README.Rmd

---
output:
  md_document:
    variant: markdown_github
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# tycho2

Author: Eric Marty  
This R package provides a simple wrapper for the [Project Tycho](https://www.tycho.pitt.edu/) 2.0 web API. 

The development of this package was supported by the National Institute of General Medical Sciences 
of the National Institutes of Health under Award Number U01GM110744. The content is solely the 
responsibility of the authors and does not necessarily reflect the official views of the National 
Institutes of Health.

## Project Tycho

Project Tycho is a repository for global health data in a standardized format compliant with FAIR (Findable, Accessible, Interoperable, and Reusable) guidelines. 

Version 2.0 of the database currently contains:

- weekly case counts for 78 notifiable conditions for 50 states and 1284 cities between 1888 and 2014, reported by health agencies in the United States.
- data for dengue-related conditions for 100 countries between 1955 and 2010, obtained from the World Health Organization and national health agencies. 

Project Tycho 2.0 datasets are represented in a standard format registered with FAIRsharing (bsg-s000718) and include standard SNOMED-CT codes for reported conditions, ISO 3166 codes for countries and first administrative level subdivisions, and NCBI TaxonID numbers for pathogens. 

Precompiled datasets with DOI's are also available for download directly from the [Project Tycho](https://www.tycho.pitt.edu/).

See <https://www.tycho.pitt.edu/dataset/api/> for complete documentation of the API. 

Project Tycho database, website and API are by:   
[Wilbert van Panhuis](https://www.tycho.pitt.edu/people/person/49/) (Principal Investogator)  
[Donald Burke](https://www.tycho.pitt.edu/people/person/66/) (Principal Investogator)  
[Anne Cross](https://www.tycho.pitt.edu/people/person/50/) (Database Programmer)  
Project Tycho is published under a
[Creative Commons Attribution 4.0 International Public License](http://creativecommons.org/licenses/by/4.0/).

## tycho2 package

* `apicall()` - Helper function to assemble arbitrary web api call URLs from a base URL and query string terms. Returns a URL as a string.
* `tycho2()` - Wrapper for the Tycho 2.0 web API. Calls `apicall()` with Tycho's default base URL and applies some automation to facilitate downloading large datasets with a single call. Returns a dataframe.