popEpi

Epidemiological analysis for population-based data.

https://github.com/finnishcancerregistry/popepi

Science Score: 13.0%

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CITATION.cff file
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Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary

Keywords

adjust-estimates age-adjusting direct-adjusting epidemiology indirect-adjusting r r-package survival

Last synced: 11 months ago · JSON representation

Repository

Epidemiological analysis for population-based data.

Basic Info

Host: GitHub
Owner: FinnishCancerRegistry
License: other
Language: R
Default Branch: master
Homepage:
Size: 11.3 MB

Statistics

Stars: 8
Watchers: 4
Forks: 7
Open Issues: 39
Releases: 7

Topics

adjust-estimates age-adjusting direct-adjusting epidemiology indirect-adjusting r r-package survival

Created almost 11 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License

README.Rmd

---
output:
  md_document:
    variant: markdown_github
---


```{r, echo = FALSE, results='hide', message = FALSE, warning=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
library(popEpi)
```

[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/popEpi)](https://cran.r-project.org/package=popEpi)
[![Codecov test coverage](https://codecov.io/gh/FinnishCancerRegistry/popEpi/branch/master/graph/badge.svg)](https://app.codecov.io/gh/FinnishCancerRegistry/popEpi?branch=master)
[![CRAN_DLs_via_RStudio](https://cranlogs.r-pkg.org/badges/popEpi)](https://cran.r-project.org/package=popEpi)
[![R-CMD-check](https://github.com/FinnishCancerRegistry/popEpi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FinnishCancerRegistry/popEpi/actions/workflows/R-CMD-check.yaml)

# popEpi: Epidemiology with population data

The purpose of popEpi is to facilitate computing certain epidemiological 
statistics where population data is used. Current main attractions:

## Splitting, merging population hazards, and aggregating

the `lexpand` function allows users to split their subject-level follow-up data into sub-intervals along age, follow-up time and calendar time, 
merge corresponding population hazard information to those intervals, 
and to aggregate the resulting data if needed.

```{r lexpand}
data(sire)
sr <- sire[1,]
print(sr)
```

```{r lexpand2}
x <- lexpand(sr, birth = bi_date, entry = dg_date, exit = ex_date,
             status = status %in% 1:2, 
             fot = 0:5, per = 1994:2000)
print(x)
```

```{r lexpand3}
data(popmort)
x <- lexpand(sr, birth = bi_date, entry = dg_date, exit = ex_date,
             status = status %in% 1:2, 
             fot = 0:5, per = 1994:2000, pophaz = popmort)
print(x)
```

```{r aggre}
a <- lexpand(sr, birth = bi_date, entry = dg_date, exit = ex_date,
             status = status %in% 1:2,
             fot = 0:5, per = 1994:2000, aggre = list(fot, per))
print(a)
```


## SIRs / SMRs

One can make use of the `sir` function to estimate indirectly standardised incidence or
mortality ratios (SIRs/SMRs). The data can be aggregated by `lexpand` or by other means.
While `sir` is simple and flexible in itself, one may also use `sirspline` to fit
spline functions for the effect of e.g. age as a continuous variable on SIRs.

```{r sir}
data(popmort)
data(sire)
c <- lexpand( sire, status = status %in% 1:2, birth = bi_date, exit = ex_date, entry = dg_date,
              breaks = list(per = 1950:2013, age = 1:100, fot = c(0,10,20,Inf)), 
              aggre = list(fot, agegroup = age, year = per, sex) )

se <- sir( coh.data = c, coh.obs = 'from0to1', coh.pyrs = 'pyrs', 
           ref.data = popmort, ref.rate = 'haz', 
           adjust = c('agegroup', 'year', 'sex'), print = 'fot')
se
```


## (Relative) survival

The `survtab` function computes observed, net/relative and cause-specific
survivals as well as  cumulative incidence functions for `Lexis` data. 
Any of the supported survival time functions can be
easily adjusted by any number of categorical variables if needed.

