rprev
Development of the rprev R package for estimating disease prevalence through simulation
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: pubmed.ncbi, ncbi.nlm.nih.gov, zenodo.org -
✓Committers with academic emails
3 of 5 committers (60.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
Repository
Development of the rprev R package for estimating disease prevalence through simulation
Basic Info
- Host: GitHub
- Owner: stulacy
- Language: R
- Default Branch: master
- Size: 80.6 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
rprev
rprev estimates disease prevalence at a specified index date from incomplete registry data. It is designed to be used when estimates of point prevalence from registry data are required, but the registry hasn't been running for sufficiently long to count the number of prevalent cases. Monte Carlo simulation techniques are used to simulate incident cases in years for which incidence data is unavailable, and then estimate survival at the index date.
Prevalence arises from two independent stochastic processes: disease incidence and survival. Default models are provided that model incidence as a homogeneous Poisson process and survival as a standard parameteric distribution, although both of these models can be user specified for further control. See the user_guide vignette for more details about the implementation, and the original publication for details of the algorithm, available at https://pubmed.ncbi.nlm.nih.gov/24656754/.
Installation
To install from CRAN, simply use install.packages('rprev'), while the latest development version can be installed from GitHub using devtools::install_github("stulacy/rprev-dev").
Owner
- Name: Stuart Lacy
- Login: stulacy
- Kind: user
- Location: York, UK
- Website: http://www.stuartlacy.co.uk
- Repositories: 4
- Profile: https://github.com/stulacy
Research Software Engineer @wacl-york and R enthusiast.
GitHub Events
Total
Last Year
Committers
Last synced: over 3 years ago
All Time
- Total Commits: 510
- Total Committers: 5
- Avg Commits per committer: 102.0
- Development Distribution Score (DDS): 0.692
Top Committers
| Name | Commits | |
|---|---|---|
| Stuart Lacy | s****y@e****k | 157 |
| stulacy | s****y@g****m | 148 |
| Steph Lax | s****x@e****k | 142 |
| Stuart Lacy | s****t@l****n | 38 |
| Stuart Lacy | s****y@y****k | 25 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- 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
Pull Request Authors
- stulacy (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 385 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 12
- Total maintainers: 1
cran.r-project.org: rprev
Estimating Disease Prevalence from Registry Data
- Homepage: https://github.com/stulacy/rprev-dev
- Documentation: http://cran.r-project.org/web/packages/rprev/rprev.pdf
- License: GPL-2
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Latest release: 1.0.6
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.10 depends
- survival * depends
- data.table * imports
- dplyr * imports
- ggplot2 * imports
- lazyeval * imports
- lubridate * imports
- magrittr * imports
- tidyr * imports
- covr * suggests
- flexsurv * suggests
- flexsurvcure * suggests
- knitr * suggests
- rmarkdown * suggests
- rms * suggests
- testthat * suggests