From 14984500584cc8f352b705f1a219a22c5cca7e65 Mon Sep 17 00:00:00 2001 From: nrosed Date: Wed, 16 Mar 2022 14:40:04 -0600 Subject: [PATCH 1/2] updated citeproc to pandoc-citeproc and now DOCx and citations work --- build/pandoc/defaults/common.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/pandoc/defaults/common.yaml b/build/pandoc/defaults/common.yaml index bfa5d97..12c0c34 100644 --- a/build/pandoc/defaults/common.yaml +++ b/build/pandoc/defaults/common.yaml @@ -6,7 +6,7 @@ filters: - pandoc-eqnos - pandoc-tablenos - pandoc-manubot-cite -- citeproc +- pandoc-citeproc wrap: preserve metadata: csl: build/assets/style.csl From 5159ad96fefdc1c73eedc84f7d2940f5459bfcc4 Mon Sep 17 00:00:00 2001 From: nrosed Date: Wed, 16 Mar 2022 14:40:32 -0600 Subject: [PATCH 2/2] seperated the data and resources section into two sections Data Availability and Code availability --- content/06.resources.md | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/content/06.resources.md b/content/06.resources.md index ad344fe..4feccaf 100644 --- a/content/06.resources.md +++ b/content/06.resources.md @@ -1,14 +1,20 @@ -### Data and Resource availability +### Data availability + +Due to copyright, we are unable to provide the unprocessed scraped data used in this analysis. +To ensure reproducability without violating copyright, we provide the word frequencies for each news article, the coreNLP output, all analyzed names with an article identifier, as well as any other associated data used in the analyses such as quotes and citations. +We provide all of this data on [github](https://github.com/greenelab/nature_news_disparities/tree/main/data). +We also provide data descriptions in our github README, under the header "Quick data folder overview". + + +### Code availability This manuscript was written using Manubot [@doi:10.1371/journal.pcbi.1007128] and is available on github: [manuscript repository link](https://github.com/greenelab/nature_news_manuscript). All code and metadata is also available on github, [full analysis repository link](https://github.com/greenelab/nature_news_disparities), under a BSD 3-Clause License. The code to generate all main and supplemental figures are available as R markdown documents within our main analysis github, in the following subfolder: [notebooks](https://github.com/greenelab/nature_news_disparities/tree/main/figure_notebooks). -Due to copyright, we are unable to provide the scraped data used in this analysis. -However, scraping code is available on our main analysis github, in the following subfolder: [scraper](https://github.com/greenelab/nature_news_disparities/tree/main/nature_news_scraper). -To ensure reproducability without violating copyright, we provide the word frequencies for each news article and the coreNLP output. -Furthermore, we provide a docker image that can re-run the analysis pipeline using intermediate, pre-processed data and produce all the main and supplemental figures. +We provide a docker image that can re-run the analysis pipeline using intermediate, pre-processed data and produce all the main and supplemental figures. To re-run the entire pipeline (including scraping), the docker image contains all necessary packages and code. +Scraping code is available on our main analysis github, in the following subfolder: [scraper](https://github.com/greenelab/nature_news_disparities/tree/main/nature_news_scraper). The shell scripts to re-run the entire analysis are provided in the README file in the github repository.