simplexity
Hopefully taking out the complexity of using the simplex: functions to generate, manipulate and plot data on the simplex
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
Keywords
Repository
Hopefully taking out the complexity of using the simplex: functions to generate, manipulate and plot data on the simplex
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Topics
Metadata Files
README.md
simplexity package
Hopefully taking out the complexity of using the simplex.
The simplexity package contains functions to generate, manipulate and plot data on the simplex
Getting started
Installation
(platform independent) If you have devtools installed you can use:
r
library(devtools) # see https://www.r-project.org/nosvn/pandoc/devtools.html
devtools::install_github('tystan/simplexity') # see DESCRIPTION file for required and suggested packages
If you don't have devtools installed but are using Windows, you can download and install the below zip file:
Loading and using simplexity
```r library(simplexity)
now package loaded, see help file to run example
?mksimplexgrid
or create an example 4-simplex plot
example("plotfourcomp", package = "simplexity") ```
Example usage
```r
create a grid of evenly spaced simplex values
number of cores = 1 faster for small computations
remove observations that are on the edge of the simplex (rm_edges = TRUE)
grid4simplex <- mksimplexgrid(4, 0.2, nc = 1, rmedges = TRUE) colnames(grid4simplex) <- paste0("comp", 1:ncol(grid4simplex)) grid_4simplex
comp1 comp2 comp3 comp4
[1,] 0.2 0.2 0.2 0.4
[2,] 0.2 0.2 0.4 0.2
[3,] 0.2 0.4 0.2 0.2
[4,] 0.4 0.2 0.2 0.2
simulate a fictitious response variable based on 4-simplex ilrs
y <- simplextoilr(grid_4simplex) %*% matrix(c(-1, 1, 0.5), ncol = 1) colnames(y) <- "outcome"
outcome
[1,] -0.3279463
[2,] 0.1621827
[3,] 0.7660467
[4,] -0.6002831
add the response variable to the simplex data for plotting
grid4simplex <- as.data.frame(cbind(y, grid4simplex))
this is an interactive/movable plotly 3D scatterplot
plotfourcomp(grid_4simplex, "comp1", "comp2", "comp3", "comp4", col = "outcome")
```
Owner
- Name: Ty Stanford
- Login: tystan
- Kind: user
- Location: Adelaide, Australia
- Website: https://people.unisa.edu.au/Ty.Stanford/
- Repositories: 6
- Profile: https://github.com/tystan
(Bio)statistician
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: simplexity
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Ty
family-names: Stanford
email: tystan@gmail.com
orcid: 'https://orcid.org/0000-0002-8570-5493'
identifiers:
- type: doi
value: 10.5281/zenodo.7943409
description: v0.1.1
repository-code: 'https://github.com/tystan/simplexity'
abstract: >-
Hopefully taking out the complexity of using the simplex -
functions to generate, manipulate and plot data on the
simplex
keywords:
- 'compositional-data'
- simplex
- plotting
- R
license: GPL-2.0
commit: e6043c6
version: v0.1.1
date-released: '2023-05-17'
GitHub Events
Total
- Release event: 1
- Watch event: 1
- Push event: 3
- Create event: 1
Last Year
- Release event: 1
- Watch event: 1
- Push event: 3
- Create event: 1
Dependencies
- GGally * imports
- ParallelLogger * imports
- doParallel * imports
- dplyr * imports
- foreach * imports
- gMOIP * imports
- geometry * imports
- ggplot2 * imports
- parallel * imports
- plotly * imports
- purrr * imports
- viridisLite * imports
- deltacomp * suggests
- testthat * suggests