One can also use `survtab_ag` for aggregated data. This means the data does
not have to be on the subject-level to compute survival time function estimates.

```{r survtab}
library(Epi)

data(sibr)
sire$cancer <- "rectal"
sibr$cancer <- "breast"
sr <- rbind(sire, sibr)

sr$cancer <- factor(sr$cancer)
sr <- sr[sr$dg_date < sr$ex_date, ]

sr$status <- factor(sr$status, levels = 0:2, 
                    labels = c("alive", "canD", "othD"))

x <- Lexis(entry = list(FUT = 0, AGE = dg_age, CAL = get.yrs(dg_date)), 
           exit = list(CAL = get.yrs(ex_date)), 
           data = sr,
           exit.status = status)

st <- survtab(FUT ~ cancer, data = x,
              breaks = list(FUT = seq(0, 5, 1/12)),
              surv.type = "cif.obs")
st
```

Owner

Name: Finnish Cancer Registry
Login: FinnishCancerRegistry
Kind: organization
Location: Finland

Website: https://cancerregistry.fi/
Repositories: 6
Profile: https://github.com/FinnishCancerRegistry

GitHub Events

Total

Push event: 7

Last Year

Push event: 7

Committers

Last synced: over 1 year ago

All Time

Total Commits: 982
Total Committers: 7
Avg Commits per committer: 140.286
Development Distribution Score (DDS): 0.436

Past Year

Commits: 30
Committers: 1
Avg Commits per committer: 30.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Joonas Miettinen	j**n@g**m	554
Joonas Miettinen	j**n@c**i	389
Matti Rantanen	m**n@c**i	31
=	=	4
unknown	m**n@T**l	2
Joonas Miettinen	J****n	1
mattdowle	m**e@g**m	1

Committer Domains (Top 20 + Academic)

cancer.fi: 2

Issues and Pull Requests

Last synced: 12 months ago

All Time

Total issues: 98
Total pull requests: 2
Average time to close issues: about 1 month
Average time to close pull requests: 12 days
Total issue authors: 8
Total pull request authors: 2
Average comments per issue: 0.52
Average comments per pull request: 1.0
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

View more stats

Top Authors

Issue Authors

WetRobot (66)
mattirantanen (21)
kseppa (6)
MichaelChirico (1)
jangorecki (1)
anddis (1)
oladav (1)
jwdebelius (1)

Pull Request Authors

mattdowle (1)
MichaelChirico (1)

Top Labels

Issue Labels

bug (42) enhancement (35) minor (19) major (14) feature change (3) docs (1) suggestion (1) deprecated (1) duplicate (1) wontfix (1) help wanted (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 1,797 last-month
Total docker downloads: 43,477

Total dependent packages: 1
Total dependent repositories: 4
Total versions: 17
Total maintainers: 1

cran.r-project.org: popEpi

Functions for Epidemiological Analysis using Population Data

Homepage: https://github.com/FinnishCancerRegistry/popEpi
Documentation: http://cran.r-project.org/web/packages/popEpi/popEpi.pdf
License: MIT + file LICENSE
Latest release: 0.4.13
published over 1 year ago

Versions: 17
Dependent Packages: 1
Dependent Repositories: 4
Downloads: 1,797 Last month
Docker Downloads: 43,477

Rankings

Docker downloads count: 0.6%

Forks count: 8.0%

Downloads: 10.3%

Average: 11.9%

Dependent repos count: 14.7%

Dependent packages count: 18.3%

Stargazers count: 19.5%

Maintainers (1)

joonas.miettinen@cancer.fi

Last synced: 12 months ago

Dependencies

DESCRIPTION cran

R >= 3.2.0 depends
Epi >= 2.0 imports
data.table >= 1.10.4 imports
survival * imports
covr * suggests
date * suggests
ggplot2 * suggests
knitr * suggests
methods * suggests
mstate * suggests
relsurv * suggests
reshape2 * suggests
rmarkdown * suggests
roxygen2 * suggests
splines * suggests
testthat * suggests

ecosyste.ms

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Open Source Science

popEpi

Science Score: 13.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

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Packages

cran.r-project.org: popEpi

Rankings

Maintainers (1)

Dependencies