Data

Tools

Indexes

Applications

Experiments

Open Source Science

sparr

Spatial (and spatio-temporal) relative risk estimation in R

https://github.com/tilmandavies/sparr

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Spatial (and spatio-temporal) relative risk estimation in R

Basic Info
  • Host: GitHub
  • Owner: tilmandavies
  • Language: R
  • Default Branch: master
  • Size: 389 MB
Statistics
  • Stars: 8
  • Watchers: 2
  • Forks: 4
  • Open Issues: 4
  • Releases: 0
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```

# sparr: Spatial and Spatiotemporal Relative Risk

The `sparr` package for R provides functions to estimate fixed and adaptive kernel-smoothed
spatial relative risk surfaces via the density-ratio method and perform subsequent inference.
Fixed-bandwidth spatiotemporal density and relative risk estimation is also supported.

## Installation

This package is available on CRAN, and we recommend installing it from there using the standard

```{r cran-installation, eval = FALSE}
install.packages('sparr')
```

If you wish to live on the bleeding edge, you may install from github using `devtools`:

```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github('tilmandavies/sparr')
```

## Example

This is a basic example of relative risk estimation for primary biliary cirrhosis cases
from north east England.

```{r pbc-example}
# Load library
library(sparr)

# Load data on cases of primary biliary cirrhosis from north east England
data(pbc)

# Split into cases and controls
pbc_case <- split(pbc)$case
pbc_cont <- split(pbc)$control

# Estimate global bandwidth for smoothing
h0 <- OS(pbc, nstar="geometric")

# Compute a symmetric (pooled) adaptive relative risk estimate
# with tolerance contours
pbc_rr <- risk(pbc_case, pbc_cont, h0=h0, adapt=TRUE, tolerate=TRUE,
               hp=OS(pbc)/2, pilot.symmetry="pooled", davies.baddeley=0.05)

# And produce a plot
plot(pbc_rr)
```

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 3
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 146
  • Total Committers: 8
  • Avg Commits per committer: 18.25
  • Development Distribution Score (DDS): 0.699
Past Year
  • Commits: 7
  • Committers: 1
  • Avg Commits per committer: 7.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
tilmandavies t****s@m****z 44
Jonathan Marshall j****l@n****d 44
Tilman Davies t****s@S****x 21
Tilman Davies t****s@S****l 17
Jonathan Marshall j****l@x****g 13
Tilman Davies t****s@S****x 4
Tilman Davies t****s@k****z 2
rubak r****k@m****k 1
Committer Domains (Top 20 + Academic)
math.aau.dk: 1 kernel.otago.ac.nz: 1 syss-macbook-pro.fritz.box: 1 xbmc.org: 1 syss-mbp.fritz.box: 1 never.you.mind: 1 maths.otago.ac.nz: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 5
  • Total pull requests: 23
  • Average time to close issues: 11 months
  • Average time to close pull requests: 12 months
  • Total issue authors: 5
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.17
  • Merged pull requests: 16
  • 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: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wangtai123 (1)
  • barryrowlingson (1)
  • spacecadet333 (1)
  • Stophface (1)
  • lambichr (1)
Pull Request Authors
  • jmarshallnz (18)
  • rubak (5)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 940 last-month
  • Total docker downloads: 43,438
  • Total dependent packages: 9
  • Total dependent repositories: 11
  • Total versions: 28
  • Total maintainers: 1
cran.r-project.org: sparr

Spatial and Spatiotemporal Relative Risk

  • Versions: 28
  • Dependent Packages: 9
  • Dependent Repositories: 11
  • Downloads: 940 Last month
  • Docker Downloads: 43,438
Rankings
Docker downloads count: 0.6%
Dependent packages count: 5.7%
Dependent repos count: 8.7%
Average: 10.5%
Forks count: 12.2%
Downloads: 13.7%
Stargazers count: 22.0%
Maintainers (1)
tilman.davies@otago.ac.nz
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10.1 depends
  • spatstat >= 2.3 depends
  • doParallel * imports
  • foreach * imports
  • misc3d * imports
  • parallel * imports
  • spatstat.core * imports
  • spatstat.geom * imports
  • spatstat.random * imports
  • spatstat.utils * imports
  • fftwtools >= 0.9.8 suggests