Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/uscbiostats/software-dev
Coding Standards for the USC Biostats group
https://github.com/uscbiostats/software-dev
hpc r reproducibility reproducible-research standards
Last synced: 3 months ago
JSON representation
Coding Standards for the USC Biostats group
- Host: GitHub
- URL: https://github.com/uscbiostats/software-dev
- Owner: USCbiostats
- Created: 2017-01-13T00:00:44.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2024-06-19T19:15:07.000Z (7 months ago)
- Last Synced: 2024-06-20T08:33:57.492Z (7 months ago)
- Topics: hpc, r, reproducibility, reproducible-research, standards
- Language: HTML
- Size: 74.1 MB
- Stars: 34
- Watchers: 24
- Forks: 7
- Open Issues: 2
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
output:
rmarkdown::github_document:
html_preview: false
---
# Software Development Standards 
This project's main contents are located in the project's [Wiki](wiki#welcome-to-the-software-development-wiki).
# USCbiostats R packages
```{r setup, include=FALSE}
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
```
```{r listing-pkgs, echo = FALSE}
pkgs <- read.csv("packages.csv", comment.char = "#", stringsAsFactors = FALSE)
# Alphabetically ordered
pkgs <- pkgs[order(pkgs$name),,drop=FALSE]
# Checking cran status
pkgs$on_cran <- TRUE
for (i in seq_len(nrow(pkgs))) {
pkg_status <- tryCatch(
httr::GET(sprintf("https://cran.r-project.org/package=%s", pkgs$name[i])),
error = function(e) e
)
# Error fetching a status
if (inherits(pkg_status, "error")) {
pkgs$on_cran[i] <- FALSE
next
}
if (httr::status_code(pkg_status) != 200) {
pkgs$on_cran[i] <- FALSE
next
}
}
dat <- with(pkgs, data.frame(
Name = sprintf(
"[**%s**](%s)", name, ifelse(!is.na(repo) & repo != "", repo, paste0("https://github.com/USCbiostats/", name))
),
Description = paste(
description,
sprintf(
"[](https://CRAN.R-project.org/package=%1$s)",
name
),
sprintf(
"[](https://cran.r-project.org/package=%1$s)",
name
),
sprintf(
"[](https://CRAN.R-project.org/package=%1$s)",
name
)
), stringsAsFactors = FALSE))
test <- with(pkgs, !on_cran & is.na(on_bioc))
dat$Description[!pkgs$on_cran] <- pkgs$description[!pkgs$on_cran]
for (pkg in pkgs$name[which(pkgs$on_bioc)]) {
dat[which(pkgs$name == pkg), "Description"] <-
paste0(pkgs$description[pkgs$name == pkg],
sprintf("[](https://www.bioconductor.org/packages/%s)", pkg),
badger::badge_bioc_download(pkg, "total", "blue", "total"))
}
```
```{r citations, include=FALSE}
regex <- "([0-9,]+)[\\s\\n]+results?[\\s\\n]+\\([\\s\\n]*[0-9]+" #[\\s\\n]+[(][0-9]*[.]?[0-9]+\\s+secs?
dat$Citations <- ""
tot_citations <- 0L
for (i in seq_len(nrow(pkgs))) {
# If no URL, then continue
if (nchar(pkgs$google_scholar[i]) == 0) {
next
}
# Otherwise, take a look at the cictations
address <- pkgs$google_scholar[i]
page <- tryCatch(readLines(address, warn = FALSE), error = function(e) e)
if (inherits(page, "error"))
next
# Removing blocks of bold, italic, etc
page <- gsub("\\<[[:alnum:]_/-]+\\>", "",page, perl = TRUE)
citations <- which(grepl(regex, page, perl = TRUE))
if (!length(citations))
next
citations <- stringr::str_extract(page[citations], "[0-9,]+(?=[\\s\\n]+results?)")
citations <- as.integer(gsub("[,.]", "", citations, perl = TRUE))
tot_citations <- tot_citations + citations
dat$Citations[i] <- sprintf("[%i](%s)", as.integer(citations), address)
}
if (tot_citations == 0L)
stop("There can't be 0 citations! Make sure things are running as expected!")
```
As of `r Sys.Date()`, the packages listed here have been cited **`r tot_citations`** times
(source: Google Scholar).
```{r printing, echo = FALSE}
knitr::kable(dat, row.names = FALSE)
```
To update this list, modify the file [packages.csv](packages.csv). The
`README.md` file is updated automatically using GitHub Actions, so there's no
need to "manually" recompile the README file after updating the list.
# Coding Standards
1. [Coding Standards](wiki#coding-standards)
2. [Software Thinking](wiki/coding-standards.md#software-thinking)
3. [Development Workflow](wiki/coding-standards.md#development-workflow)
4. [Misc](wiki/coding-standards.md#misc)
We do have some direct guidelines developed as issue templates [here](templates).
# Bioghost Server
1. [Introduction](wiki/Bioghost-server.md#introduction)
2. [Setup](wiki/Bioghost-server.md#setup)
3. [Cheat Sheet](wiki/Bioghost-server.md#cheat-sheet)
# HPC in R
* [Parallel computing in R](wiki/HPC-in-R.md#parallel-computing-in-r)
* [parallel](wiki/HPC-in-R.md#parallel)
* [iterators+foreach](wiki/HPC-in-R.md#foreach)
* [RcppArmadillo + OpenMP](wiki/HPC-in-R.md#rcpparmadillo-and-openmp)
# Happy Scientist Seminars
The Happy Scientist Seminars are educational seminars sponsored by Cores C and D of IMAGE, the Biostats Program Project award. This series, the "Happy Scientist" seminar series, is aimed at providing educational material for members of Biostats, both students and faculty, about a variety of tools and methods that might prove useful to them. If you have any suggestions for subjects that you would like to learn about in future, please send email to Paul Marjoram at ([email protected]). Our agenda will be driven by your specific interests as far as is possible.
List of past seminars with material can be found [here](/happy_scientist/).