README.Rmd

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output: github_document
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```{r, include = FALSE}
knitr::opts_chunk$set(
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# `eyeris`: flexible reproducible pupil preprocessing pipelines in R <a href="http://shawnschwartz.com/eyeris/" title="eyeris website"><img src="man/figures/logo.png" align="right" height="139" alt="eyeris website" /></a>

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<!-- The goal of eyeris is to ... -->

## Installation

You can install the development version of eyeris from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("shawntz/eyeris")
```

or

``` r
# install.packages("pak")
pak::pak("shawntz/eyeris")
```

## Example

### the `glassbox()` "prescription" function

This is a basic example of how to use `eyeris` out of the box with our very
*opinionated* set of steps and parameters that one should start out with when
preprocessing pupillometry data. Critically, this is a "glassbox" -- as opposed
to a "blackbox" -- since each step and parameter implemented herein is fully
open and accessible to you. We designed each pipeline step / function to be like
legos -- they are intentionally and carefully designed in a way that allows you
to flexibly construct and compare different pipelines.

We hope you enjoy! -shawn

```{r glassbox-example, fig.dpi=300}
set.seed(32)

library(eyeris)

demo_data <- system.file("extdata", "memory.asc", package = "eyeris")

eyeris_preproc <- glassbox(
  demo_data,
  detrend_data = F,
  lpfilt = list(plot_freqz = T)
)
```

### step-wise correction of pupillary signal
```{r glassbox-plot, echo=TRUE, fig.width=12, fig.height=5, fig.dpi=300}
plot(eyeris_preproc)
```

### final pre-post correction of pupillary signal (raw ➡ preprocessed)
```{r timeseries-plot, echo=TRUE, fig.width=8, fig.height=5, fig.dpi=300}
plot(eyeris_preproc,
     steps = c(1, 5),
     preview_window = c(0, nrow(eyeris_preproc$timeseries)))
```

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# Comments, suggestions, questions, issues?

Please use the issues tab (https://github.com/shawntz/eyeris/issues) to make note of any bugs, comments, suggestions, feedback, etc... all are welcomed and appreciated, thanks!