EndoMineR for the extraction of endoscopic and associated pathology data from medical reports

EndoMineR for the extraction of endoscopic and associated pathology data from medical reports - Published in JOSS (2018)

https://github.com/ropensci/endominer

Keywords

Repository

Endoscopic and Pathological data extraction for various endo-pathological data extraction

README.Rmd

---
output: github_document
---


[![Build Status](https://travis-ci.org/sebastiz/EndoMineR.svg?branch=master)](https://travis-ci.org/sebastiz/EndoMineR)
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```{r, echo = FALSE}
library(pander)
library(EndoMineR)
library(here)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```


This package has undergone a major revision to make it much more user friendly. THe documentation has been updated to reflect this. I am always happy to hear of any feedback, positive and negative.

## **Aims of EndoMineR**

The goal of EndoMineR is to extract as much information as possible from free or semi-structured endoscopy reports and their associated pathology specimens.  A full tutorial can be found [here](https://docs.ropensci.org/EndoMineR/articles/EndoMineR.html)

## Installation

You can install EndoMineR from github with:

```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github("ropenSci/EndoMineR")
```

If you dont have access to github, then download the zip and change the working dirctory to the place you have downloaded it, then do

```{r gh-installation2, eval = FALSE}
setwd("C:/Users/Desktop/")

#On windows you cand cd to change the directory or us pushd to create a temporary directory indtead of cd and then setwd to the temporary directory
unzip("EndoMineR.zip")
file.rename("EndoMineR.zip-master", "EndoMineR.zip")
shell("R CMD build EndoMineR.zip")

#Then install the resulting tarball with:

install.packages("EndoMineR_0.2.0.9000.tar.gz", repos = NULL)
```


### How to contribute

Contributions to this project are most welcome. There are just a few small guidelines you need to follow.

#### Submitting a patch

It's generally best to start by opening a new issue describing the bug or feature you're intending to fix. Even if you think it's relatively minor, it's helpful to know what people are working on. Mention in the initial issue that you are planning to work on that bug or feature so that it can be assigned to you.

Follow the normal process of forking the project, and setup a new branch to work in. It's important that each group of changes be done in separate branches in order to ensure that a pull request only includes the commits related to that bug or feature.

The best way to ensure your code is properly formatted is to use lint. Various packages in R provide this.

Any significant changes should almost always be accompanied by tests. The project already has good test coverage, so look at some of the existing tests if you're unsure how to go about it. 

Do your best to have well-formed commit messages for each change. This provides consistency throughout the project, and ensures that commit messages are able to be formatted properly by various git tools.

Finally, push the commits to your fork and submit a pull request. Please, remember to rebase properly in order to maintain a clean, linear git history.


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Owner

JOSS Publication

EndoMineR for the extraction of endoscopic and associated pathology data from medical reports

Published

April 27, 2018

DOI

10.21105/joss.00701

Volume 3, Issue 24, Page 701

Authors

Sebastian S. Zeki
Department of Gastroenterology, St Thomas' Hospital, Westminster Bridge Bridge Road, London SE1 7EH

Editor

Arfon Smith

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