Full package review for v0.2.0

NEWS.md

@@ -2,6 +2,8 @@
 
 The second release of the {epiparameter} R package focuses on interoperability with the [{epireview} R package](https://mrc-ide.github.io/epireview/). Several functions have been refactored and enhanced.
 
+This release benefited from feedback from the participants of an [EpiParameter Community workshop hosted by the World Health Organisation](https://who-collaboratory.github.io/collaboratory-epiparameter-community/#/pages/news).
+
 ## New features
 
 * The `as_epidist()` S3 generic has been added to the package for the coercion of other R objects into `<epidist>` objects. The `as_epidist.data.frame()` method is added, as well as the internal functions `is_epireview()` which determines if a `<data.frame>` is from {epireview}, and `epireview_to_epidist()` performs the conversion  (#298, #334 & #335)

R/coercion.R

@@ -29,15 +29,13 @@ as.function.epidist <- function(x,
     )
   }
   epidist <- x
-  x <- switch(func_type,
+  # return distribution function
+  switch(func_type,
     density = function(x) density(x = epidist, at = x),
     cdf = function(x) epiparameter::cdf(x = epidist, q = x),
     generate = function(x) epiparameter::generate(x = epidist, times = x),
     quantile = function(x) quantile(x = epidist, p = x)
   )
-
-  # return distribution function
-  x
 }
 
 
@@ -60,8 +58,7 @@ as.data.frame.epidist <- function(x, ...) {
   # check object as could be invalidated by user
   validate_epidist(x)
 
-  # make data frame
-  df <- data.frame(
+  data.frame(
     disease = x$disease,
     pathogen = x$pathogen,
     epi_distribution = x$epi_dist,
@@ -71,12 +68,9 @@ as.data.frame.epidist <- function(x, ...) {
     citation = I(x$citation),
     metadata = I(list(metadata = x$metadata)),
     method_assess = I(list(method_assess = x$method_assess)),
-    notes = x$notes
+    notes = x$notes,
+    row.names = NULL
   )
-  row.names(df) <- NULL
-
-  # return data frame
-  df
 }
 
 #' [as.data.frame()] method for `<multi_epidist>` class

R/convert_params.R

@@ -29,6 +29,8 @@
 #' statistics used to convert to parameter(s). An example is the `mean`
 #' and `sd` summary statistics for the lognormal (`lnorm`) distribution.
 #'
+#' @seealso [convert_params_to_summary_stats()]
+#'
 #' @return A list of either one or two elements (depending on how many
 #' parameters the distribution has).
 #' @export
@@ -154,6 +156,8 @@ convert_summary_stats_to_params.epidist <- function(x, ...) {
 #' used to convert to summary statistics. An example is the `meanlog` and
 #' `sdlog` parameters of the lognormal (`lnorm`) distribution.
 #'
+#' @seealso [convert_summary_stats_to_params()]
+#'
 #' @return A list of eight elements including: mean, median, mode,
 #' variance (`var`), standard deviation (`sd`), coefficient of variation (`cv`),
 #' skewness, and excess kurtosis (`ex_kurtosis`).

R/epidist.R

@@ -438,7 +438,7 @@ format.epidist <- function(x, header = TRUE, vb = NULL, ...) {
     )
     writeLines(sprintf(dist_string, family(x)))
   } else {
-    writeLines(sprintf("Parameters: <no parameters>"))
+    writeLines("Parameters: <no parameters>")
   }
 
   if (is.object(x$prob_dist)) {

R/print.R

@@ -80,8 +80,8 @@ print.multi_epidist <- function(x, ..., n = NULL) {
         " Use `parameter_tbl()` to see a summary table of the parameters.\n",
         "# ", cli::symbol$info, " Explore database online at: ",
         cli::style_hyperlink(
-          text = "https://epiverse-trace.github.io/epiparameter/dev/articles/database.html", # nolint line_length_linter
-          url = "https://epiverse-trace.github.io/epiparameter/dev/articles/database.html" # nolint line_length_linter
+          text = "https://epiverse-trace.github.io/epiparameter/articles/database.html", # nolint line_length_linter
+          url = "https://epiverse-trace.github.io/epiparameter/articles/database.html" # nolint line_length_linter
         )
       )
     )

README.Rmd

@@ -24,7 +24,7 @@ knitr::opts_chunk$set(
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11110881.svg)](https://doi.org/10.5281/zenodo.11110881)
 <!-- badges: end -->
 
-`{epiparameter}` is an `R` package that contains a library of epidemiological parameters for infectious diseases and a set classes and helper functions to be able to work with the data. It also includes functions to extract and convert parameters from reported summary statistics.
+`{epiparameter}` is an `R` package that contains a library of epidemiological parameters for infectious diseases and a set of 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/).
 
