lectures.Rmd

---
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)