diff --git a/README.Rmd b/README.Rmd index e8e3b8a02..5980c5da1 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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 diff --git a/README.md b/README.md index 8e41ea118..83969d515 100644 --- a/README.md +++ b/README.md @@ -74,7 +74,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-6 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.723 #> sdlog: 0.231 @@ -88,7 +88,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-7 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.163 #> sdlog: 0.140 @@ -102,7 +102,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-8 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.386 #> sdlog: 0.593 @@ -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 . -#> Distribution: weibull +#> Distribution: weibull (days) #> Parameters: #> shape: 2.101 #> scale: 3.839 @@ -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 @@ -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 #> , @@ -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/}, #> }