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Add _pkgdown.yml with echoverse dark theme and improve vignette
Add pkgdown site config with organized reference sections and echoverse dark theme. Add has_internet() guards to all vignette API calls so the vignette builds offline without errors. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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‎_pkgdown.yml‎

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url: https://rajlabmssm.github.io/echogithub/
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template:
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bootstrap: 5
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bslib:
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bg: "#1a2744"
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fg: "#e8f4f4"
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primary: "#4ecdc4"
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secondary: "#3a8d8c"
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success: "#2ee8d6"
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info: "#5bc0be"
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code-bg: "#d6e4ee"
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code-color: "#1a2744"
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border-color: "#2a4060"
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link-color: "#4ecdc4"
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link-hover-color: "#2ee8d6"
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font-size-base: "1rem"
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includes:
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in_header: |
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<style>
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.navbar {
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background-color: #162038 !important;
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border-bottom: 2px solid #4ecdc4;
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}
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.navbar-brand, .nav-link { color: #e8f4f4 !important; }
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.nav-link:hover { color: #2ee8d6 !important; }
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.nav-link.active { color: #2ee8d6 !important; border-bottom: 2px solid #2ee8d6; }
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pre {
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background-color: #d6e4ee !important;
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color: #1a2744 !important;
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border: none !important;
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border-radius: 12px;
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margin: 0;
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padding: 0.8em 1em;
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}
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code { color: #1a6b68 !important; border: none !important; }
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pre code { color: #1a2744 !important; border: none !important; background: transparent !important; }
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pre code span { border: none !important; background: transparent !important; }
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.table { color: #e8f4f4 !important; }
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.table-striped > tbody > tr:nth-of-type(odd) > * {
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background-color: rgba(78, 205, 196, 0.05) !important;
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color: #e8f4f4 !important;
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}
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.table-striped > tbody > tr:nth-of-type(even) > * {
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background-color: transparent !important;
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color: #e8f4f4 !important;
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}
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.table > thead { border-bottom: 2px solid #4ecdc4; }
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h1, h2, h3, h4, h5, h6 { color: #4ecdc4 !important; }
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a { color: #5bc0be; }
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a:hover { color: #2ee8d6; }
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.card { background-color: #1e3050; border-color: #2a4060; }
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.footer { background-color: #162038 !important; border-top: 1px solid #2a4060; }
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.page-header { border-bottom: 2px solid #3a8d8c; }
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.sourceCode {
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background-color: #d6e4ee !important;
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border: 1px solid #3a8d8c;
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border-radius: 12px !important;
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overflow: hidden;
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}
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.sourceCode code span,
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.sourceCode code a {
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border: none !important;
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outline: none !important;
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box-shadow: none !important;
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background: transparent !important;
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}
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</style>
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navbar:
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structure:
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left: [intro, reference, articles, news]
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right: [search, github]
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components:
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github:
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icon: fa-github
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href: https://github.com/RajLabMSSM/echogithub
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articles:
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- title: Getting started
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contents:
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- echogithub
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reference:
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- title: GitHub repository queries
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desc: Functions for querying GitHub repository metadata and content
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contents:
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- github_branches
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- github_code
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- github_commits
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- github_files
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- github_files_download
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- github_metadata
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- github_permissions
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- github_repositories
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- github_traffic
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- github_user_events
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- github_workflows
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- title: GitHub dependencies
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desc: Discover package dependencies and reverse dependencies
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contents:
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- github_dependencies
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- github_dependents
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- title: GitHub Pages
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desc: Query and scrape GitHub Pages websites
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contents:
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- github_pages
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- github_pages_files
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- github_pages_vignettes
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- title: DESCRIPTION file utilities
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desc: Extract and parse R package DESCRIPTION files
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contents:
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- description_extract
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- add_owner_repo
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- title: R package repositories
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desc: Query and compare R packages across CRAN, Bioconductor, and GitHub
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contents:
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- r_repos
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- r_repos_data
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- r_repos_downloads
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- r_repos_opts
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- r_repos_upset_queries

