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lectures.Rmd
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lectures.Rmd
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---
title: "Lectures"
---
```{r include = FALSE}
library(tidyverse)
library(stringr)
library(httr)
```
```{r include = FALSE}
# Import schedule
rawdat <- read.csv(file.path("course-admin", "schedule_2024.csv"), stringsAsFactors = FALSE, colClasses = list(course = 'factor', dow = 'factor'))
rawdat$course <- as.factor(rawdat$course)
# Class meetings
rawdat_cm <- rawdat[rawdat$course == "STAT540",]
cdat <- rawdat_cm %>%
mutate(ugly_date = ISOdate(2024, match(month, month.name), day),
date = sprintf("%s %s %s",
dow, months(ugly_date, abbreviate = TRUE),
day),
notes = ifelse(grepl("^lect", lect) & raw_notes != "",
sprintf("%s: %s", lect, raw_notes), raw_notes))
## link to the class page of any class meetings where such exists
req <- GET("https://api.github.com/repos/STAT540-UBC/lectures/git/trees/main?recursive=1")
stop_for_status(req)
filelist <- unlist(lapply(content(req)$tree, "[", "path"), use.names = F)
# now grab pdf & html file names
cmdat <-
data.frame(file = filelist[grepl('^lect.*pdf|^lect.*html', basename(filelist))],
stringsAsFactors = FALSE) %>%
mutate(lect = str_extract(file, "lect[0-9]+")) %>%
mutate(lect = sapply(lect, str_replace, pattern="lect0*([0-9]+)",
replacement="lecture-\\1")) %>%
mutate(type = ifelse(grepl("pdf", file), "pdf", "html")) %>%
pivot_wider(id_cols = lect, names_from = type, values_from = file)
if (nrow(cmdat) >0){
cdat <- cdat %>% left_join(cmdat, by="lect")
}else{
cdat$file <- NA
}
pdf_exists <- grepl("*.pdf", cdat$pdf)
html_exists <- grepl("*.html", cdat$html)
if (length(html_exists) == 0){
if (length(pdf_exists) > 0){
html_exists <- rep(FALSE, length(pdf_exists))
}
}
if (length(pdf_exists) == 0){
if (length(html_exists) > 0){
pdf_exists <- rep(FALSE, length(html_exists))
}
}
# Insert placeholder link to notes
#cdat$notes[pdf_exists] <-
# str_replace(cdat$notes[which(pdf_exists)],
# "(lecture-[0-9]+)|(lecture-[1-9]+)", '<a href="LINK">\\1</a>')
cdat$notes <- gsub("lecture-", "Lecture ", cdat$notes)
cdat$notes[pdf_exists|html_exists] <-
str_replace(cdat$notes[which(pdf_exists|html_exists)],
"(Lecture [0-9]+)|(Lecture [1-9]+)", '[\\1](LINK)')
for (i in seq_along(html_exists)){
if (html_exists[i]){
# Replace placeholder "LINK" with html file names
cdat$notes[i] <- str_replace(cdat$notes[i], "LINK",
paste0("https://stat540-ubc.github.io/lectures/",
cdat$html[i]))
if (pdf_exists[i]){
# Append pdf files
cdat$notes[i] <- paste0(cdat$notes[i],
paste0("\ [(pdf)](https://github.com/STAT540-UBC/lectures/raw/main/",
cdat$pdf[i], ")"))
}
}else if (pdf_exists[i]){
# Replace placeholder "LINK" with pdf file names
cdat$notes[i] <- str_replace(cdat$notes[i], "LINK",
paste0("https://github.com/STAT540-UBC/lectures/raw/main/",
cdat$pdf[i]))
}}
dat_cm <- cdat %>% split(cdat$course)
dat_cm <- lapply(dat_cm, 'rownames<-', NULL)
```
### Class meetings and schedule
**Time** : Tues Thurs 9:00 - 10:30am
**Location**: Building and room number listed on Canvas
```{r results = 'asis', echo = FALSE}
# add readings
sched <- dat_cm[["STAT540"]] %>%
mutate(readings = "") %>%
select(date, readings, notes, instructor)
# lect 1
sched$readings[1] <- "[1](https://stat540-ubc.github.io/syllabus.html)"
# lect 3
sched$readings[3] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect03-eda/README.md)"
# lect 4
sched$readings[4] <- "
[1](http://genomicsclass.github.io/book/pages/populations_and_samples.html),
[2](http://genomicsclass.github.io/book/pages/random_variables.html),
[3](http://genomicsclass.github.io/book/pages/clt_and_t-distribution.html)
"
# lect 5
sched$readings[5] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect05-twoGroup/README.md)"
# lect 6
sched$readings[6] <- "
[1](http://genomicsclass.github.io/book/pages/matrix_notation.html),
[2](http://genomicsclass.github.io/book/pages/matrix_operations.html),
[3](http://genomicsclass.github.io/book/pages/expressing_design_formula.html)
"
# lect 7
sched$readings[8] <- "[1](http://genomicsclass.github.io/book/pages/interactions_and_contrasts.html)"
# lect 8
sched$readings[9] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect08-continuous/README.md)"
# lect 9
sched$readings[10] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect09-multipleTesting/README.md)"
# lect 10
sched$readings[11] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect10-RNAseq/README.md)"
# lect 12
sched$readings[15] <- "[1](https://github.com/STAT540-UBC/lectures/blob/main/lect12-gsea/README.md)"
# print final table
knitr::kable(sched %>%
dplyr::rename(Date=date, "Pre-reading"=readings, Topic=notes, Instructor=instructor),
"html", escape = FALSE) %>%
kableExtra::column_spec(1, width = "6em") %>%
kableExtra::kable_styling(full_width = TRUE)
```
**Supplemental Files**:
* Additional companion notes can be found in the [STAT540-UBC/resources GitHub repo](https://github.com/STAT540-UBC/resources)
* Source files for lectures can be found the [STAT540-UBC/lectures GitHub repo](https://github.com/STAT540-UBC/lectures)