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README.Rmd
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README.Rmd
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---
output: github_document
---
```{r knitr.opts, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
```
# nihexporter
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[](https://github.com/rnabioco/nihexporter/actions/workflows/R-CMD-check.yaml)
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The `nihexporter` R package provides a minimal set of data from the [NIH EXPORTER](https://reporter.nih.gov/exporter) database, which contains information on NIH biomedical research funding from 1985-2021.
To keep the package lightweight, many details are omitted but can be easily retrieved from [NIH RePORTER](https://reporter.nih.gov/).
## Installation
Install the package from github with:
``` r
# install.packages('pak')
pak::pkg_install("jayhesselberth/nihexporter")
```
**Note: this is a large data package (>40 Mb)**
## Tables
* `projects`: provides data on funded projects by NIH.
* `project_pis`: links project numbers (`project.num`) to principal investigator IDs (`pi.id`).
* `publinks`: links Pubmed IDs (`pmid`) to project numbers (`project.num`).
* `publications`: provides information for individual publications, including their [Relative Citation Ratio](https://icite.od.nih.gov) values (`rcr`).
* `patents`: links project IDs (`project.num`) to `patent.id`.
* `clinical_studies`: links project IDs to associated [clinical trials](https://clinicaltrials.gov/).
* `project_io`: pre-computed `n.pubs`, `n.patents` and `project.cost` for each `project.num`.
**Note:** [Abstracts](https://exporter.nih.gov/ExPORTER_Catalog.aspx?sid=0&index=1) from NIH EXPORTER are not provided as they significantly increase the size of the package.
## Functions
* `rcr()` retrieves [Relative Citation Ratios](https://icite.od.nih.gov/) and associated information for PubMed IDs.
* `nihexporter_sqlite()` can be used to cache data in a local SQLite database.
## Variables
* `nih.institutes`: 27 NIH institutes in two-letter format
## Resources
+ [`nihexporter` pre-print on bioRxiv](https://biorxiv.org/content/early/2015/12/02/033456)
+ [RePORTER / EXPORTER mailing list archives](https://list.nih.gov/cgi-bin/wa.exe?A0=NIH-REPORT-PUBLIC-L)
+ [Relative Citation Ratio manuscript at PLoS](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002541)