-Slurm.pdf) |
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| 10 | 10/29/26 | Lab | Slurm practice | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/10-slurm-practice/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/10-slurm-practice/lab.qmd)) |
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| 11 | 11/3/26 | Lecture | Slurm | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/11-slurm-week1/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/11-slurm-week1/slides.qmd)) |
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| 11 | 11/5/26 | Lab | Slurm | \+ Homework 4 (Slurm) |
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| 12 | 11/10/26 | Lecture | More practice with slurm | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/12-slurm-week2/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/12-slurm-week2/slides.qmd)) |
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| 12 | 11/12/26 | Lab | More practice with slurm | [Homework 4](https://UofUEpiBio.github.io/PHS7045-advanced-programming/12-slurm-week2/12-slurm-hw.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/12-slurm-week2/12-slurm-hw.qmd)) |
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| 13 | 11/17/26 | Lecture | R packages I | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/13-rpkgs-i/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/13-rpkgs-i/slides.qmd)) |
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| 13 | 11/19/26 | Lab | R packages I | [lab](https://UofUEpiBio.github.io/PHS7045-advanced-programming/13-rpkgs-i/lab.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/13-rpkgs-i/lab.qmd)) |
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| 14 | 11/24/26 | Lecture | R packages II | |
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| 14 | 11/26/26 | Off | Thanksgiving recess | |
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| 15 | 12/1/26 | Lecture | Automatic Reports with GitHub Actions | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/15-autoreport/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/15-autoreport/slides.qmd)) |
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| 15 | 12/3/26 | Lab | R packages II | |
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| 16 | 12/8/26 | Hybrid | Final Prep (Hackathon) | |
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| 16 | 12/10/26 | Hybrid | Final Prep (Hackathon) | |
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| 17 | 12/15/26 | Package | Final | |
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| 17 | 12/17/26 | Talk | Final | [Requirements](https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/02-final.html) |
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## Assignment workflow
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‎README.qmd‎

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# PHS 7045: Advanced Programming
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Welcome to Advanced Programming in R and HPC! You can find the syllabus [here](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/syllabus.md). Readings for the week can be found in the GitHub issues associated with them.
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Welcome to Advanced Programming in R and HPC! You can find the syllabus [here](https://github.com/UofUEpiBio/PHS7045-advanced-programming/tree/main/syllabus.md). Readings for each session can be found in the GitHub issues associated with them.
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## Contents
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@@ -17,61 +17,66 @@ library(data.table)
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dat <- fread("pages.csv")
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urlgit <- "https://github.com/UofUEpiBio/PHS7045-advanced-programming/"
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urlraw <- "https://UofUEpiBio.github.io/PHS7045-advanced-programming"
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dat[, has_lecture := file.exists(sprintf("%s/slides.html", id))]
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dat[, has_lecture_source := file.exists(sprintf("%s/slides.qmd", id))]
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dat[, has_lab := file.exists(sprintf("%s/lab.html", id))]
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dat[, has_lab_source := file.exists(sprintf("%s/lab.qmd", id))]
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# Iterating through the weeks
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weeks <- sort(unique(dat$week))
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tab <- NULL
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for (i in 1:nrow(dat)) {
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# Adding the entry to the table
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tab <- rbind(
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tab,
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with(dat[i,,drop=FALSE], data.frame(
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Week = date,
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# Title of the week
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Title = fifelse(
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!is.na(issue),
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sprintf(
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"%s (Issue [%i](%s/issues/%i))",
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name, issue, urlgit, issue
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),
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sprintf("%s", name)
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),
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# Lecture links
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Lecture = if (has_lecture & has_lecture_source) {
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sprintf(
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"[slides](%s/%s/slides.html) ([source](%s/tree/main/%s/slides.qmd))",
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urlraw, id, urlgit, id
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)
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} else {""},
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# Lab links
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Lab = if (has_lab & has_lab_source) {
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sprintf(
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"[lab](%s/%s/lab.html) ([source](%s/tree/main/%s/lab.qmd))",
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urlraw, id, urlgit, id
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)
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} else {""}
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)
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))
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if (!is.na(dat[i,,drop=FALSE]$extra) && (dat[i,,drop=FALSE]$extra != ""))
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tab[nrow(tab),]$Title <- paste(
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tab[nrow(tab),]$Title,
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dat[i,,drop=FALSE]$extra
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urlraw <- "https://UofUEpiBio.github.io/PHS7045-advanced-programming"
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make_url <- function(path, base) {
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if (is.na(path) || path == "") {
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return(NA_character_)
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}
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if (grepl("^https?://", path)) {
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return(path)
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}
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sprintf("%s/%s", base, path)
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}
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make_material <- function(link_text, link, source) {
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if (is.na(link) || link == "") {
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return("")
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}
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out <- sprintf("[%s](%s)", link_text, make_url(link, urlraw))
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if (!is.na(source) && source != "") {
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out <- sprintf(
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"%s ([source](%s))",
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out,
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make_url(source, paste0(urlgit, "tree/main"))
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)
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}
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out
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}
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knitr::kable(tab, row.names = FALSE)
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dat[, title := fifelse(
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!is.na(issue),
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sprintf("%s (Issue [%i](%s/issues/%i))", name, issue, urlgit, issue),
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name
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)]
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dat[, materials := mapply(
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make_material, link_text, link, source, USE.NAMES = FALSE
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)]
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dat[
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!is.na(extra) & extra != "",
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materials := fifelse(
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materials == "",
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extra,
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paste0(materials, "<br>", extra)
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)
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]
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tab <- dat[, .(
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Week = week,
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Date = date,
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Session = session,
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Title = title,
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Materials = materials
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)]
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knitr::kable(tab, row.names = FALSE, escape = FALSE)
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```
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## Assignment workflow
@@ -122,4 +127,3 @@ git push -u origin master
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```
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And you are done!
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