‎vignettes/echogithub.Rmd‎

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---
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title: "echogithub: Getting started"
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author: "<h4>Author: <i>Brian M. Schilder</i></h4>"
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title: "echogithub: Getting started"
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author: "<h4>Author: <i>Brian M. Schilder</i></h4>"
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date: "<h4>Most recent update: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
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output:
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BiocStyle::html_document
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vignette: >
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%\VignetteIndexEntry{echogithub}
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%\VignetteIndexEntry{echogithub}
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%\usepackage[utf8]{inputenc}
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%\VignetteEngine{knitr::rmarkdown}
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---
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```{r setup}
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```{r setup, include = FALSE}
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library(echogithub)
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has_internet <- function() {
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tryCatch({
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con <- url("https://github.com", open = "r")
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close(con)
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TRUE
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}, error = function(e) FALSE)
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}
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```
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# GitHub branches
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Easily find all available branches for a given GitHub repo.
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```{r}
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```{r, eval = has_internet()}
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branches <- echogithub::github_branches(owner = "RajLabMSSM",
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repo = "echolocatoR")
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print(branches)
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## Check
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You can also check whether a particular branch exists.
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By default, `github_branches()` interprets "master" and "main" as synonymous and
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By default, `github_branches()` interprets "master" and "main" as synonymous and
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returns whichever one actually exists.
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```{r}
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branches <- echogithub::github_branches(owner = "RajLabMSSM",
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repo = "echolocatoR",
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```{r, eval = has_internet()}
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branches <- echogithub::github_branches(owner = "RajLabMSSM",
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repo = "echolocatoR",
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branch = "main")
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print(branches)
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```
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# GitHub files
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# GitHub files
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`github_files()` lets you easily:
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1. Search any GitHub repo
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(that you have access to) for files.
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2. Filter those files by a *regex* `query`,
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3. Download those files to your local compute
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(can increase `nThread` to speed up download via parallelization).
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*NOTE*:
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To search your private repos, make sure you
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GitHub token is supplied to the `token` argument, or is saved as in your
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*~.Renviron* file, e.g.: `GITHUB_TOKEN=<token_here>`
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1. Search any GitHub repo (that you have access to) for files.
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2. Filter those files by a *regex* `query`.
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3. Download those files to your local computer
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(can increase `nThread` to speed up download via parallelisation).
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*NOTE*:
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To search your private repos, make sure your
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GitHub token is supplied to the `token` argument, or is saved in your
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*~/.Renviron* file, e.g.: `GITHUB_TOKEN=<token_here>`
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## Search / filter / downlaod
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## Search / filter / download
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```{r}
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files <- echogithub::github_files(owner = "RajLabMSSM",
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```{r, eval = has_internet()}
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files <- echogithub::github_files(owner = "RajLabMSSM",
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repo = "Fine_Mapping_Shiny",
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query = ".md$",
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ignore.case = TRUE,
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# GitHub Pages
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There are several functions to searching GitHub Pages websites associated
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There are several functions for searching GitHub Pages websites associated
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with specific GitHub repos.
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## Find GitHub Pages URL
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First, since not all GitHub repos use GitHub Pages, we should find out
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whether the one we are interested in exists.
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First, since not all GitHub repo have use GitHub Pages, we should find out
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whether the one we're interested in exist.
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```{r}
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ghpages_url <- echogithub::github_pages(owner ="RajLabMSSM",
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```{r, eval = has_internet()}
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ghpages_url <- echogithub::github_pages(owner = "RajLabMSSM",
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repo = "echolocatoR")
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print(ghpages_url)
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```
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If it doesn't exist, the function will simply return `NULL` when you set
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`error=FALSE`.
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If it does not exist, the function will simply return `NULL` when you set
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`error = FALSE`.
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```{r}
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ghpages_null <- echogithub::github_pages(owner ="RajLabMSSM",
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repo = "Fine_Mapping_Shiny",
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error = FALSE)
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```{r, eval = has_internet()}
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ghpages_null <- echogithub::github_pages(owner = "RajLabMSSM",
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repo = "Fine_Mapping_Shiny",
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error = FALSE)
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print(ghpages_null)
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```
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## Find vignettes
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`github_pages_vignettes` allows you to easily gather all vignettes
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`github_pages_vignettes` allows you to easily gather all vignettes
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across multiple GitHub Pages websites at once.
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### As `data.table`
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```{r}
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vdt <- echogithub::github_pages_vignettes(owner = c("RajLabMSSM","neurogenomics"),
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repo = c("echodata","MungeSumstats"))
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```{r, eval = has_internet()}
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vdt <- echogithub::github_pages_vignettes(
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owner = c("RajLabMSSM", "neurogenomics"),
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repo = c("echodata", "MungeSumstats")
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)
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knitr::kable(utils::head(vdt))
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```
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### As table of contents
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You can also use the `as_toc=TRUE` argument to turn the vignettes `data.table`
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into an HTML Table of Contents (TOC).
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You can also use the `as_toc = TRUE` argument to turn the vignettes
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`data.table` into an HTML Table of Contents (TOC).
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```{r, results='asis'}
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toc <- echogithub::github_pages_vignettes(owner = c("RajLabMSSM","neurogenomics"),
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repo = c("echodata","MungeSumstats"),
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as_toc = TRUE)
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```{r, results='asis', eval = has_internet()}
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toc <- echogithub::github_pages_vignettes(
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owner = c("RajLabMSSM", "neurogenomics"),
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repo = c("echodata", "MungeSumstats"),
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as_toc = TRUE
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)
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```
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# *DESCRIPTION* files
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*DESCRIPTION* files contains essential information about each R package.
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However finding and importing them is not always straightforward
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*DESCRIPTION* files contain essential information about each R package.
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However, finding and importing them is not always straightforward
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(e.g. when the package is not yet installed).
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`echogithub::description_extract` searches a variety of sources
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(e.g. local files, local installations, GitHub) to find the correct
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`echogithub::description_extract` searches a variety of sources
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(e.g. local files, local installations, GitHub) to find the correct
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*DESCRIPTION* file and import it into the easy-to-use `description` format.
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It then parses it to extract the relevant information.
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## Find and extract
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`description_extract` then takes that object and extracts and parses
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`description_extract` takes that object and extracts and parses
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just the fields you need, returning them as a named list.
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```{r}
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res <- echogithub::description_extract(refs = c("RajLabMSSM/echolocatoR",
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"RajLabMSSM/echogithub",
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"RajLabMSSM/rworkflows"))
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```{r, eval = has_internet()}
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res <- echogithub::description_extract(
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refs = c("RajLabMSSM/echolocatoR",
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"RajLabMSSM/echogithub",
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"RajLabMSSM/rworkflows")
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)
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methods::show(res)
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```
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# Session Info
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# Session Info
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<details>
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<details>
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```{r Session Info}
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utils::sessionInfo()
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```
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</details>
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</details>
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<hr>
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