epiparameter

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

https://github.com/epiverse-trace/epiparameter

Science Score: 77.0%

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Keywords

data-access data-package epidemiology epiverse probability-distribution r r-package

Keywords from Contributors

standards standard-operating-procedure r-package-development stan onboarding internal-docs best-practices scenario-analysis epidemic-modelling epidemic-simulations

Last synced: 6 months ago · JSON representation ·

Repository

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

Basic Info

Host: GitHub
Owner: epiverse-trace
License: other
Language: R
Default Branch: main
Homepage: https://epiverse-trace.github.io/epiparameter
Size: 30.7 MB

Statistics

Stars: 37
Watchers: 8
Forks: 13
Open Issues: 62
Releases: 5

Topics

data-access data-package epidemiology epiverse probability-distribution r r-package

Created almost 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "75%",
  fig.align = "center"
)
```

# epiparameter 


[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![R-CMD-check](https://github.com/epiverse-trace/epiparameter/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameter/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/epiverse-trace/epiparameter/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameter?branch=main)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11110881.svg)](https://doi.org/10.5281/zenodo.11110881)
[![CRAN status](https://www.r-pkg.org/badges/version/epiparameter)](https://CRAN.R-project.org/package=epiparameter)
[![CRAN downloads](https://cranlogs.r-pkg.org/badges/epiparameter)](https://cran.r-project.org/package=epiparameter)


`{epiparameter}` is an `R` package that contains a library of epidemiological parameters for infectious diseases as well as classes and helper functions to work with the data. It also includes functions to extract and convert parameters from reported summary statistics.

`{epiparameter}` is developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the [London School of Hygiene and Tropical Medicine](https://www.lshtm.ac.uk/) as part of [Epiverse-TRACE](https://data.org/initiatives/epiverse/).


## Installation

The package can be installed from CRAN using

```r
install.packages("epiparameter")
```

The development version of `{epiparameter}` can be installed from [GitHub](https://github.com/epiverse-trace/epiparameter) using the `{pak}` package:

``` r
# check whether {pak} is installed
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/epiparameter")
```

Alternatively, install pre-compiled binaries from [the Epiverse TRACE R-universe](https://epiverse-trace.r-universe.dev/epiparameter)

``` r
install.packages("epiparameter", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
```

## Quick start

```{r load-epiparameter}
library(epiparameter)
```

To load the library of epidemiological parameters into `R`:

```{r load-data}
epiparameters <- epiparameter_db()
epiparameters
```

This results in a list of database entries. Each entry of the library is an `` object.

Alternatively, the library of epiparameters can be viewed as a vignette locally (`vignette("database", package = "epiparameter")`) or on the [{epiparameter} website](https://epiverse-trace.github.io/epiparameter/articles/database.html).

The results can be filtered by disease and epidemiological distribution. Here we set `single_epiparameter = TRUE` as we only want a single database entry returned, and by default (`single_epiparameter = FALSE`) it will return all database entries that match the disease (`disease`) and epidemiological parameter (`epi_name`).

```{r load-single-epiparameter}
influenza_incubation <- epiparameter_db(
  disease = "influenza",
  epi_name = "incubation period",
  single_epiparameter = TRUE
)
influenza_incubation
```

To quickly view the list of epidemiological distributions returned by `epiparameter_db()` in a table, the `parameter_tbl()` gives a summary of the data, and offers the ability to subset you data by `disease`, `pathogen` and epidemiological parameter (`epi_name`).

```{r parameter-tbl}
parameter_tbl(epiparameters)
parameter_tbl(
  epiparameters,
  epi_name = "onset to hospitalisation"
)
```

The `` object can be plotted.

```{r plot-epiparameter}
plot(influenza_incubation)
```

The CDF can also be plotted by setting `cumulative = TRUE`.

```{r, plot-epiparameter-cdf}
plot(influenza_incubation, cumulative = TRUE)
```

### Parameter conversion and extraction

The parameters of a distribution can be converted to and from mean and standard deviation. In `{epiparameter}` we implement this for a variety of distributions:

- gamma
- lognormal
- Weibull
- negative binomial
- geometric

The parameters of a probability distribution can also be extracted from other summary statistics, for example, percentiles of the distribution, or the median and range of the data. This can be done for:

- gamma
- lognormal
- Weibull
- normal

## Contributing to library of epidemiological parameters

The library of epidemiological parameters that can be loaded by `{epiparameter}` using the `epiparameter_db()` function is stored in the [`{epiparameterDB}` R package](https://github.com/epiverse-trace/epiparameterDB). If you would like to contribute to the library of epiparameters you can either: 

1. Add data to a public [google sheet](https://docs.google.com/spreadsheets/d/1eCL3n_woseg5Npu7XD7TcuNoLUIhMBu8ZoLCkVdATUE/edit?usp=sharing). This spreadsheet contains two example entries as a guide to what fields are accepted. We are monitoring this sheet for new entries that will subsequently be included in the package.

2. Add to the [JSON file holding the database](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/parameters.json) directly via a Pull Request. See the [contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md) for instructions.

You can find a description of the epidemiological parameter data structure and contents in the [data dictionary](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/data_dictionary.json). This documents the valid format and data types to ensure consistency and accuracy. All entries in the parameter library are automatically validated against the data dictionary using an GitHub action workflow.

## Help 

To report a bug please open an [issue](https://github.com/epiverse-trace/epiparameter/issues/new/choose)

## Contribute 

Contributions to `{epiparameter}` are welcomed. [package contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md).

## Code of Conduct

Please note that the `{epiparameter}` project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

## Citing this package