@@ -60,6 +60,8 @@ epidists
 
 This results a list of database entries. Each entry of the library is an `<epidist>` 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_epidist = TRUE` as we only want a single database entry returned, and by default (`single_epidist = FALSE`) it will return all database entries that match the disease (`disease`) and epidemiological distribution (`epi_dist`).
 
 ```{r load-single-epidist}
@@ -112,7 +114,7 @@ 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/1zVpaaKkQ7aeMdRN2r0p-W4d2TtccL5HcIOp_w-lfkEQ/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.
+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.
 

README.md

@@ -16,10 +16,9 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 <!-- badges: end -->
 
 `{epiparameter}` is an `R` package that contains a library of
-epidemiological parameters for infectious diseases and a set classes and
-helper functions to be able to work with the data. It also includes
-functions to extract and convert parameters from reported summary
-statistics.
+epidemiological parameters for infectious diseases and a set of 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
@@ -59,9 +58,6 @@ epidists <- epidist_db()
 #> Returning 122 results that match the criteria (99 are parameterised). 
 #> Use subset to filter by entry variables or single_epidist to return a single entry. 
 #> To retrieve the citation for each use the 'get_citation' function
-```
-
-``` r
 epidists
 #> # List of 122 <epidist> objects
 #> Number of diseases: 23
@@ -113,12 +109,17 @@ epidists
 #> # ℹ 119 more elements
 #> # ℹ Use `print(n = ...)` to see more elements.
 #> # ℹ Use `parameter_tbl()` to see a summary table of the parameters.
-#> # ℹ Explore database online at: https://epiverse-trace.github.io/epiparameter/dev/articles/database.html
+#> # ℹ Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html
 ```
 
 This results a list of database entries. Each entry of the library is an
 `<epidist>` 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_epidist = TRUE` as we only want a single database
 entry returned, and by default (`single_epidist = FALSE`) it will return
@@ -137,9 +138,6 @@ influenza_incubation <- epidist_db(
 #> Virus Infections." _American Journal of Epidemiology_.
 #> doi:10.1093/aje/kwv115 <https://doi.org/10.1093/aje/kwv115>.. 
 #> To retrieve the citation use the 'get_citation' function
-```
-
-``` r
 influenza_incubation
 #> Disease: Influenza
 #> Pathogen: Influenza-A-H7N9
@@ -177,9 +175,6 @@ parameter_tbl(epidists)
 #>  9 RSV      RSV      incubation peri… lnorm             Lessl…  2009          24
 #> 10 Rhinovi… Rhinovi… incubation peri… lnorm             Lessl…  2009          28
 #> # ℹ 112 more rows
-```
-
-``` r
 parameter_tbl(
   epidists,
   epi_dist = "onset to hospitalisation"
@@ -237,7 +232,7 @@ or the median and range of the data. This can be done for:
 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/1zVpaaKkQ7aeMdRN2r0p-W4d2TtccL5HcIOp_w-lfkEQ/edit?usp=sharing).
+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.
@@ -277,7 +272,7 @@ citation("epiparameter")
 #>   Epidemiological Parameters with Helper Functions and Classes_.
 #>   doi:10.5281/zenodo.11110881
 #>   <https://doi.org/10.5281/zenodo.11110881>,
-#>   <https://github.com/epiverse-trace/epiparameter/,https://epiverse-trace.github.io/epiparameter/>.
+#>   <https://epiverse-trace.github.io/epiparameter>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
@@ -286,7 +281,6 @@ citation("epiparameter")
 #>     author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo},
 #>     year = {2024},
 #>     doi = {10.5281/zenodo.11110881},
-#>     url = {https://github.com/epiverse-trace/epiparameter/,
-#> https://epiverse-trace.github.io/epiparameter/},
+#>     url = {https://epiverse-trace.github.io/epiparameter},
 #>   }
 ```

inst/CITATION

@@ -20,5 +20,5 @@ bibentry(
   author  = author,
   year    = date,
   doi     = "10.5281/zenodo.11110881",
-  url     = meta$URL
+  url     = "https://epiverse-trace.github.io/epiparameter"
 )

inst/WORDLIST

@@ -12,6 +12,8 @@ distcrete
 dplyr
 ebola
 epidist
+EpiParameter
+epiparameters
 epireview
 episoap
 Epiverse

tests/testthat/_snaps/print.md

@@ -57,7 +57,7 @@
       # i 119 more elements
       # i Use `print(n = ...)` to see more elements.
       # i Use `parameter_tbl()` to see a summary table of the parameters.
-      # i Explore database online at: https://epiverse-trace.github.io/epiparameter/dev/articles/database.html
+      # i Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html
 
 # epidist_db print method works as expected for <= 5 <epidist>
 
@@ -98,5 +98,5 @@
         dispersion: 0.170
 
       # i Use `parameter_tbl()` to see a summary table of the parameters.
-      # i Explore database online at: https://epiverse-trace.github.io/epiparameter/dev/articles/database.html
+      # i Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html