epiverse-trace · pratikunterwegs · Mar 14, 2024 · Feb 9, 2024 · Feb 9, 2024 · Feb 9, 2024
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "epidemics" in publications use:'
 type: software
 license: MIT
 title: 'epidemics: A Library of Compartmental Epidemic Scenario Models'
-version: 0.1.0
+version: 0.1.0.9000
 abstract: A library of compartmental epidemic models taken from the published literature,
   and classes to represent populations with heterogeneous characteristics, public
   health response measures including non-pharmaceutical interventions on social contacts,
@@ -98,27 +98,6 @@ references:
     given-names: Toby
     orcid: https://orcid.org/0000-0002-3146-0865
   year: '2024'
-- type: software
-  title: deSolve
-  abstract: 'deSolve: Solvers for Initial Value Problems of Differential Equations
-    (''ODE'', ''DAE'', ''DDE'')'
-  notes: Imports
-  url: http://desolve.r-forge.r-project.org/
-  repository: https://CRAN.R-project.org/package=deSolve
-  authors:
-  - family-names: Soetaert
-    given-names: Karline
-    email: [email protected]
-    orcid: https://orcid.org/0000-0003-4603-7100
-  - family-names: Petzoldt
-    given-names: Thomas
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-4951-6468
-  - family-names: Setzer
-    given-names: R. Woodrow
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-6709-9186
-  year: '2024'
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
@@ -319,6 +298,17 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-8814-9421
   year: '2024'
+- type: software
+  title: ggdist
+  abstract: 'ggdist: Visualizations of Distributions and Uncertainty'
+  notes: Suggests
+  url: https://mjskay.github.io/ggdist/
+  repository: https://CRAN.R-project.org/package=ggdist
+  authors:
+  - family-names: Kay
+    given-names: Matthew
+    email: [email protected]
+  year: '2024'
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -369,6 +359,21 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+- type: software
+  title: purrr
+  abstract: 'purrr: Functional Programming Tools'
+  notes: Suggests
+  url: https://purrr.tidyverse.org/
+  repository: https://CRAN.R-project.org/package=purrr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4757-117X
+  - family-names: Henry
+    given-names: Lionel
+    email: [email protected]
+  year: '2024'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -448,7 +453,7 @@ references:
   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
@@ -502,6 +507,30 @@ references:
   - family-names: Girlich
     given-names: Maximilian
   year: '2024'
+- type: software
+  title: withr
+  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
+  notes: Suggests
+  url: https://withr.r-lib.org
+  repository: https://CRAN.R-project.org/package=withr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Henry
+    given-names: Lionel
+    email: [email protected]
+  - family-names: Müller
+    given-names: Kirill
+    email: [email protected]
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Chang
+    given-names: Winston
+  year: '2024'
 - type: software
   title: BH
   abstract: 'BH: Boost C++ Header Files'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: epidemics
 Title: A Library of Compartmental Epidemic Scenario Models
-Version: 0.1.0
+Version: 0.1.0.9000
 Authors@R: c(
     person("Pratik", "Gupte", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-5294-7819")),
@@ -32,7 +32,6 @@ Imports:
     checkmate,
     cli,
     data.table,
-    deSolve,
     glue,
     Rcpp,
     RcppEigen,
@@ -45,15 +44,18 @@ Suggests:
     dplyr,
     EpiEstim,
     finalsize,
+    ggdist,
     ggplot2,
     knitr,
+    purrr,
     rmarkdown,
     scales,
     socialmixr,
     spelling,
     testthat (>= 3.0.0),
     tibble,
-    tidyr
+    tidyr,
+    withr
 LinkingTo: 
     BH,
     Rcpp,

