Add new package infrastructure (epichains classes and methods)

.github/workflows/update-citation-cff.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+      - .github/workflows/update-citation-cff.yaml
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+      - name: Update CITATION.cff
+        run: |
+          library(cffr)
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+          # Write your own keys
+          mykeys <- list()
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.lintr

@@ -6,7 +6,11 @@ linters: linters_with_tags(
     extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
     function_argument_linter = NULL,
-    cyclocomp_linter = NULL,
-    # Use minimum R declared in DESCRIPTION or fall back to current R version
+    indentation_linter = NULL, # unstable as of lintr 3.1.0
+    # Use minimum R declared in DESCRIPTION or fall back to current R version.
+    # Install etdev package from https://github.com/epiverse-trace/etdev
     backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
-    )
+  )
+exclusions: list(
+    "tests/testthat.R" = list(unused_import_linter = Inf)
+  )

CITATION.cff

@@ -1,47 +1,57 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.4.1
+# CITATION file created with {cffr} R package, v0.5.0
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
 
 cff-version: 1.2.0
-message: 'To cite package "bpmodels" in publications use:'
+message: 'To cite package "epichains" in publications use:'
 type: software
 license: MIT
-title: 'bpmodels: Analysing transmission chain statistics using branching process
-  models'
-version: 0.2.0
-abstract: Provides methods to analyse and simulate the size and length of branching
+title: 'epichains: Simulating and Analysing Transmission Chain Statistics Using Branching
+  Process Models'
+version: 0.1.0
+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>.
 authors:
-- family-names: Funk
-  given-names: Sebastian
-  email: [email protected]
-  orcid: https://orcid.org/0000-0002-2842-3406
-- family-names: Finger
-  given-names: Flavio
-  email: [email protected]
-  orcid: https://orcid.org/0000-0002-8613-5170
 - family-names: Azam
   given-names: James M.
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5782-7330
-repository-code: https://github.com/epiverse-trace/bpmodels
-url: https://epiverse-trace.github.io/bpmodels/
+- family-names: Finger
+  given-names: Flavio
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-8613-5170
+- family-names: Funk
+  given-names: Sebastian
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-2842-3406
+preferred-citation:
+  type: manual
+  title: 'epichains: Analysing transmission chain statistics using branching process
+    models'
+  authors:
+  - name: Sebastian Funk
+  - name: Flavio Finger
+  - name: James M. Azam
+  year: '2023'
+  url: https://github.com/epiverse-trace/epichains/
+repository-code: https://github.com/epiverse-trace/epichains
+url: https://epiverse-trace.github.io/epichains/
 contact:
 - family-names: Azam
   given-names: James M.
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5782-7330
 keywords:
-- branching-process
+- branching-processes
 - epidemic-dynamics
 - epidemic-modelling
 - epidemic-simulations
 - outbreak-simulator
-- r
 - r-package
+- r-stats
 - transmission-chain
 - transmission-chain-reconstruction
 references:
@@ -56,7 +66,41 @@ references:
   year: '2023'
   institution:
     name: R Foundation for Statistical Computing
-  version: '>= 3.0.0'
+  version: '>= 3.6.0'
+- type: software
+  title: checkmate
+  abstract: 'checkmate: Fast and Versatile Argument Checks'
+  notes: Imports
+  url: https://mllg.github.io/checkmate/
+  repository: https://CRAN.R-project.org/package=checkmate
+  authors:
+  - family-names: Lang
+    given-names: Michel
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-9754-0393
+  year: '2023'
+- type: software
+  title: stats
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+- type: software
+  title: utils
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
 - type: software
   title: bookdown
   abstract: 'bookdown: Authoring Books and Technical Documents with R Markdown'
@@ -190,37 +234,55 @@ references:
   authors:
   - family-names: Allaire
     given-names: JJ
-    email: jj@rstudio.com
+    email: jj@posit.co
   - family-names: Xie
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Dervieux
+    given-names: Christophe
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4474-2498
   - family-names: McPherson
     given-names: Jonathan
-    email: jonathan@rstudio.com
+    email: jonathan@posit.co
   - family-names: Luraschi
     given-names: Javier
-    email: [email protected]
   - family-names: Ushey
     given-names: Kevin
-    email: kevin@rstudio.com
+    email: kevin@posit.co
   - family-names: Atkins
     given-names: Aron
-    email: aron@rstudio.com
+    email: aron@posit.co
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
   - family-names: Cheng
     given-names: Joe
-    email: joe@rstudio.com
+    email: joe@posit.co
   - family-names: Chang
     given-names: Winston
-    email: winston@rstudio.com
+    email: winston@posit.co
   - family-names: Iannone
     given-names: Richard
-    email: rich@rstudio.com
+    email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2023'
+- type: software
+  title: spelling
+  abstract: 'spelling: Tools for Spell Checking in R'
+  notes: Suggests
+  url: https://docs.ropensci.org/spelling/
+  repository: https://CRAN.R-project.org/package=spelling
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-4035-0289
+  - family-names: Hester
+    given-names: Jim
+    email: [email protected]
+  year: '2023'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -230,7 +292,7 @@ references:
   authors:
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
   year: '2023'
 - type: software
   title: truncdist
@@ -254,14 +316,18 @@ references:
   authors:
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
     orcid: https://orcid.org/0000-0003-4757-117X
   - family-names: Bryan
     given-names: Jennifer
-    email: jenny@rstudio.com
+    email: jenny@posit.co
     orcid: https://orcid.org/0000-0002-6983-2759
   - family-names: Barrett
     given-names: Malcolm
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0299-5825
+  - family-names: Teucher
+    given-names: Andy
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-7840-692X
   year: '2023'

