{"id":15555431,"url":"https://github.com/sckott/mstext","last_synced_at":"2026-01-07T15:07:42.961Z","repository":{"id":140973570,"uuid":"46182995","full_name":"sckott/mstext","owner":"sckott","description":"Manuscript on rOpenSci scholarly text packages","archived":false,"fork":false,"pushed_at":"2015-11-14T16:53:06.000Z","size":0,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-23T23:36:11.549Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sckott.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-11-14T16:52:59.000Z","updated_at":"2015-11-14T23:43:44.000Z","dependencies_parsed_at":"2023-03-13T18:01:47.933Z","dependency_job_id":null,"html_url":"https://github.com/sckott/mstext","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fmstext","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fmstext/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fmstext/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fmstext/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sckott","download_url":"https://codeload.github.com/sckott/mstext/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246131244,"owners_count":20728299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-02T15:09:19.678Z","updated_at":"2026-01-07T15:07:42.917Z","avatar_url":"https://github.com/sckott.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"MS on rOpenSci text pkgs\n======================================\n\n[![Circle CI](https://circleci.com/gh/sckott/mstext.svg?style=svg)](https://circleci.com/gh/sckott/mstext)\n\nMS on rOpenSci text pacakges: `fulltext`, `rcrossref`, `rentrez`, `rplos`, `bmc`, `aRxiv`, etc.\n\nInstall dependencies\n--------------------\n\nInstall the `fulltext`:\n\n```r\ninstall.packages(c('rcrossref', 'rentrez', 'rplos', 'aRxiv', 'fulltext', 'rmarkdown'), dependencies=TRUE)\n```\n\nNote that `rmarkdown` requires `pandoc` (\u003e= 0.12.3) and `pandoc-citeproc` be installed. These ship with the current version of RStudio (`\u003e=0.98`). Additionally, a LaTeX environment is required to generate the output pdf.\n\n\n\nBuild the manuscript\n--------------------\n\n\n```r\nrmarkdown::render(\"manuscript.Rmd\")\n```\n\nor use the `knit2pdf` button in your RStudio console.\n\n\nAlternately: Using Docker\n-------------------------\n\nInstead of installing R packages seperately, you can try out `rgbif`\nby running RStudio in a Docker container.  This (a) avoids having to install\nsoftware dependencies, and (b) avoids altering anything on your local\nlibrary. If the above doesn't work, or just for fun, give this a try.\n\nThe `rgbif` package and all dependencies are installed on the [rocker/ropensci](http://registry.hub.docker.com/u/rocker/ropensci) Docker container.  You will still need all the files from this directory to build the manuscript. Users can decide to run either an R console (accessed through a terminal)\nor an RStudio instance (accessed through the browser) on the container.\n\n\n### Docker Installation\n\nIn a Mac or Windows machine, this will aslo install boot2docker\n(easy point \u0026 click install, ~24 MB). On Linux, this installs\nnatively and we can run everything in the terminal instead of in\nthe boot2docker window.\n([[Mac](https://docs.docker.com/installation/mac/)],\n[[Windows](https://docs.docker.com/installation/windows/),\n[[Linux](https://docs.docker.com/installation)]).\n\n### R console\n\nWith boot2docker running, run `R` on the `rocker/ropensci` image,\nlinking the location of your copy of this directory to\n`/home/rstudio` on the container, setting the container's\nworking directory to the same, and setting user as `rstudio`:\n\n```bash\ndocker run -v /path/to/rgbif:/home/rstudio \\\n  -w /home/rstudio -u rstudio -ti --rm rocker/ropensci R\n```\n\nAt the R prompt, you can use `rmarkdown` to render the manuscript PDF from the `Rmd` file:\n\n```r\nrmarkdown::render('manuscript.Rmd')\n```\n\n`manuscript.pdf` should now be created in the manuscripts directory.\n\n### Using RStudio\n\n1) From the command line (with boot2docker running on Mac/Windows), do:\n\n```bash\nsudo docker run -d -p 8787:8787 rocker/ropensci\n```\n\nThat will take a while to download the image the first time you run it.\n\n2) Once it is done, try:\n\n```bash\nboot2docker ip\n```\n\nthat should return an ip address you can paste into your browser.\n\n3) Add a `:8787` to the end of this address and paste it into your\nbrowser address bar. (e.g. it's probably `http://92.168.59.103:8787`\nbut that can change).\n\n4) You should get the RStudio welcome screen.  you should be able to\nlogin with user/password `rstudio/rstudio`.\n\n5) Clone the `msrgbif` repository from https://github.com/sckott/msrgbif, and you should be good to go as above.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fmstext","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsckott%2Fmstext","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fmstext/lists"}