Package updates for v0.3.0 CRAN submission

.Rbuildignore

@@ -17,3 +17,5 @@
 ^vignettes/*.orig$
 ^vignettes/figure$
 ^vignettes/articles$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epiparameter
 Title: Library of Epidemiological Parameters with Helper Functions and
     Classes
-Version: 0.2.0.9000
+Version: 0.3.0
 Authors@R: c(
     person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-5218-3046")),
@@ -23,7 +23,8 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-8587-7113"))
   )
 Description: Library of epidemiological parameters for infectious diseases
-    and a set of classes and helper functions.
+    extracted from the literature, and a set of classes and helper functions
+    for working with parameters.
 License: MIT + file LICENSE
 URL: https://github.com/epiverse-trace/epiparameter/,
     https://epiverse-trace.github.io/epiparameter/

NEWS.md

@@ -1,4 +1,4 @@
-# epiparameter (development version)
+# epiparameter 0.3.0
 
 The third minor release of the {epiparameter} R package contains a range of updates and improvements to the package. The principal aim of this release is to simplify, clarify and enhance the classes and class methods when working with epidemiological parameters in R. 
 
@@ -10,7 +10,7 @@ This is the first version of {epiparameter} to be released on CRAN.
 
 * The library of epidemiological parameters has been updated to include 3 new Chikungunya parameter entries. The Mpox parameters previously missing from the Guzzetta et al. entry have been added (#346 & #374).
 * A `c()` method has been added for `<epiparameter>` and `<multi_epiparameter>` objects (#368).
-* An `aggregate()` method has been added for `<multi_epiparameter>` to enable consensus distributions to be built utilising the mixture distribution class from [{distributional}](https://cran.r-project.org/web/packages/distributional/index.html) (#388).
+* An `aggregate()` method has been added for `<multi_epiparameter>` to enable consensus distributions to be built utilising the mixture distribution class from [{distributional}](https://CRAN.R-project.org/package=distributional) (#388).
 * Infrastructure has been added to the package to allow translations of messages/warnings/errors printed to the console. (@Bisaloo, #367).
 * `convert_summary_stats_to_params()` can now convert from median and dispersion for a lognormal distribution (#378).
 * The `data_dictionary.json` has been enhanced to improve validation of the library of epidemiological parameters (`parameters.json`) (#379).

R/accessors.R

@@ -64,6 +64,7 @@ get_parameters.epiparameter <- function(x, ...) {
   params
 }
 
+#' @rdname get_parameters.epiparameter
 #' @export
 get_parameters.multi_epiparameter <- function(x, ...) {
   params <- lapply(x, get_parameters)

R/checkers.R

@@ -41,13 +41,15 @@ is_parameterised <- function(x, ...) {
 #' @export
 is_parameterized <- is_parameterised
 
+#' @rdname is_parameterised
 #' @export
 is_parameterised.epiparameter <- function(x, ...) {
   chkDots(...)
   # probability distribution object
   return(is.object(x$prob_distribution))
 }
 
+#' @rdname is_parameterised
 #' @export
 is_parameterised.multi_epiparameter <- function(x, ...) {
   chkDots(...)

R/coercion.R

@@ -15,6 +15,16 @@
 #'
 #' @return A [function] object.
 #' @export
+#'
+#' @examples
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' # by default it will convert to a density function
+#' f <- as.function(ep)
+#' # use function
+#' f(10)
+#'
+#' f <- as.function(ep, func_type = "cdf")
+#' f(10)
 as.function.epiparameter <- function(x,
                                      func_type = c(
                                        "density", "cdf", "generate", "quantile"
@@ -53,6 +63,10 @@ as.function.epiparameter <- function(x,
 #'
 #' @return A `<data.frame>` with a single row.
 #' @export
+#'
+#' @examples
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' as.data.frame(ep)
 as.data.frame.epiparameter <- function(x, ...) {
   chkDots(...)
   # check object as could be invalidated by user
@@ -82,6 +96,10 @@ as.data.frame.epiparameter <- function(x, ...) {
 #'
 #' @return A `<data.frame>` with as many rows as length of input list.
 #' @export
+#'
+#' @examples
+#' db <- epiparameter_db()
+#' as.data.frame(db)
 as.data.frame.multi_epiparameter <- function(x, ...) {
   chkDots(...)
   do.call(rbind, lapply(x, as.data.frame))
@@ -133,6 +151,11 @@ as_epiparameter <- function(x, ...) {
 #'
 #' @inherit epiparameter_db return
 #' @export
+#'
+#' @examples
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' df <- as.data.frame(ep)
+#' ep <- as_epiparameter(df)
 as_epiparameter.data.frame <- function(x, ...) {
   if (is_epiparameter_df(x)) {
     epiparameter <- .epiparameter_df_to_epiparameter(x, ...)
@@ -189,19 +212,12 @@ is_epiparameter_df <- function(x) {
 #' @inherit epiparameter return
 #' @keywords internal
 .epiparameter_df_to_epiparameter <- function(x, ...) { # nolint object_length_linter
-  # extract probability distribution from list and extract parameters
-  # and truncation if available
   prob_dist <- x$prob_distribution[[1]]
   if (inherits(prob_dist, "distribution")) {
     prob_distribution_params <- unlist(
       distributional::parameters(x$prob_distribution[[1]])
     )
   }
-  if (identical(family(prob_dist), "truncated")) {
-    truncation <- distributional::parameters(x$prob_distribution)$upper
-  } else {
-    truncation <- NA_real_
-  }
   # create uncertainty list of parameters if not provided
   if (all(unlist(lapply(x$uncertainty$uncertainty, is.na)))) {
     uncertainty <- x$uncertainty$uncertainty
@@ -212,23 +228,15 @@ is_epiparameter_df <- function(x) {
     )
   }
 
