Ensure non-zero negative binomial offspring parameters

CITATION.cff

@@ -1,19 +1,19 @@
-# -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.5.0
+# --------------------------------------------
+# CITATION file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# -----------------------------------------------------------
+# --------------------------------------------
 
 cff-version: 1.2.0
 message: 'To cite package "bpmodels" in publications use:'
 type: software
 license: MIT
 title: 'bpmodels: Simulating and Analysing Transmission Chain Statistics using Branching
   Process Models'
-version: 0.3.1
+version: 0.3.2
 abstract: Provides methods to simulate and analyse the size and length of branching
   processes with an arbitrary offspring distribution. These can be used, for example,
   to analyse the distribution of chain sizes or length of infectious disease outbreaks,
-  as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>.
+  as discussed in Farrington et al. (2003) <https://doi.org/10.1093/biostatistics/4.2.279>.
 authors:
 - family-names: Azam
   given-names: James M.
@@ -37,8 +37,8 @@ preferred-citation:
   - name: James M. Azam
   year: '2023'
   url: https://github.com/epiverse-trace/bpmodels/
-repository-code: https://github.com/epiverse-trace/bpmodels
-url: https://epiverse-trace.github.io/bpmodels/
+repository-code: https://github.com/epiforecasts/bpmodels
+url: https://epiforecasts.io/bpmodels/
 contact:
 - family-names: Azam
   given-names: James M.
@@ -63,11 +63,10 @@ references:
   url: https://www.R-project.org/
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 3.6.0'
 - type: software
   title: bookdown
@@ -80,7 +79,8 @@ references:
     given-names: Yihui
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.bookdown
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -104,7 +104,8 @@ references:
     given-names: Davis
     email: davis@posit.co
     orcid: https://orcid.org/0000-0003-4777-038X
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.dplyr
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -139,7 +140,12 @@ references:
   - family-names: Dunnington
     given-names: Dewey
     orcid: https://orcid.org/0000-0002-9415-4582
-  year: '2023'
+  - family-names: Brand
+    given-names: Teun
+    name-particle: van den
+    orcid: https://orcid.org/0000-0002-9335-7468
+  year: '2024'
+  doi: 10.32614/CRAN.package.ggplot2
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -151,7 +157,8 @@ references:
     given-names: Yihui
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.knitr
 - type: software
   title: lubridate
   abstract: 'lubridate: Make Dealing with Dates a Little Easier'
@@ -166,7 +173,8 @@ references:
     given-names: Garrett
   - family-names: Wickham
     given-names: Hadley
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.lubridate
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -209,12 +217,13 @@ references:
     given-names: Richard
     email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.rmarkdown
 - type: software
   title: spelling
   abstract: 'spelling: Tools for Spell Checking in R'
   notes: Suggests
-  url: https://docs.ropensci.org/spelling/
+  url: https://ropensci.r-universe.dev/spelling
   repository: https://CRAN.R-project.org/package=spelling
   authors:
   - family-names: Ooms
@@ -224,7 +233,8 @@ references:
   - family-names: Hester
     given-names: Jim
     email: james.hester@rstudio.com
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.spelling
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -235,7 +245,8 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: hadley@posit.co
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.testthat
 - type: software
   title: truncdist
   abstract: 'truncdist: Truncated Random Variables'
@@ -248,7 +259,8 @@ references:
   - family-names: Nadarajah
     given-names: Saralees
     email: saralees.nadarajah@manchester.ac.uk
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.truncdist
 - type: software
   title: checkmate
   abstract: 'checkmate: Fast and Versatile Argument Checks'
@@ -260,4 +272,6 @@ references:
     given-names: Michel
     email: michellang@gmail.com
     orcid: https://orcid.org/0000-0001-9754-0393
-  year: '2023'
+  year: '2024'
+  doi: 10.32614/CRAN.package.checkmate
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bpmodels
 Title: Simulating and Analysing Transmission Chain Statistics using Branching Process
     Models
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
     person("James M.", "Azam", , "james.azam@lshtm.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "https://orcid.org/0000-0001-5782-7330")),

NEWS.md

@@ -1,3 +1,9 @@
+# bpmodels 0.3.2
+
+## Model
+
+* `chain_sim()` now ensures that the parameters of the negative binomial offspring are not both zero else returns an informative error.
+
 # bpmodels 0.3.1
 
 ## Unit tests and input validation

R/simulate.r

@@ -128,6 +128,13 @@ chain_sim <- function(n, offspring, stat = c("size", "length"), infinite = Inf,
   if (!(exists(roffspring_name)) || !is.function(get(roffspring_name))) {
     stop("Function ", roffspring_name, " does not exist.")
   }
+  # If both parameters of the negative binomial are zero, you get NaNs
+  if (roffspring_name == "rnbinom" && all(c(...) == 0)) {
+    stop(
+      "The negative binomial parameters must have at least one ",
+      "non-zero parameter."
+    )
+  }
 
   if (!missing(serial)) {
     if (!is.function(serial)) {

inst/WORDLIST

@@ -1,6 +1,8 @@
 Borel
 CMD
 COVID
+Eq
+Lifecycle
 Marivate
 ORCID
 Poisson
@@ -9,16 +11,25 @@ README's
 Vukosi
 Zhian
 codecov
+cutoff
 dfrac
 doi
 ecdf
+epichains
+frac
 gborel
+geq
 immunes
+infectee
 infectees
+infector
 infectors
 json
+kS
 linelist
 ln
+mathbf
+mathrm
 nbinom
 nolint
 pois
@@ -27,4 +38,6 @@ quickstart
 sim
 superspreading
 susceptibles
+th
+unnormalised
 var

tests/testthat/tests-sim.r

@@ -134,6 +134,16 @@ test_that("Errors are thrown", {
     ),
     "If `tf` is specified, `serial` must be specified too."
   )
+  expect_error(
+    chain_sim(
+      n = 10,
+      offspring = "nbinom",
+      stat = "size",
+      mu = 0,
+      size = 0
+    ),
+    "must have at least one non-zero parameter"
+  )
 })
 
 test_that("Chains can be simulated", {