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,23 +9,17 @@ S3method(print,vaccination)
 export(as.intervention)
 export(as.vaccination)
 export(epidemic_size)
-export(get_parameter)
 export(intervention)
 export(is_contacts_intervention)
 export(is_intervention)
 export(is_population)
 export(is_rate_intervention)
 export(is_vaccination)
-export(model_default_cpp)
-export(model_default_r)
-export(model_diphtheria_cpp)
-export(model_ebola_r)
-export(model_vacamole_cpp)
-export(model_vacamole_r)
+export(model_default)
+export(model_diphtheria)
+export(model_ebola)
+export(model_vacamole)
 export(new_infections)
-export(no_contacts_intervention)
-export(no_rate_intervention)
-export(no_vaccination)
 export(population)
 export(vaccination)
 import(RcppEigen)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,54 @@
+# epidemics (development version)
+
+The development version of _epidemics_ makes substantial additions to the functionality in v0.1.0, and introduces significant breaking changes in #176.
+
+## Breaking changes
+
+1. The "Vacamole" model has been refactored with the arguments `*_reduction_vax` for the effect of double vaccination on compartmental transition rates renamed to `*_vax`, where `*` may be one of susceptibility, hospitalisation, and mortality. Previously, these parameters were implemented in the internal C++ code, but presented as inverse values to users (i.e., `susceptibility_vax = susceptibility * (1 - (susceptibility_reduction_vax)))`). This change brings the user-facing representation in line with the internal implementation, and allows these parameters to be targeted by rate interventions and time-dependence, which was not possible earlier.
+
+2. All model function have been renamed to `model_<NAME>()`, removing the language suffix.
+
+3. The wrappers around R-only implementations of the 'default' and 'Vacamole' models have been removed, but the ODE system functions have been retained.
+
+4. The function `get_parameter()` has been removed.
+
+## Model structures
+
+There is no change to the model structures.
+
+## Classes
+
+No substantial changes to classes; small additions of input checking to `<population>` class.
+
+## Helper functions
+
+1. Internal helper functions `.check_args_model_*()` and `.prepare_args_model_*()` have been combined into single functions `.check_prepare_args_*()` that are called both for their output and for input checking side effects.
+
+2. The new internal functions `.prepare_population()`, `.cross_check_intervention()`, `.cross_check_vaccination()`, `.cross_check_timedep()`, and `.cross_check_popchange()` check and prepare a model population and check other inputs for compatibility with it. These are used in `.check_prepare_args_*()`.
+
+3. New internal functions have been added to check and recycle lists of vectors; original implementations by @TimTaylor.
+
+4. `output_to_df()` is renamed to `.output_to_df()`.
+
+## Documentation
+
+1. The benchmarking vignette has been removed as the R-only model implementations are no longer provided to users.
+
+2. The vignette on parameter uncertainty has been rewritten to show how to pass vectors of infection parameters and model composable elements to model functions, and renamed to "Modelling parameter uncertainty and epidemic scenarios".
+
+3. All function documentation has been updated to reflect name changes and other minor improvements.
+
+## Package
+
+1. All ODE model functions have received a more extensive and more standardised (as much as possible) test suite.
+
+2. Filenames have been standardised to show which files are related, e.g. `R/model_default.R`, `src/model_default.cpp`, and `inst/include/model_default.h`; references to filenames such as in the package header have been updated.
+
+3. Removed {deSolve} from dependencies.
+
+4. Updated NEWS.md file to track changes to the package.
+
+
 # epidemics 0.1.0
 
 This is an initial GitHub release of _epidemics_, an R package that ships a library of compartmental epidemic model structures that can be used, along with supplied classes that help define population characteristics and epidemic response interventions including vaccinations, to compose and model epidemic scenarios.

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -36,7 +36,7 @@
 #' The second list element is a vector of timesteps.
 #' @keywords internal
 .model_default_cpp <- function(initial_state, transmissibility, infectiousness_rate, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
-    .Call(`_epidemics_model_default_cpp_internal`, initial_state, transmissibility, infectiousness_rate, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
+    .Call(`_epidemics_model_default_internal`, initial_state, transmissibility, infectiousness_rate, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
 }
 
 #' @title Run an SEIHR ODE model for diphtheria using a Boost solver
@@ -74,7 +74,7 @@
 #' The second list element is a vector of timesteps.
 #' @keywords internal
 .model_diphtheria_cpp <- function(initial_state, transmissibility, infectiousness_rate, recovery_rate, reporting_rate, prop_hosp, hosp_entry_rate, hosp_exit_rate, rate_interventions, time_dependence, pop_change_times, pop_change_values, time_end = 100.0, increment = 1.0) {
-    .Call(`_epidemics_model_diphtheria_cpp_internal`, initial_state, transmissibility, infectiousness_rate, recovery_rate, reporting_rate, prop_hosp, hosp_entry_rate, hosp_exit_rate, rate_interventions, time_dependence, pop_change_times, pop_change_values, time_end, increment)
+    .Call(`_epidemics_model_diphtheria_internal`, initial_state, transmissibility, infectiousness_rate, recovery_rate, reporting_rate, prop_hosp, hosp_entry_rate, hosp_exit_rate, rate_interventions, time_dependence, pop_change_times, pop_change_values, time_end, increment)
 }
 
 #' @title Run the RIVM Vacamole model
@@ -128,6 +128,6 @@
 #' The second list element is a vector of timesteps.
 #' @keywords internal
 .model_vacamole_cpp <- function(initial_state, transmissibility, transmissibility_vax, infectiousness_rate, mortality_rate, mortality_rate_vax, hospitalisation_rate, hospitalisation_rate_vax, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
-    .Call(`_epidemics_model_vacamole_cpp_internal`, initial_state, transmissibility, transmissibility_vax, infectiousness_rate, mortality_rate, mortality_rate_vax, hospitalisation_rate, hospitalisation_rate_vax, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
+    .Call(`_epidemics_model_vacamole_internal`, initial_state, transmissibility, transmissibility_vax, infectiousness_rate, mortality_rate, mortality_rate_vax, hospitalisation_rate, hospitalisation_rate_vax, recovery_rate, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
 }