Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary
Last synced: 11 months ago
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Repository
Gaussian processes for Bayesian emulation
Basic Info
- Host: GitHub
- Owner: RobinHankin
- Language: R
- Default Branch: master
- Size: 268 KB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 4
- Releases: 0
Created over 8 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
README.Rmd
---
title: "Gaussian processes for complex code evaluation: the emulator package"
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# 
[](https://cran.r-project.org/package=emulator)
# Overview
To cite the `emulator` package in publications please use Hankin 2005.
The `emulator` package provides R-centric functionality for working
with Gaussian processes. The focus is on approximate evaluation of
complex computer codes. The package is part of the the `BACCO` suite
of software.
# Installation
You can install the released version of `emulator` from [CRAN](https://CRAN.R-project.org) with:
```{r}
# install.packages("emulator") # uncomment this to use the package
library("emulator")
```
The package is maintained on
[github](https://github.com/RobinHankin/emulator).
# The `emulator` package in use
```{r echo = FALSE}
set.seed(0)
options(digits=3)
fish <- c(1,1,4) # roughness scales
var <- 0.3 # variance
real.relation <- function(x){sum( (1:3)*x )} # real relation
val <- latin.hypercube(7,3)
colnames(val) <- c("alpha","beta","gamma")
A <- corr.matrix(val,scales=fish)
d <- as.vector(rmvnorm(n=1,mean=apply(val,1,real.relation),var*A))
```
Suppose we have a complicated computer program which takes three
parameters as input, and we can run it a total of seven times at
different points in parameter space:
```{r}
val
d
```
Above, `val` shows the seven points in parameter space at which we
have run the code, and `d` shows the output at those points. Now
suppose we wish to know what the code would have produced at point
$p=(0.5, 0.5, 0.5)$, at which the point has not actually been run.
This is straightforward with the package:
```{r}
p <- c(0.5,0.5,0.)
fish <- c(1,1,4)
A <- corr.matrix(val,scales=fish)
interpolant(p, d, val, A = A, scales=fish, give=TRUE)
```
Above, object `fish` is a vector of roughness length ("scales")
corresponding to the small-scale covariance properties of our
function. This may be estimated from the problem or from the
datapoints. Matrix `A` is a normalized variance-covariance matrix for
the points of `val`.
The output gives various aspects of the Gaussian process associated
with the original observations. The most interesting one is
`mstar.star` which indicates that the best estimate for the code's
output, if it were to be run at point $p$, would be about 2.41.
## References
R. K. S. Hankin 2005. "Introducing `BACCO`, an R bundle for Bayesian
analysis of computer code output". _Journal of Statistical Software_,
14(16)
Owner
- Name: Robin Hankin
- Login: RobinHankin
- Kind: user
- Location: Auckland
- Company: AUT
- Repositories: 30
- Profile: https://github.com/RobinHankin
pushing the boundaries of R in non-statistical contexts
GitHub Events
Total
- Issues event: 1
- Push event: 2
Last Year
- Issues event: 1
- Push event: 2
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| RobinHankin | h****n@g****m | 36 |
| Robin Hankin | R****n@u****m | 1 |
| Robin Hankin | r****n@a****z | 1 |
Committer Domains (Top 20 + Academic)
aut.ac.nz: 1
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 14
- Total pull requests: 0
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.57
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- RobinHankin (14)
Pull Request Authors
Top Labels
Issue Labels
enhancement (1)
bug (1)
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- cran 3,424 last-month
- Total docker downloads: 105,675
-
Total dependent packages: 15
(may contain duplicates) -
Total dependent repositories: 21
(may contain duplicates) - Total versions: 16
- Total maintainers: 1
cran.r-project.org: emulator
Bayesian Emulation of Computer Programs
- Homepage: https://github.com/RobinHankin/emulator
- Documentation: http://cran.r-project.org/web/packages/emulator/emulator.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL]
-
Latest release: 1.2-24
published over 2 years ago
Rankings
Docker downloads count: 0.6%
Dependent packages count: 4.4%
Dependent repos count: 6.0%
Average: 13.0%
Downloads: 13.5%
Stargazers count: 25.5%
Forks count: 27.8%
Maintainers (1)
Last synced:
11 months ago
conda-forge.org: r-emulator
- Homepage: https://github.com/RobinHankin/emulator
- License: GPL-2.0-or-later
-
Latest release: 1.2_21
published over 4 years ago
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 46.0%
Stargazers count: 60.1%
Forks count: 61.1%
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.0.1 depends
- mvtnorm * depends
- knitr * suggests
- rmarkdown * suggests