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Update contributing to library in README #430

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update contributing to library of epiparameters section in README
joshwlambert Jan 6, 2025
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Automatic readme update
actions-user Jan 6, 2025
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8 changes: 5 additions & 3 deletions README.Rmd
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Expand Up @@ -114,11 +114,13 @@ The parameters of a probability distribution can also be extracted from other su

## Contributing to library of epidemiological parameters

If you would like to contribute to the different epidemiological parameters stored in the `{epiparameter}` package, you can 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 can accept. We are monitoring this sheet for new entries that will subsequently be included in the package.
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:

Alternatively, parameters can be added to the [JSON file holding the data](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/parameters.json) base directly via a Pull Request.
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.

You can find explanation of accepted entries for each column in the [data dictionary](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/data_dictionary.json).
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

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51 changes: 30 additions & 21 deletions README.md
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Expand Up @@ -74,7 +74,7 @@ epiparameters
#> review." _The Lancet Infectious Diseases_.
#> doi:10.1016/S1473-3099(09)70069-6
#> <https://doi.org/10.1016/S1473-3099%2809%2970069-6>.
#> Distribution: lnorm
#> Distribution: lnorm (days)
#> Parameters:
#> meanlog: 1.723
#> sdlog: 0.231
Expand All @@ -88,7 +88,7 @@ epiparameters
#> review." _The Lancet Infectious Diseases_.
#> doi:10.1016/S1473-3099(09)70069-7
#> <https://doi.org/10.1016/S1473-3099%2809%2970069-7>.
#> Distribution: lnorm
#> Distribution: lnorm (days)
#> Parameters:
#> meanlog: 1.163
#> sdlog: 0.140
Expand All @@ -102,7 +102,7 @@ epiparameters
#> review." _The Lancet Infectious Diseases_.
#> doi:10.1016/S1473-3099(09)70069-8
#> <https://doi.org/10.1016/S1473-3099%2809%2970069-8>.
#> Distribution: lnorm
#> Distribution: lnorm (days)
#> Parameters:
#> meanlog: 1.386
#> sdlog: 0.593
Expand Down Expand Up @@ -148,7 +148,7 @@ influenza_incubation
#> Distribution of the Incubation Periods of Human Avian Influenza A(H7N9)
#> Virus Infections." _American Journal of Epidemiology_.
#> doi:10.1093/aje/kwv115 <https://doi.org/10.1093/aje/kwv115>.
#> Distribution: weibull
#> Distribution: weibull (days)
#> Parameters:
#> shape: 2.101
#> scale: 3.839
Expand Down Expand Up @@ -230,21 +230,30 @@ or the median and range of the data. This can be done for:

## Contributing to library of epidemiological parameters

If you would like to contribute to the different epidemiological
parameters stored in the `{epiparameter}` package, you can 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
can accept. We are monitoring this sheet for new entries that will
subsequently be included in the package.

Alternatively, parameters can be added to the [JSON file holding the
data](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/parameters.json)
base directly via a Pull Request.

You can find explanation of accepted entries for each column in the
[data
dictionary](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/data_dictionary.json).
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

Expand All @@ -269,7 +278,7 @@ By contributing to this project, you agree to abide by its terms.
citation("epiparameter")
#> To cite package 'epiparameter' in publications use:
#>
#> Lambert J, Kucharski A, Tamayo C (2024). _epiparameter: Library of
#> Lambert J, Kucharski A, Tamayo C (2025). _epiparameter: Library of
#> Epidemiological Parameters with Helper Functions and Classes_.
#> doi:10.5281/zenodo.11110881
#> <https://doi.org/10.5281/zenodo.11110881>,
Expand All @@ -280,7 +289,7 @@ citation("epiparameter")
#> @Manual{,
#> title = {epiparameter: Library of Epidemiological Parameters with Helper Functions and Classes},
#> author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo},
#> year = {2024},
#> year = {2025},
#> doi = {10.5281/zenodo.11110881},
#> url = {https://epiverse-trace.github.io/epiparameter/},
#> }
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