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effectclass

Interpret effects and visualise uncertainty

https://github.com/inbo/effectclass

Science Score: 44.0%

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Keywords

effect-size fan-chart r r-package r-stats
Last synced: 6 months ago · JSON representation ·

Repository

Interpret effects and visualise uncertainty

Basic Info
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  • Stars: 6
  • Watchers: 7
  • Forks: 1
  • Open Issues: 1
  • Releases: 2
Topics
effect-size fan-chart r r-package r-stats
Created almost 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Zenodo

README.md

effectclass

Project Status: Active – The project has reached a stable, usable state and is being actively developed. Lifecycle: stable GitHub License Release R build status r-universe name r-universe package Codecov test coverage GitHub code size in bytes GitHub repo size <!-- badges: end -->

The effectclass package helps interpreting effects and visualising uncertainty.

It classifies the effects by comparing a coverage interval with a reference, lower and upper threshold. The result is a 10 scale classification of the effect. You can reduced it to a 4 scale classification. effectclass provides stat_effect() and scale_effect() to visualise the effects as points with different shapes.

The Bank of England visualises uncertainty by using a fan plot^[Britton, E.; Fisher, P. & J. Whitley (1998). The Inflation Report Projections: Understanding the Fan Chart. Bank of England Quarterly Bulletin. Retrieved 2019-05-22.]. Instead of displaying a single coverage interval, they recommend to display a bunch of coverage intervals with different levels of transparency.

Installation

You can install the released version of effectclass from GitHub with:

``` r

installation requires the "remotes" package

install.package("remotes")

remotes::install_github("inbo/effectclass") ```

Example

Classifying effect for usage in a table

r library(effectclass) z <- data.frame( effect = c("unknown\neffect", "potential\npositive\neffect", "potential\nnegative\neffect", "no effect", "positive\neffect", "negative\neffect", "moderate\npositive\neffect", "moderate\nnegative\neffect", "strong\npositive\neffect", "strong\nnegative\neffect"), estimate = c( 0, 0, 0, 0, 1, -1, 0.5, -0.5, 1.5, -1.5), lcl = c(-2, -0.9, -2, -0.9, 0.1, -2, 0.1, -0.9, 1.1, -2), ucl = c( 2, 2, 0.9, 0.9, 2, -0.1, 0.9, -0.1, 2, -1.1) ) classification(z$lcl, z$ucl, threshold = c(-1, 1), reference = 0)

Adding a classification to a plot

r library(ggplot2) ggplot(z, aes(x = effect, y = estimate, ymin = lcl, ymax = ucl)) + stat_effect(threshold = c(-1, 1), reference = 0, size = 3)

Creating a fan plot

r z <- data.frame(year = 1990:2019, dx = rnorm(30), s = rnorm(30, 1, 0.05)) z$index <- cumsum(z$dx) library(ggplot2) ggplot(z, aes(x = year, y = index, link_sd = s)) + stat_fan() + geom_line()

Owner

  • Name: Research Institute for Nature and Forest (INBO)
  • Login: inbo
  • Kind: organization
  • Location: Belgium

Open source, data and science initiatives of the Research Institute for Nature and Forest (INBO)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "effectclass: Classification and Visualisation of Effects"
authors:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
keywords:
- classification
- effect size
- uncertainty
- visualisation
contact:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
doi: ~
license: GPL-3.0
repository-code: https://github.com/inbo/effectclass/
type: software
abstract: "Classify effects by comparing the confidence intervals with thresholds."
identifiers:
- type: url
  value: https://inbo.github.io/effectclass/
version: 0.1.5

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Top Authors
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  • wlangera (1)
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  • ThierryO (11)
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  • florisvdh (2)
  • wlangera (1)
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Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • assertthat * imports
  • ggplot2 * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests