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Open Source Science

https://github.com/connordonegan/surveil

Public Health Surveillance

https://github.com/connordonegan/surveil

Science Score: 23.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    2 of 5 committers (40.0%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary

Keywords

bayesian-statistics cancer health-equity public-health r-stats rstan rstats-package

Keywords from Contributors

bayesian-inference epidemiology stan
Last synced: 5 months ago · JSON representation

Repository

Public Health Surveillance

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 4
Topics
bayesian-statistics cancer health-equity public-health r-stats rstan rstats-package
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output:
  md_document:
    variant: markdown_github
editor_options: 
  chunk_output_type: console
---



## surveil: Public health surveillance 



The *surveil* R package provides time series models for routine public health surveillance tasks: model time trends in mortality or disease incidence rates to make inferences about levels of risk, cumulative and period percent change, age-standardized rates, and health inequalities. 

*surveil* is an interface to [Stan](https://mc-stan.org), a state-of-the-art platform for Bayesian inference. For analysis of spatial health data see the [*geostan*](https://connordonegan.github.io/geostan/) R package.

### Installation

*surveil* is available on CRAN; install from R using:

```{r eval = FALSE}
install.packages("surveil")
```

### Vignettes

Review the package vignettes to get started:

 - `vignette("surveil-demo")`: An introduction to public health modeling with *surveil*
 - `vignette("age-standardization")`: How to age-standardize *surveil* model results 
 - `vignette("measuring-inequality")`: Assessing pairwise health differences with measures of inequality
 - `vignette("surveil-mcmc")`: A brief introduction to Markov chain Monte Carlo (MCMC) with *surveil*

Also see the online [documentation](https://connordonegan.github.io/surveil/reference/index.html).

### Usage

Model time series data of mortality or disease incidence by loading the *surveil* package into R together with disease surveillance data. Tables exported from CDC WONDER are automatically in the correct format.

```{r}
library(surveil)
library(knitr)
data(cancer)

kable(head(cancer), 
      booktabs = TRUE,
      caption = "Table 1. A glimpse of cancer surveillance data")
```

Model trends in risk and easily view functions of risk estimates, such as cumulative percent change:

```{r eval = FALSE}
fit <- stan_rw(data = cancer,
               time = Year, 
               group = Age,
	       cores = 4 # multi-core processing for speed
	       )

fit_apc <- apc(fit)
plot(fit_apc, cumulative = TRUE)
```


*Cumulative percent change in US cancer incidence by age group*

Owner

  • Name: Connor Donegan
  • Login: ConnorDonegan
  • Kind: user
  • Company: UT Dallas & UTSW Medical Center

GitHub Events

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Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 67
  • Total Committers: 5
  • Avg Commits per committer: 13.4
  • Development Distribution Score (DDS): 0.209
Past Year
  • Commits: 8
  • Committers: 2
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.125
Top Committers
Name Email Commits
ConnorDonegan c****n@g****m 53
Connor Donegan c****n@u****u 10
Connor Donegan C****n@U****u 2
Andrew Johnson a****n@a****m 1
Pietro Monticone 3****e 1
Committer Domains (Top 20 + Academic)
utdallas.edu: 2 arjohnsonau.com: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 days
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 19 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
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  • pitmonticone (1)
  • andrjohns (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 305 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
cran.r-project.org: surveil

Time Series Models for Disease Surveillance

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 305 Last month
Rankings
Forks count: 21.9%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Average: 32.7%
Dependent repos count: 35.5%
Downloads: 47.9%
Maintainers (1)
connor.donegan@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Rcpp >= 0.12.0 imports
  • RcppParallel >= 5.0.1 imports
  • dplyr >= 1.0.7 imports
  • ggdist >= 3.0.0 imports
  • ggplot2 >= 3.0.0 imports
  • gridExtra >= 2.0 imports
  • methods * imports
  • rlang >= 0.4.0 imports
  • rstan >= 2.18.1 imports
  • rstantools >= 2.1.1 imports
  • scales >= 0.4.0 imports
  • tidybayes >= 3.0.0 imports
  • tidyr >= 1.1.0 imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests