epiverse-trace · joshwlambert · Jan 28, 2025 · Jan 22, 2025 · Jan 22, 2025 · Jan 22, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,5 @@
 ^Meta$
 ^CITATION\.cff$
 ^tools$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,96 +1,60 @@
 Package: superspreading
-Title: Estimate Individual-Level Variation in Transmission
-Version: 0.2.0.9000
-Authors@R: 
-    c(
-        person(
-            given = "Joshua W.",
-            family = "Lambert",
-            role = c("aut", "cre", "cph"),
-            email = "joshua.lambert@lshtm.ac.uk",
-            comment = c(ORCID = "0000-0001-5218-3046")
-        ),
-        person(
-            given = "Adam", 
-            family = "Kucharski",
-            role = c("aut", "cph"),
-            email = "adam.kucharski@lshtm.ac.uk", 
-            comment = c(ORCID = "0000-0001-8814-9421")
-        ),
-        person(
-            given = "Dillon C.",
-            family = "Adam",
-            role = c("aut"),
-            email = "dcadam@hku.hk",
-            comment = c(ORCID = "0000-0002-7485-9905")
-        ),
-        person(
-            given = "Sebastian",
-            family = "Funk",
-            role = c("ctb", "cph"),
-            email = "sebastian.funk@lshtm.ac.uk",
-            comment = c(
-              ORCID = "0000-0002-2842-3406",
-              ".chain_sim uses code from bpmodels::chain_sim"
-            )
-        ),
-        person(
-            given = "Pratik",
-            family = "Gupte",
-            role = c("rev"),
-            email = "pratik.gupte@lshtm.ac.uk",
-            comment = c(ORCID = "0000-0001-5294-7819")
-        ),
-        person(
-            given = "Hugo",
-            family = "Gruson",
-            role = c("rev"),
-            email = "hugo@data.org",
-            comment = c(ORCID = "0000-0002-4094-1476")
-        ),
-        person(
-            given = "James M.",
-            family = "Azam", 
-            role = c("rev", "ctb"),
-            email = "james.azam@lshtm.ac.uk",
-            comment = c(ORCID = "0000-0001-5782-7330")
-        ),
-        person(
-            given = "Chris", 
-            family = "Hartgerink",
-            role = "rev",
-            email = "chris@data.org",
-            comment = c(ORCID = "0000-0003-1050-6809")
-        )
-    )
-Description: Implements functions to estimate individual-level variation in 
-    transmission.
+Title: Understand Individual-Level Variation in Infectious Disease
+    Transmission
+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")),
+    person("Adam", "Kucharski", , "adam.kucharski@lshtm.ac.uk", role = c("aut", "cph"),
+           comment = c(ORCID = "0000-0001-8814-9421")),
+    person("Dillon C.", "Adam", , "dcadam@hku.hk", role = "aut",
+           comment = c(ORCID = "0000-0002-7485-9905")),
+    person("Sebastian", "Funk", , "sebastian.funk@lshtm.ac.uk", role = c("ctb", "cph"),
+           comment = c(ORCID = "0000-0002-2842-3406", ".chain_sim uses code from bpmodels::chain_sim")),
+    person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = "rev",
+           comment = c(ORCID = "0000-0001-5294-7819")),
+    person("Hugo", "Gruson", , "hugo@data.org", role = "rev",
+           comment = c(ORCID = "0000-0002-4094-1476")),
+    person("James M.", "Azam", , "james.azam@lshtm.ac.uk", role = c("rev", "ctb"),
+           comment = c(ORCID = "0000-0001-5782-7330")),
+    person("Chris", "Hartgerink", , "chris@data.org", role = "rev",
+           comment = c(ORCID = "0000-0003-1050-6809"))
+  )
+Description: Estimate and understand individual-level variation in
+    transmission. Implements density and cumulative compound Poisson
+    discrete distribution functions ('Kremer et al.' (2021) 
+    <doi:10.1038/s41598-021-93578-x>), as well as functions to calculate
+    infectious disease outbreak statistics given epidemiological
+    parameters on individual-level transmission; including the probability
+    of an outbreak becoming an epidemic/extinct ('Kucharski et al.' (2020) 
+    <doi:10.1016/S1473-3099(20)30144-4>), or the cluster size
+    statistics, e.g. what proportion of cases cause X\% of transmission
+    ('Lloyd-Smith et al.' (2005) <doi:10.1038/nature04153>).
 License: MIT + file LICENSE
-URL: https://github.com/epiverse-trace/superspreading, https://epiverse-trace.github.io/superspreading/
+URL: https://github.com/epiverse-trace/superspreading,
+    https://epiverse-trace.github.io/superspreading/
 BugReports: https://github.com/epiverse-trace/superspreading/issues
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
 Imports:
     checkmate,
-    stats,
-    rlang
+    rlang,
+    stats
 Suggests: 
-    epiparameter,
+    dplyr,
+    epiparameter (>= 0.4.0),
     fitdistrplus,
-    knitr,
-    rmarkdown,
     ggplot2,
-    spelling,
     ggtext,
-    scales,
+    knitr,
     purrr,
-    dplyr,
+    rmarkdown,
+    scales,
+    spelling,
     testthat (>= 3.0.0)
-Remotes:
-    epiverse-trace/epiparameter
+VignetteBuilder: 
+    knitr
+Config/Needs/website: epiverse-trace/epiversetheme
 Config/testthat/edition: 3
-Config/Needs/website:
-    epiverse-trace/epiversetheme
-VignetteBuilder: knitr
+Encoding: UTF-8
 Language: en-GB
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# superspreading (development version)
+# superspreading 0.3.0
 
 The third minor release of the _superspreading_ package contains enhancements to several functions and a new vignette. 
 

diff --git a/R/probability_contain.R b/R/probability_contain.R
@@ -87,11 +87,11 @@
 #'   rlnorm(n, meanlog = 1, sdlog = 1.5)
 #' }
 #' probability_contain(
-#'   R = 1.5,
+#'   R = 1.2,
 #'   k = 0.5,
 #'   num_init_infect = 1,
 #'   simulate = TRUE,
-#'   case_threshold = 100,
+#'   case_threshold = 50,
 #'   outbreak_time = 20,
 #'   generation_time = gt
 #' )

diff --git a/R/utils.R b/R/utils.R
@@ -46,7 +46,7 @@ get_epiparameter_param <- function(epiparameter,
 #' @description This is a helper function for creating a model comparison
 #' `<data.frame>` primarily for use in the \pkg{superspreading} vignettes. It
 #' is designed specifically for handling [fitdistrplus::fitdist()] output and
-#' not a generalised function. See [bbmle::ICtab()] for a more general use
+#' not a generalised function. See `bbmle::ICtab()` for a more general use
 #' function to create information criteria tables.
 #'
 #' @param ... [dots] One or more model fit results from

diff --git a/README.Rmd b/README.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 # _superspreading_: Estimate individual-level variation in transmission <img src="man/figures/logo.svg" align="right" width="120"/>
 
 <!-- badges: start -->
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
 [![R-CMD-check](https://github.com/epiverse-trace/superspreading/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/superspreading/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/epiverse-trace/superspreading/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/superspreading?branch=main)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
@@ -34,15 +34,27 @@ from data on secondary cases.
 
 ## Installation
 
+The package can be installed from CRAN using
+
+```r
+install.packages("superspreading")
+```
+
 The easiest way to install the development version of `{superspreading}` from
 [GitHub](https://github.com/) is to use the `{pak}` package:
 
-  ``` r
+``` r
 # check whether {pak} is installed
 if(!require("pak")) install.packages("pak")
 pak::pak("epiverse-trace/superspreading")
 ```
 
+Alternatively, install pre-compiled binaries from [the Epiverse TRACE R-universe](https://epiverse-trace.r-universe.dev/superspreading)
+
+``` r
+install.packages("superspreading", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
+```
+
 ## Quick start
 
 ```{r load-superspreading}

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![License:
-MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
 [![R-CMD-check](https://github.com/epiverse-trace/superspreading/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/superspreading/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/epiverse-trace/superspreading/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/superspreading?branch=main)
@@ -34,6 +34,12 @@ Medicine](https://www.lshtm.ac.uk/) as part of
 
 ## Installation
 
+The package can be installed from CRAN using
+
+``` r
+install.packages("superspreading")
+```
+
 The easiest way to install the development version of `{superspreading}`
 from [GitHub](https://github.com/) is to use the `{pak}` package:
 
@@ -43,6 +49,13 @@ if(!require("pak")) install.packages("pak")
 pak::pak("epiverse-trace/superspreading")
 ```
 
+Alternatively, install pre-compiled binaries from [the Epiverse TRACE
+R-universe](https://epiverse-trace.r-universe.dev/superspreading)
+
+``` r
+install.packages("superspreading", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
+```
+
 ## Quick start
 
 ``` r
@@ -197,17 +210,19 @@ By contributing to this project, you agree to abide by its terms.
 citation("superspreading")
 #> To cite package 'superspreading' in publications use:
 #> 
-#>   Lambert J, Kucharski A, Adam D (2024). _superspreading: Estimate
-#>   Individual-Level Variation in Transmission_. R package version
-#>   0.2.0.9000, https://epiverse-trace.github.io/superspreading/,
+#>   Lambert J, Kucharski A, Adam D (2025). _superspreading: Understand
+#>   Individual-Level Variation in Infectious Disease Transmission_. R
+#>   package version 0.2.0.9000,
+#>   https://epiverse-trace.github.io/superspreading/,
 #>   <https://github.com/epiverse-trace/superspreading>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {superspreading: Estimate Individual-Level Variation in Transmission},
+#>     title = {superspreading: Understand Individual-Level Variation in Infectious Disease
+#> Transmission},
 #>     author = {Joshua W. Lambert and Adam Kucharski and Dillon C. Adam},
-#>     year = {2024},
+#>     year = {2025},
 #>     note = {R package version 0.2.0.9000, 
 #> https://epiverse-trace.github.io/superspreading/},
 #>     url = {https://github.com/epiverse-trace/superspreading},

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,7 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
+
+* The author names in the `Description:` in the `DESCRIPTION` file were flagged in the initial submission with the message "Possibly misspelled words in DESCRIPTION", I've surrounded the names in single quotes as suggestion in Writing R Extensions. 
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -18,6 +18,7 @@ CoV
 COVID
 Delaporte
 Delignette
+doi
 dplyr
 Driessche
 du

diff --git a/man/ic_tbl.Rd b/man/ic_tbl.Rd
diff --git a/man/probability_contain.Rd b/man/probability_contain.Rd
diff --git a/man/superspreading-package.Rd b/man/superspreading-package.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,6 +18,7 @@ CoV @@
     COVID
     Delaporte
     Delignette
+    doi
     dplyr
     Driessche
     du
@@ Expand Down @@