Adding references and a comparison table

UofUEpiBio · Apr 5, 2024 · ae5fe9c · ae5fe9c
1 parent c476aa6
commit ae5fe9c
Show file tree

Hide file tree

Showing 3 changed files with 182 additions and 0 deletions.
diff --git a/paper/paper.md b/paper/paper.md
@@ -72,6 +72,28 @@ package:
   different comorbidities affect the transmission and severity of the
   disease.
 
+## Other alternatives
+
+# Existing Alternatives
+
+The following table from Meyer and Vega Yon (2023) shows existing
+alternatives to epiworld, including **ABM** (Ma 2023), **abmR**
+(Gochanour, Fernandez-Lopez, and Contina 2023), **cystiSim**
+(Devleesschauwer and Braae 2016), **villager** (Thelen et al. 2022), and
+**RNetLogo** (Thiele, Kurth, and Grimm 2012).[^1]
+
+| Package                                                       | Multiple Viruses | Multiple Tools | Multiple Runs | Global Actions | Built-In Epi Models |
+|:--------------------------------------------------------------|:-----------------|:---------------|:--------------|:---------------|---------------------|
+| [**epiworldR**](https://cran.r-project.org/package=epiworldR) | yes              | yes            | yes           | yes            | yes                 |
+| [**ABM**](https://cran.r-project.org/package=ABM)             | \-               | \-             | \-            | yes            | yes                 |
+| [**abmR**](https://cran.r-project.org/package=abmR)           | \-               | \-             | yes           | \-             | \-                  |
+| [**cystiSim**](https://cran.r-project.org/package=cystiSim)   | \-               | yes            | yes           | \-             | \-                  |
+| [**villager**](https://cran.r-project.org/package=villager)   | \-               | \-             | \-            | yes            | \-                  |
+| [**RNetLogo**](https://cran.r-project.org/package=RNetLogo)   | \-               | yes            | yes           | yes            | \-                  |
+
+A benchmark comparing epiworld’s speed with other software packages can
+be found in the [benchmark section](#speed-benchmark).
+
 # Appendix
 
 ## Code example
@@ -158,8 +180,76 @@ Transition Probabilities:
 
 ## Speed benchmark
 
+The following figure shows the time measured in seconds that each of the
+benchmarked software packages took to simulate a SIR model featuring
+50,000 agents for 100 days.
+
 ![](benchmark.png)
 
 ## Implementation
 
+The following figure illustrates the model composition process used in
+epiworld. Generally, users can add an arbitrary number of states,
+viruses, tools, and events to a single model. The flexibility of
+epiworld’s API provides a simple way to extend the model’s capabilities.
+
 ![](building-models.png)
+
+# References
+
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
+
+<div id="ref-cystiSim" class="csl-entry">
+
+Devleesschauwer, Brecht, and Uffe Christian Braae. 2016. *cystiSim:
+Agent-Based Model for Taenia_solium Transmission and Control*.
+<https://CRAN.R-project.org/package=cystiSim>.
+
+</div>
+
+<div id="ref-abmR" class="csl-entry">
+
+Gochanour, Benjamin, Javier Fernandez-Lopez, and Andrea Contina. 2023.
+*abmR: Agent-Based Models in R*.
+<https://doi.org/10.1111/2041-210X.14014>.
+
+</div>
+
+<div id="ref-ABM" class="csl-entry">
+
+Ma, Junling. 2023. *ABM: Agent Based Model Simulation Framework*.
+<https://CRAN.R-project.org/package=ABM>.
+
+</div>
+
+<div id="ref-meyerEpiworldRFastAgentBased2023" class="csl-entry">
+
+Meyer, Derek, and George G Vega Yon. 2023.
+“<span class="nocase">epiworldR</span>: Fast Agent-Based Epi Models.”
+*Journal of Open Source Software* 8 (90): 5781.
+<https://doi.org/10.21105/joss.05781>.
+
+</div>
+
+<div id="ref-villager" class="csl-entry">
+
+Thelen, Thomas, Gerardo Aldana, Marcus Thomson, and Toni Gonzalez. 2022.
+*Villager: A Framework for Designing and Running Agent Based Models*.
+<https://CRAN.R-project.org/package=villager>.
+
+</div>
+
+<div id="ref-RNetLogo" class="csl-entry">
+
+Thiele, Jan C., Winfried Kurth, and Volker Grimm. 2012. “RNetLogo: An R
+Package for Running and Exploring Individual-Based Models Implemented in
+NetLogo.” *Methods in Ecology and Evolution* 3 (3): 480–83.
+<https://doi.org/10.1111/j.2041-210X.2011.00180.x>.
+
+</div>
+
+</div>
+
+[^1]: Although other ABM frameworks are available, the table focuses on
+    those most relevant (and popular) to epidemiological simulations.
diff --git a/paper/paper.qmd b/paper/paper.qmd
@@ -5,6 +5,7 @@ format:
   docx: default
 author: 'George G. Vega Yon, Ph.D.'
 date: April 5, 2024
+bibliography: references.bib
 ---
 
 `epiworld` is a fast and flexible agent-based modeling (ABM) framework for epidemiological simulations. Designed in C++, it can simulate large populations with complex interactions. The framework is designed to be modular, allowing users to extend and modify the model to suit their needs quickly. Besides the C++ library, an R package ([epiworldR](https://github.com/UofUEpiBio/epiworldR)), a ShinyApp ([epiworldRShiny](https://github.com/UofUEpiBio/epiworldRShiny)), and a Python library ([epiworldpy](https://github.com/UofUEpiBio/epiworldpy)) are available to interact with the model.
@@ -35,6 +36,24 @@ As a framework, `epiworld` can simulate various epidemiological scenarios. This
 
 - **Population comorbidities**: The library can model the impact of population comorbidities on the spread of the disease, including how different comorbidities affect the transmission and severity of the disease.
 
