SpatialEpi
R Package of methods and data for spatial epidemiology
Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: researchgate.net -
✓Committers with academic emails
3 of 8 committers (37.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Last synced: 11 months ago
·
JSON representation
Repository
R Package of methods and data for spatial epidemiology
Basic Info
Statistics
- Stars: 34
- Watchers: 1
- Forks: 8
- Open Issues: 1
- Releases: 4
Created about 12 years ago
· Last pushed over 3 years ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README_figure/README-"
)
```
# SpatialEpi
[](https://github.com/rudeboybert/SpatialEpi/actions)
[](https://cran.r-project.org/package=SpatialEpi) [](https://www.r-pkg.org/pkg/SpatialEpi)
Package of data and methods for spatial epidemiology.
## Installation
Get the released version from CRAN:
```{r, eval=FALSE}
install.packages("SpatialEpi")
```
Or the development version from GitHub:
```{r, eval=FALSE}
# If you haven't installed devtools yet, do so:
# install.packages("devtools")
devtools::install_github("rudeboybert/SpatialEpi")
```
Note: In order for all C++ code to compile correctly you may need to
1. Install the `cpp11` package
1. Install an older version of `RcppArmadillo` by running
```{r, eval=FALSE}
packageurl <- "https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.9.900.3.0.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
```
## Example
We load the data and convert the coordinate system from latitude/longitude to a grid-based system.
```{r, message=FALSE, warning=FALSE}
library(SpatialEpi)
```
```{r, message=FALSE, warning=FALSE}
data(NYleukemia)
sp.obj <- NYleukemia$spatial.polygon
centroids <- latlong2grid(NYleukemia$geo[, 2:3])
population <- NYleukemia$data$population
cases <- NYleukemia$data$cases
```
We plot the incidence of leukemia for each census tract.
```{r, message=FALSE, warning=FALSE, fig.height=6.5}
plotmap(cases/population, sp.obj, log=TRUE, nclr=5)
points(grid2latlong(centroids), pch=4)
```
We run the Bayesian Cluster Detection method from [Wakefield and Kim (2013)](https://www.researchgate.net/publication/235896508_A_Bayesian_model_for_cluster_detection):
```{r bayes_cluster, message=FALSE, warning=FALSE, cache=TRUE}
y <- cases
E <- expected(population, cases, 1)
max.prop <- 0.15
shape <- c(2976.3, 2.31)
rate <- c(2977.3, 1.31)
J <- 7
pi0 <- 0.95
n.sim.lambda <- 10^4
n.sim.prior <- 10^5
n.sim.post <- 10^5
# Compute output
output <- bayes_cluster(y, E, population, sp.obj, centroids, max.prop,
shape, rate, J, pi0, n.sim.lambda, n.sim.prior,
n.sim.post)
```
```{r, fig.height=6.5}
plotmap(output$post.map$high.area, sp.obj)
```
Owner
- Name: Albert Y. Kim
- Login: rudeboybert
- Kind: user
- Location: Northampton MA, USA
- Company: @SmithCollege-SDS
- Website: http://rudeboybert.rbind.io/
- Twitter: rudeboybert
- Repositories: 39
- Profile: https://github.com/rudeboybert
Assistant Professor of Statistical & Data Sciences, Smith College
GitHub Events
Total
- Watch event: 3
Last Year
- Watch event: 3
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| rudeboybert | a****m@g****m | 183 |
| arrismo | m****e@p****m | 35 |
| Arris Moise | m****0@g****m | 34 |
| Kim | a****m@f****u | 2 |
| Arris Moise | a****e@s****u | 1 |
| Ian D Buller | i****r@g****m | 1 |
| Mikael Moise | m****l@m****m | 1 |
| whoishomer | a****t@s****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 20
- Total pull requests: 20
- Average time to close issues: 2 months
- Average time to close pull requests: 7 days
- Total issue authors: 6
- Total pull request authors: 3
- Average comments per issue: 0.85
- Average comments per pull request: 1.25
- Merged pull requests: 19
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rudeboybert (11)
- arrismo (5)
- colourfulmww (1)
- rsbivand (1)
- simon-smart88 (1)
- jofmorenore (1)
Pull Request Authors
- rudeboybert (11)
- arrismo (8)
- idblr (1)
Top Labels
Issue Labels
wontfix (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 707 last-month
- Total docker downloads: 1,385
- Total dependent packages: 3
- Total dependent repositories: 8
- Total versions: 12
- Total maintainers: 1
cran.r-project.org: SpatialEpi
Methods and Data for Spatial Epidemiology
- Homepage: https://github.com/rudeboybert/SpatialEpi
- Documentation: http://cran.r-project.org/web/packages/SpatialEpi/SpatialEpi.pdf
- License: GPL-2
-
Latest release: 1.2.8
published over 3 years ago
Rankings
Forks count: 7.9%
Stargazers count: 10.3%
Dependent repos count: 10.5%
Dependent packages count: 10.9%
Average: 11.7%
Downloads: 14.6%
Docker downloads count: 16.0%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.0.2 depends
- sp * depends
- MASS * imports
- Rcpp * imports
- maptools * imports
- spdep * imports
- dplyr * suggests
- ggplot2 * suggests
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests