Course Material for PM566

The PM566 course website is here. We will be using this website to share all course material including lecture slides, labs, and assignments.

Our class meets at 1pm every Wednesday. Zoom links for each lecture session are available in the course Blackboard.

Latest week’s cross reference

This is an example of web scrapping. We built this program to extract the cross-reference links from a given GitHub issue, including details such as timestamp, the user, and the commit message.

You can download the program here

library(data.table)
library(stringr)

# API access
source("list_cross_ref_api.R", echo=FALSE)

library(httr)
# Setting up the token
if (file.exists("github_app.R")) {
  # See
  # https://github.com/r-lib/httr/blob/cb4e20c9e0b38c0c020a8756db8db7a882288eaf/demo/oauth2-github.r
  # For a detailed example
  source("github_app.R")
  token <- oauth2.0_token(
    endpoint = oauth_endpoints("github"),
    app      = github_app,
    config   = httr::config(connecttimeout = 60)
    )
  token <- httr::config(token = token)
} else {
  token <- NULL
}

# Retrieving all the cross-reference information
ans <- list_cross_ref_api(
  issue = 26,
  config = c(httr::config(connecttimeout=60), token)
  )

# Preparing to print using a nice format
ans[, user := sprintf("[%s](https://github.com/%s)", gsub("/.+", "", repo), repo)]
ans[, link := sprintf("[link](%s)", commit_url)]
setorder(ans, created_at)

# A more concise message
ans[, message := sprintf("%s (%s to this %s) (files: %s)", message, link, type, files)]
knitr::kable(ans[, .(created_at, user, message, type)])

created_at	user	message	type
2020-09-25T20:19:10Z	NA	(link to this NA) (files: )	NA
2020-09-25T20:19:19Z	NA	(link to this NA) (files: )	NA
2020-09-25T20:19:36Z	NA	(link to this NA) (files: )	NA
2020-09-30T22:42:46Z	hankezhe	add Lab 07 step 1 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: 07-lab.Rmd, 07-lab.md)	lab
2020-10-01T00:10:16Z	hankezhe	Lab 07 was done https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: 07-lab.Rmd, 07-lab.md)	lab
2020-10-01T00:10:35Z	gvegayon	Lab 7 done https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: week7/README.Rmd, week7/README.md)	lab
2020-10-01T00:10:43Z	eshkim1021	Finish Lab 7https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: Lab 7.Rmd, Lab-7.md)	lab
2020-10-01T00:11:17Z	bcruiz	Lab7 USCbiostats/PM566#26 (link to this lab) (files: Lab7.Rmd, Lab7.md)	lab
2020-10-01T00:12:12Z	slee2424	lab7 done https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: lab7.Rmd, lab7.md)	lab
2020-10-01T00:15:14Z	HopeW233	adding lab 7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: week7/README.Rmd, week7/README.md)	lab
2020-10-01T00:15:17Z	jiaheche	Lab7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: 07-lab.Rmd, 07-lab.md)	lab
2020-10-01T00:20:50Z	mbolshakova	Lab 7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: Lab-7.md, Lab-7_cache/html/__packages, Lab-7_cache/html/counter-pubmed_af9409d9095e9232821cb2dc029d80d0.RData, Lab-7_cache/html/counter-pubmed_af9409d9095e9232821cb2dc029d80d0.rdb, Lab-7_cache/html/counter-pubmed_af9409d9095e9232821cb2dc029d80d0.rdx, Lab-7_cache/markdown_github/__packages, Lab-7_cache/markdown_github/counter-pubmed_6670a29088ce78b20f5cab969c0ac0b5.RData, Lab-7_cache/markdown_github/counter-pubmed_6670a29088ce78b20f5cab969c0ac0b5.rdb, Lab-7_cache/markdown_github/counter-pubmed_6670a29088ce78b20f5cab969c0ac0b5.rdx)	lab
2020-10-01T00:23:10Z	asuasu95	finish lab7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: 07-lab/07-lab.Rmd, 07-lab/07-lab.md)	lab
2020-10-01T00:25:53Z	MingzhiYe16	lab7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: README.Rmd, README.md)	lab
2020-10-01T00:27:21Z	Luqing521	lab07 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: lab07/07-lab.Rmd, lab07/07-lab.md)	lab
2020-10-01T00:31:17Z	Shan-shan-666	Done lab 7https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: lab/07-lab.Rmd)	lab
2020-10-01T00:35:57Z	RuowenWang123	lab 07 (link to this lab) (files: lab07.Rmd, lab07.md)	lab
2020-10-01T00:35:59Z	ashwathkraj	https://github.com/USCbiostats/PM566/issues/26 (link to this NA) (files: .Rproj.user/DCB78155/sources/prop/80414198, .Rproj.user/DCB78155/sources/s-C976EDB0/31DB5E9C, .Rproj.user/DCB78155/sources/s-C976EDB0/31DB5E9C-contents, .Rproj.user/shared/notebooks/833EAC6E-README/1/DCB78155C976EDB0/chunks.json, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ccku1u4s4ntwu/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ccku1u4s4ntwu/000003.error, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ceg5hyjejvm7s/00000c.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/chunks.json, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cms8o2kwfzep2/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cot3qp8d6t7gn/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/criafkwas143o/000006.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/csetup_chunk/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cva79p0j0386v/000002.csv, pm566-07-lab/README.Rmd, pm566-07-lab/README.html)	NA
2020-10-01T00:39:05Z	ashwathkraj	https://github.com/USCbiostats/PM566/issues/26 lab 7 complete (link to this lab) (files: .Rproj.user/DCB78155/sources/prop/80414198, .Rproj.user/DCB78155/sources/s-C976EDB0/31DB5E9C, .Rproj.user/DCB78155/sources/s-C976EDB0/31DB5E9C-contents, .Rproj.user/shared/notebooks/833EAC6E-README/1/DCB78155C976EDB0/chunks.json, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ccku1u4s4ntwu/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ccku1u4s4ntwu/000003.error, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/ceg5hyjejvm7s/00000c.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/chunks.json, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cms8o2kwfzep2/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cot3qp8d6t7gn/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/criafkwas143o/000006.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/csetup_chunk/000002.csv, .Rproj.user/shared/notebooks/833EAC6E-README/1/s/cva79p0j0386v/000002.csv, pm566-07-lab/README.Rmd, pm566-07-lab/README.html)	lab
2020-10-01T00:41:50Z	Weijia-H	Add files via upload (link to this NA) (files: 07-lab.Rmd, 07-lab.md)	NA
2020-10-01T01:59:39Z	cbegay89	Lab 7 Complete (link to this lab) (files: Week 7/READMELab7.md, Week 7/READMELab7.rmd)	lab
2020-10-01T03:10:18Z	shawnyeusc	lab07 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: Lab07.Rmd)	lab
2020-10-01T03:54:36Z	yina-liu	lab07 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: Lab07-Yina.Rmd, Lab07-Yina.md)	lab
2020-10-01T04:07:30Z	jiqingwu1997	lab 7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: lab7.Rmd, lab7.html)	lab
2020-10-01T07:17:24Z	ameihao	Finalizing lab 7 https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: .DS_Store, lab07.Rmd, lab07.html)	lab
2020-10-01T09:36:26Z	shiyushen	lab07 done https://github.com/USCbiostats/PM566/issues/26 (link to this lab) (files: 07-lab/07-lab.Rmd, 07-lab/07-lab.md)	lab
2020-10-03T04:41:53Z	stephtring	Lab 7 “https://github.com/USCbiostats/PM566/issues/26” (link to this lab) (files: Lab7/README.md)	lab