README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---

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

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
options(tibble.print_min = 5, tibble.print_max = 5)
```

# wranglEHR <a href='https://inform-health-informatics.github.io/wranglEHR/'><img src='man/figures/logo.png' align="right" height="139" /></a>

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## Overview

wranglEHR is a data wrangling tool for EMAP. It is designed to run against OMOP CDM 5.3.1. Please see the `R` vignettes for further details on how to use the package to perform the most common tasks:

* `extract()` produces a rectangular table in a "long" format that is suitable for most statistial packages.
* `clean()` cleans the above table in accordance with pre-defined standards (pending)

## Installation

```{r, eval = FALSE}
# install directly from github with
remotes::install_github("inform-health-informatics/wranglEHR")
```

## Usage

More documentation to follow

```{r, message = FALSE, eval = FALSE}
library(wranglEHR)

ctn <- ctn <- DBI::dbConnect(
  RPostgres::Postgres(),
  host = "****", # Host target for the UDS
  port = 5432,
  user = "****",
  password = rstudioapi::askForPassword(),
  dbname = "uds")

# Extract variables.
# Rename on the fly.
# Dynamically set time cadance.
ltb <- extract(
  connection = ctn,
  target_schema = "ops_dev",
  visit_occurrence_ids = 600000:600005,
  concept_names = c(3013502, 44809212),
  relabel = c("spo2", "spo2_target"),
  coalesce_rows = dplyr::first,
  chunk_size = 5000,
  cadance = 1
)

head(ltb)

# Add in bed movement data
ltb <- attach_locations(ctn, ltb)
head(ltb)

# Regularise the underlying time cadance of the table
ltb <- regularise(ltb, cadance = 1)

# Don't forget to switch of the lights after you leave
DBI::dbDisconnect(ctn)
```

## Getting help

If you find a bug, please file a minimal reproducible example on [github](https://github.com/inform-health-informatics/wranglEHR/issues).