-  # remove <AsIs> from citation
-  class(x$citation) <- setdiff(class(x$citation), "AsIs")
-
   # return <epiparameter> from class constructor
   epiparameter(
     disease = x$disease,
     pathogen = x$pathogen,
     epi_name = x$epi_name,
-    prob_distribution = create_prob_distribution(
-      prob_distribution = family(x$prob_distribution[[1]]),
-        prob_distribution_params = prob_distribution_params,
-      discretise = inherits(x$prob_distribution[[1]], "distcrete"),
-      truncation = truncation
-    ),
+    prob_distribution = prob_dist,
     uncertainty = uncertainty,
     summary_stats = x$summary_stats$summary_stats,
-    citation = x$citation,
+    citation = x$citation[[1]],
     metadata = x$metadata,
     method_assess = x$method_assess,
     notes = x$notes

R/epiparameter.R

@@ -302,6 +302,14 @@ epiparameter <- function(disease,
 #' (errors when invalid `<epiparameter>` object is provided).
 #'
 #' @export
+#'
+#' @examples
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' assert_epiparameter(ep)
+#'
+#' # example with invalid <epiparameter>
+#' ep$disease <- NULL
+#' try(assert_epiparameter(ep))
 assert_epiparameter <- function(x) {
   msg <- .validate_epiparameter(x)
   if (length(msg) > 0) {
@@ -320,6 +328,14 @@ assert_epiparameter <- function(x) {
 #' @return A boolean `logical` whether the object is a valid `<epiparameter>`
 #' object (prints message when invalid `<epiparameter>` object is provided).
 #' @export
+#'
+#' @examples
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' test_epiparameter(ep)
+#'
+#' # example with invalid <epiparameter>
+#' ep$disease <- NULL
+#' test_epiparameter(ep)
 test_epiparameter <- function(x) {
   msg <- .validate_epiparameter(x)
   if (length(msg) > 0) {
@@ -987,6 +1003,7 @@ c.epiparameter <- function(...) {
   ep_list
 }
 
+#' @rdname c.epiparameter
 #' @export
 c.multi_epiparameter <- function(...) {
   c.epiparameter(...)

R/parameter_tbl.R

@@ -10,8 +10,10 @@
 #' @param multi_epiparameter Either an `<epiparameter>` object or a list of
 #' `<epiparameter>` objects.
 #'
-#' @author Joshua W. Lambert, Adam Kucharski
+#' @return A `<parameter_tbl>` object which is a subclass of `<data.frame>`.
 #' @export
+#' @author Joshua W. Lambert, Adam Kucharski
+#'
 #' @examples
 #' epiparameter_list <- epiparameter_db(disease = "COVID-19")
 #' parameter_tbl(multi_epiparameter = epiparameter_list)

README.Rmd

@@ -31,7 +31,13 @@ knitr::opts_chunk$set(
 
 ## Installation
 
-The easiest way to install the development version of `{epiparameter}` is to use the `{pak}` package:
+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
@@ -41,7 +47,7 @@ pak::pak("epiverse-trace/epiparameter")
 
 Alternatively, install pre-compiled binaries from [the Epiverse TRACE R-universe](https://epiverse-trace.r-universe.dev/epiparameter)
 
-```r
+``` r
 install.packages("epiparameter", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
 ```
 

README.md

@@ -29,8 +29,15 @@ Medicine](https://www.lshtm.ac.uk/) as part of
 
 ## Installation
 
-The easiest way to install the development version of `{epiparameter}`
-is to use the `{pak}` package:
+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
@@ -272,7 +279,7 @@ citation("epiparameter")
 #>   Epidemiological Parameters with Helper Functions and Classes_.
 #>   doi:10.5281/zenodo.11110881
 #>   <https://doi.org/10.5281/zenodo.11110881>,
-#>   <https://epiverse-trace.github.io/epiparameter>.
+#>   <https://epiverse-trace.github.io/epiparameter/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
@@ -281,6 +288,6 @@ citation("epiparameter")
 #>     author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo},
 #>     year = {2024},
 #>     doi = {10.5281/zenodo.11110881},
-#>     url = {https://epiverse-trace.github.io/epiparameter},
+#>     url = {https://epiverse-trace.github.io/epiparameter/},
 #>   }
 ```

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

inst/CITATION

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

inst/WORDLIST

@@ -33,6 +33,7 @@ medRxiv
 MERS
 monkeypox
 mpox
+Mpox
 ORCID
 parameterisations
 parameterised