From e85556ba4e31c5d5ce742b9292330902beec419c Mon Sep 17 00:00:00 2001 From: Christopher Cole Date: Sun, 23 Oct 2016 12:00:51 -0400 Subject: [PATCH 1/4] Update README.md --- README.md | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/README.md b/README.md index aeb7cb3..5b0f243 100644 --- a/README.md +++ b/README.md @@ -76,23 +76,17 @@ Q: **What if I don't have my text in R, but instead as a text or PDF file?** Q: **Installation from CRAN is not working and it says something about `slam`, what's going on?** -Newer versions of the `tm` package, which is a dependency of `goldi` require a package named `slam` which needs to be compiled from Fortran. Try the following, and if it doesn't work, raise an issue on the repository and we'll get it fixed! - +> A: Newer versions of the `tm` package, which is a dependency of `goldi` require a package named `slam` which needs to be compiled from Fortran. Try the following, and if it doesn't work, raise an issue on the repository and we'll get it fixed! Type the following into terminal (on Mac OSX): - ```sh curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C / ``` - Install `slam`: - ```R install.packages("slam") ``` - Reinstall `goldi`: - ```R install.packages("goldi") ``` From 173e6f1c3f8b1c30b4dd2fb008a2bbae68a5ae56 Mon Sep 17 00:00:00 2001 From: Christopher Cole Date: Sun, 23 Oct 2016 12:21:45 -0400 Subject: [PATCH 2/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5b0f243..bc90974 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ Status: | Branch | Travis-CI | Appveyor | Coverage | CRAN | Downloads | Publication | | :--- | :---: | :---: | :--: | :---: | :---: | :---: | | `master` | ![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=master) | ![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=master)](https://codecov.io/github/Chris1221/goldi?branch=master) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/goldi) | [bioRχiv](http://biorxiv.org/content/early/2016/09/05/073460) | -| `devel` |![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=devel) | [![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true)](https://ci.appveyor.com/project/Chris1221/miner) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=devel)](https://codecov.io/github/Chris1221/goldi?branch=devel) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/goldi) |
| +| `devel` |![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=devel) | [![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true)](https://ci.appveyor.com/project/Chris1221/miner) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=devel)](https://codecov.io/github/Chris1221/goldi?branch=devel) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/grand-total/heatmaply?color=yellowgreen) |
| -------------------------------- ### Overview From 00b38722c518bf6903183b4e13fa72bc0a097c2b Mon Sep 17 00:00:00 2001 From: Christopher Cole Date: Sun, 23 Oct 2016 12:22:11 -0400 Subject: [PATCH 3/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bc90974..7eae212 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ Status: | Branch | Travis-CI | Appveyor | Coverage | CRAN | Downloads | Publication | | :--- | :---: | :---: | :--: | :---: | :---: | :---: | | `master` | ![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=master) | ![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=master)](https://codecov.io/github/Chris1221/goldi?branch=master) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/goldi) | [bioRχiv](http://biorxiv.org/content/early/2016/09/05/073460) | -| `devel` |![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=devel) | [![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true)](https://ci.appveyor.com/project/Chris1221/miner) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=devel)](https://codecov.io/github/Chris1221/goldi?branch=devel) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/grand-total/heatmaply?color=yellowgreen) |
| +| `devel` |![Build Status](https://travis-ci.org/Chris1221/goldi.svg?branch=devel) | [![Build status](https://ci.appveyor.com/api/projects/status/v64oe85q29btxln9?svg=true)](https://ci.appveyor.com/project/Chris1221/miner) | [![codecov.io](https://codecov.io/github/Chris1221/goldi/coverage.svg?branch=devel)](https://codecov.io/github/Chris1221/goldi?branch=devel) | ![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/goldi) | ![](http://cranlogs.r-pkg.org/badges/grand-total/goldi) |
| -------------------------------- ### Overview From 0dc61b1dc443fc5ddd848b09bf23e34620f34d07 Mon Sep 17 00:00:00 2001 From: Christopher Cole Date: Sun, 30 Oct 2016 15:34:35 -0400 Subject: [PATCH 4/4] Update README.md --- README.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/README.md b/README.md index 7eae212..df02a71 100644 --- a/README.md +++ b/README.md @@ -106,5 +106,17 @@ Q: **I am looking for a project to work on with `goldi`, do you have any ideas?* Q: **Nothing is working, who can I complain to?** > A: Please raise an issue on this repository, that's most likely to get answered. +### Citation +Cole, Christopher B., et al. "Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi." bioRxiv (2016): 073460. +``` +@article{cole2016semi, + title={Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi}, + author={Cole, Christopher B and Patel, Sejal and French, Leon and Knight, Jo}, + journal={bioRxiv}, + pages={073460}, + year={2016}, + publisher={Cold Spring Harbor Labs Journals} +} +```