README.Rmd

---
title: "fizzr: A tidy port of PhysioScripts"
output: github_document
bibliography: fizzr.bib
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, error = FALSE, message = FALSE)
```

# fizzr <img src="man/figures/fizzr_sticker_small.png" align="right" />

***DISCLAIMER*** Very much a work in progress!

The `fizzr` package (*phys*iological analysis in *r*) is a tidy implementation/port
of the `PhysioScripts` suite of functions, originally published by @christie2013physioscripts.
Further documentation and relevant publication can be found online in the
journal [*Behavioral Research Methods*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767411/).

The original `.RData` file for the `PhysioScripts` package is included in the `data` folder.
However, all of these original functions have been transferred to the package as "legacy"
functions that are still callable (as of now).

## Installing

    devtools::install_github('d-bohn/fizzr')
    library(fizzr)

## Browsing

Each function is being re-evaluated for 'tidiness', and then ported (slowly) to this package.
If you would like to browse the original `PhysioScripts` suite of functions that
will be available once this package is finished, you can do so by:

    library(fizzr)
    ls('package:fizzr')
    
## Timeline/Steps
1). Import all of the `PhysioScripts` functions "as is" into the `fizzr` package (complete)

2). Tidy and re-write the functions

  - Clean/format code according to [style guide](http://adv-r.had.co.nz/Style.html)
  
  - Add documentation to separate files

  - Remove ability to use interactive file selection
  
      - Remove dependency for `tcltk`
      
      - Remove unnecessary interactive functions (e.g., `confirm.file.replace`)
  
  - Replace `.` with `_` to emulate tidy logic
  
  - Alter code to allow "pipe-able" chains

3). Deploy version 1.0 with example data

## Currently 'tidied' Functions
So far, the following functions are be called directly from the package without having to
load the `PhysioScripts` suite:

- `process_ecg()`

# Motivation and Rationale
The current motivation for porting these functions to a new package is three-fold.
First, `PhysioScripts` is no longer maintained by the original author(s). Providing
appropriate documentation and package structure will allow for the community to easily
add to, modify, and continue development on this package.

Second, `R` lacks an intuitive and straightforward package to do physiological data
pre-processing. While the functions provided by `PhysioScripts` are meant to be an
end-to-end solution, most of the currently ported functions are used for
pre-processing heart rate data. The pre-processed data can then passed to
other packages that require cleaned data (e.g., [`RHRV`](http://rhrv.r-forge.r-project.org/)).

Finally, porting code that you did not write yourself is an excellent learning
opportunity for working with second-hand code and package building. Creating
a package of functions from original code that both maintains its functionality
while also fitting into a larger ecosystem (e.g., the tidyverse) is a great
learning exercise. One immediate change from `PhysioScripts` that I made was
renaming functions to fit the "underscore" naming convention often used in
the tidy ecosystem. This convention is desirable over the "period" naming
convention for a number of reasons, one of which being that periods are 
used in `python` to denote "within", much like the `$` operator in `R`.

# References