```{r message=FALSE, warning=FALSE}
citation("epiparameter")
```

Owner

Name: Epiverse-TRACE
Login: epiverse-trace
Kind: organization

Website: https://epiverse.org
Repositories: 17
Profile: https://github.com/epiverse-trace

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
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title: 'epiparameter: Classes and Helper Functions for Working with Epidemiological
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version: 0.4.1.9000
doi: 10.5281/zenodo.11110881
identifiers:
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abstract: Classes and helper functions for loading, extracting, converting, manipulating,
  plotting and aggregating epidemiological parameters for infectious diseases. Epidemiological
  parameters extracted from the literature are loaded from the 'epiparameterDB' R
  package.
authors:
- family-names: Lambert
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- family-names: Tamayo Cuartero
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  email: carmen.tamayo-cuartero@lshtm.ac.uk
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  orcid: https://orcid.org/0000-0001-5218-3046
keywords:
- data-access
- data-package
- epidemiology
- epiverse
- probability-distribution
- r
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  doi: 10.32614/CRAN.package.visNetwork

GitHub Events

Total

Create event: 47
Release event: 3
Issues event: 18
Watch event: 6
Delete event: 42
Issue comment event: 58
Push event: 94
Pull request review comment event: 13
Pull request review event: 15
Pull request event: 86
Fork event: 2

Last Year

Create event: 47
Release event: 3
Issues event: 18
Watch event: 6
Delete event: 42
Issue comment event: 58
Push event: 94
Pull request review comment event: 13
Pull request review event: 15
Pull request event: 86
Fork event: 2

Name	Email	Commits
Joshua Lambert	j**t@l**k	616
adamkucharski	a**i@l**k	27
GitHub Action	a**n@g**m	18
Hugo Gruson	B****o	14
Andree Valle Campos	a**m@g**m	1
Maëlle Salmon	m**n@y**e	1
Pietro Monticone	3****e	1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 113
Total pull requests: 164
Average time to close issues: 4 months
Average time to close pull requests: 6 days
Total issue authors: 14
Total pull request authors: 7
Average comments per issue: 1.31
Average comments per pull request: 0.57
Merged pull requests: 147
Bot issues: 0
Bot pull requests: 20

Past Year

Issues: 16
Pull requests: 78
Average time to close issues: 13 days
Average time to close pull requests: about 21 hours
Issue authors: 7
Pull request authors: 3
Average comments per issue: 0.44
Average comments per pull request: 0.35
Merged pull requests: 66
Bot issues: 0
Bot pull requests: 16

View more stats

Top Authors

Issue Authors

joshwlambert (79)
adamkucharski (13)
avallecam (10)
Bisaloo (8)
jamesmbaazam (7)
sbfnk (6)
chloerice48 (3)
pratikunterwegs (3)
CarmenTamayo (3)
chartgerink (2)
nlinton (1)
prabasaj (1)
jlessler (1)
Karim-Mane (1)
thibautjombart (1)

Pull Request Authors

joshwlambert (203)
github-actions[bot] (40)
Bisaloo (15)
jamesmbaazam (3)
cm401 (3)
chartgerink (2)
CarmenTamayo (2)
sbfnk (2)
avallecam (1)
wzmli (1)

Top Labels

Issue Labels

enhancement (24) documentation (10) dev day (6) discussion (5) S3-method (5) v0.1 (4) question (4) bug (4) S3-class (4) data management (3) good first issue (1) interoperability (1) scope (1) workflow (1) reminder (1) consideration (1) citations (1)

Pull Request Labels

documentation (39) pkg infrastructure (38) enhancement (35) S3-method (24) S3-class (19) CI (13) data management (12) JSON (9) internal (8) website (6) Pkg review (5) citations (2) CRAN (2) bug (1) interoperability (1)

Packages

Total packages: 1
Total downloads:
- cran 287 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2
Total maintainers: 1

cran.r-project.org: epiparameter

Classes and Helper Functions for Working with Epidemiological Parameters

Homepage: https://github.com/epiverse-trace/epiparameter/
Documentation: http://cran.r-project.org/web/packages/epiparameter/epiparameter.pdf
License: MIT + file LICENSE
Latest release: 0.4.1
published about 1 year ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 287 Last month

Rankings

Forks count: 6.4%

Stargazers count: 9.1%

Dependent packages count: 27.5%

Average: 32.8%

Dependent repos count: 33.8%

Downloads: 87.0%

Maintainers (1)

joshua.lambert@lshtm.ac.uk

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

dplyr * imports
magrittr * imports

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/lint-changed-files.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/render_readme.yml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

epiparameter

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

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

Top Authors

Issue Authors

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Issue Labels

Pull Request Labels

Packages

cran.r-project.org: epiparameter

Rankings

Maintainers (1)

Dependencies