DESCRIPTION

@@ -1,45 +1,32 @@
 Package: epichains
-Title: Analysing transmission chain statistics using branching process models
-Version: 0.2.1
+Title: Simulating and Analysing Transmission Chain Statistics Using Branching Process
+    Models
+Version: 0.1.0
 Authors@R: c(
-    person(
-    given = "Sebastian",
-    family = "Funk",
-    email = "[email protected]",
-    role = "aut",
-    comment = c(ORCHID = "https://orcid.org/0000-0002-2842-3406")
-    ),
-    person(
-    given = "Zhian N.",
-    family = "Kamvar",
-    email = "[email protected]",
-    role = "ctb",
-    comment = c(ORCHID = "https://orcid.org/0000-0003-1458-7108")
-    ),
-    person(
-    given = "Flavio",
-    family = "Finger",
-    email = "[email protected]",
-    role = "aut",
-    comment = c(ORCHID = "https://orcid.org/0000-0002-8613-5170")
-    ),
-    person(
-    given = "James M.",
-    family = "Azam",
-    email = "[email protected]",
-    role = c("aut", "cre"),
-    comment = c(ORCHID = "https://orcid.org/0000-0001-5782-7330"))
-  )
-Description: Provides methods to analyse and simulate the size and length
+    person("James M.", "Azam", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "https://orcid.org/0000-0001-5782-7330")),
+    person("Zhian N.", "Kamvar", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "https://orcid.org/0000-0003-1458-7108")),
+    person("Flavio", "Finger", , "[email protected]", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0002-8613-5170")),
+    person("Sebastian", "Funk", , "[email protected]", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0002-2842-3406"))
+           )
+Description: 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>.
 License: MIT + file LICENSE
-URL: https://github.com/epiverse-trace/epichains, https://epiverse-trace.github.io/epichains/
+URL: https://github.com/epiverse-trace/epichains,
+    https://epiverse-trace.github.io/epichains/
 BugReports: https://github.com/epiverse-trace/epichains/issues
 Depends:
     R (>= 3.6.0)
+Imports: 
+    checkmate,
+    stats,
+    utils
 Suggests:
     bookdown,
     covr,
@@ -53,11 +40,11 @@ Suggests:
     testthat,
     truncdist,
     usethis
-Config/testthat/edition: 3
 VignetteBuilder:
     knitr
 Remotes:
     github::epiverse-trace/epiparameter
+Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,6 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
-export(chain_ll)
-export(chain_sim)
-export(chain_sim_susc)
+S3method(aggregate,epichains)
+S3method(format,epichains)
+S3method(head,epichains)
+S3method(print,epichains)
+S3method(summary,epichains)
+S3method(tail,epichains)
+export(dborel)
+export(is_chains_summary)
+export(is_chains_tree)
+export(is_epichains)
+export(is_epichains_aggregate_df)
+export(likelihood)
+export(offspring_ll)
+export(rborel)
 export(rnbinom_mean_disp)
+export(simulate_summary)
+export(simulate_tree)
+export(simulate_tree_from_pop)
+export(validate_epichains)
+importFrom(stats,aggregate)
+importFrom(utils,head)
+importFrom(utils,tail)