https://github.com/thomased/spec.vis

A database/R data package of photoreceptor absorbance and ocular transmission spectra and their metadata
https://github.com/thomased/spec.vis

database modelling r vision

Last synced: 3 months ago
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A database/R data package of photoreceptor absorbance and ocular transmission spectra and their metadata

• Host: GitHub
• URL: https://github.com/thomased/spec.vis
• Owner: thomased
• Created: 2019-04-15T02:50:57.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-04-17T09:42:22.000Z (about 7 years ago)
• Last Synced: 2025-04-08T16:55:20.509Z (over 1 year ago)
• Topics: database, modelling, r, vision
• Language: R
• Homepage:
• Size: 4.25 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

          

# `spec.vis`

[![Project Status: WIP – Initial development is in progress, but there

has not yet been a stable, usable release suitable for the

public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

[![cran

version](https://www.r-pkg.org/badges/version-ago/spec.vis)](https://cran.r-project.org/package=spec.vis/)

[![Build

Status](https://travis-ci.org/thomased/spec.vis.svg?branch=master)](https://travis-ci.org/thomased/spec.vis/)

[![Coverage

status](https://codecov.io/gh/thomased/spec.vis/branch/master/graph/badge.svg)](https://codecov.io/github/thomased/spec.vis?branch=master)

[![cran

downloads](https://cranlogs.r-pkg.org/badges/grand-total/spec.vis)](https://cran.r-project.org/package=spec.vis/)

## Spectral sensitivity data package

`spec.vis` is a mini-database and R data package of receptor absorbance

and ocular transmission spectra with metadata, useful for

visual/colorspace modelling among other things. It currently contains

**410 spectra** from **119 species**.

## Installation

To download the development version of `spec.vis`, you can:

  - use the [`remotes`](https://github.com/r-lib/remotes) package:

``` r

# install.packages("remotes")

remotes::install_github("thomased/spec.vis")

```

  - download files from GitHub and install using `$R CMD INSTALL` or,

    from within R:

``` r

install.packages(path, type = "source", repos = NULL)

```

## Browsing and searching spectra

The entire database can be loaded into memory by simply calling

`data(specvis_spectra)`, along with the metadata `data(specvis_meta)`

and dictionary `data(specvis_dict)`.

Alternately, the `specvis_search()` function allows you to query the

available data and return a select subset based on search terms

(e.g. `specvis_search(genus == 'bombus')`), with the option of

returning either raw spectra or metadata via the `return.spectra`

argument.

Finally, if you’re not an `R` person, the ‘database’ boils down to a few

text files located in the `data.raw/` directory, which you’re free to

download and use as you please.

## Example

    # Load packages

    library(spec.vis)

    library(pavo)

    

    # Grab some spectra

    apis <- specvis_search(genus == 'apis', species == 'mellifera', return.spectra = TRUE)

    canis <- specvis_search(genus == 'canis', species == 'familiaris', return.spectra = TRUE)

    bluetit <- specvis_search(genus == 'cyanistes', species == 'caeruleus', return.spectra = TRUE)

    

    # Plot them

    par(mfrow=c(1,3))

    plot(as.rspec(canis), main = 'Canis familiaris', ylab = 'Absorbance', xlab = '')

    plot(as.rspec(apis), ylab = '', main = 'Apis mellifera (f)')

    plot(as.rspec(bluetit), ylab = '', main = 'Cyanistes caeruleus', xlab = '')



## Contributing

Contributions of spectra to the package are most welcome. There are a

few ways to do so, from most- to least-involved:

  - **via pull request**

      - Install the `spec.vis` package in the usual manner.

      - Fork and clone the package repository.

      - Append your spectra to the `data-raw/specvis_spectra.csv` file,

        and complete all metadata fields in the

        `data-raw/specvis_meta.csv` file. Spectra should follow the

        naming convention `_.`, where

        `` begins at 1 and proceeds from the shortest- to

        longest- wavelength sensitive receptor.

      - Run the function `specvis_rebuild()` to rebuild the database

        (i.e. to save the raw data as `.rda` files.

      - Commit and push your changes, and submit a pull request.

  - **via email, v1**

      - Take a look at the structure of the package’s spectral data

        (`data(specvis_spectra)`) and metadata (`data(specvis_meta)`).

      - [Email me](mailto:thomas.white@sydney.edu.au) your data in as

        similar a format as possible (but I’ll take anything).

  - **via email, v2**

      - [Email me](mailto:thomas.white@sydney.edu.au) a paper containing

        data that you’d like added (containing either lambda-max values

        or plotted absorbance curves, at a minimum).

## Citing

If you find the package useful, please cite the original data

source(s)and the `spec.vis` package (see `citation("spec.vis")` for the

reference).