+## Other alternatives
+
+# Existing Alternatives
+
+The following table from @meyerEpiworldRFastAgentBased2023 shows existing alternatives to epiworld, including **ABM** [@ABM], **abmR** [@abmR], **cystiSim** [@cystiSim], **villager** [@villager], and **RNetLogo** [@RNetLogo].[^othermodels]
+
+[^othermodels]: Although other ABM frameworks are available, the table focuses on those most relevant (and popular) to epidemiological simulations.
+
+| Package                                                                     | Multiple Viruses | Multiple Tools | Multiple Runs | Global Actions | Built-In Epi Models |
+|:--------|:--------|:--------|:--------|:--------|---------|
+| [**epiworldR**](https://cran.r-project.org/package=epiworldR)               | yes              | yes            | yes           | yes            | yes                 |
+| [**ABM**](https://cran.r-project.org/package=ABM)                           | \-               | \-             | \-            | yes            | yes                 |
+| [**abmR**](https://cran.r-project.org/package=abmR)                         | \-               | \-             | yes           | \-             | \-                  |
+| [**cystiSim**](https://cran.r-project.org/package=cystiSim)                 | \-               | yes            | yes           | \-             | \-                  |
+| [**villager**](https://cran.r-project.org/package=villager)                 | \-               | \-             | \-            | yes            | \-                  |
+| [**RNetLogo**](https://cran.r-project.org/package=RNetLogo) | \-               | yes            | yes           | yes            | \-                  |
+
+A benchmark comparing epiworld's speed with other software packages can be found in the [benchmark section](#speed-benchmark).
 
 # Appendix
 
@@ -120,9 +139,14 @@ Transition Probabilities:
 
 ## Speed benchmark
 
+The following figure shows the time measured in seconds that each of the benchmarked software packages took to simulate a SIR model featuring 50,000 agents for 100 days. 
+
 ![](benchmark.png)
 
 ## Implementation
 
+The following figure illustrates the model composition process used in epiworld. Generally, users can add an arbitrary number of states, viruses, tools, and events to a single model. The flexibility of epiworld's API provides a simple way to extend the model's capabilities.
+
 ![](building-models.png)
 
+# References
diff --git a/paper/references.bib b/paper/references.bib
@@ -0,0 +1,68 @@
+@Manual{ABM,
+    title = {ABM: Agent Based Model Simulation Framework},
+    author = {Junling Ma},
+    year = {2023},
+    note = {R package version 0.3},
+    url = {https://CRAN.R-project.org/package=ABM},
+}
+
+@Manual{abmR,
+    title = {abmR: Agent-Based Models in {R}},
+    author = {Benjamin Gochanour and Javier Fernandez-Lopez and Andrea Contina},
+    year = {2023},
+    note = {R package version 1.0.9},
+    doi = {10.1111/2041-210X.14014},
+}
+  
+@article{gochanour2021abmr,
+  title = {abmR: An R package for agent-based model analysis of large-scale movements across taxa},
+  author = {Gochanour, Benjamin and Fern{\'a}ndez-L{\'o}pez, Javier and Contina, Andrea},
+  journal = {bioRxiv},
+  pages = {2021--09},
+  year = {2021},
+  publisher = {Cold Spring Harbor Laboratory},
+  doi = {10.1101/2021.09.15.460374}
+}
+
+@Manual{cystiSim,
+    title = {cystiSim: Agent-Based Model for Taenia_solium Transmission and Control},
+    author = {Brecht Devleesschauwer and Uffe Christian Braae},
+    year = {2016},
+    note = {R package version 0.1.0},
+    url = {https://CRAN.R-project.org/package=cystiSim},
+}
+  
+@Manual{villager,
+    title = {villager: A Framework for Designing and Running Agent Based Models},
+    author = {Thomas Thelen and Gerardo Aldana and Marcus Thomson and Toni Gonzalez},
+    year = {2022},
+    note = {R package version 1.1.1},
+    url = {https://CRAN.R-project.org/package=villager},
+}
+  
+@Article{RNetLogo,
+    title = {{RNetLogo}: An {R} Package for Running and Exploring
+      Individual-Based Models Implemented in {NetLogo}},
+    author = {Jan C. Thiele and Winfried Kurth and Volker Grimm},
+    journal = {Methods in Ecology and Evolution},
+    year = {2012},
+    volume = {3},
+    number = {3},
+    pages = {480--483},
+    doi = {10.1111/j.2041-210X.2011.00180.x},
+}
+
+@article{meyerEpiworldRFastAgentBased2023,
+  title = {{{epiworldR}}: {{Fast Agent-Based Epi Models}}},
+  shorttitle = {{{epiworldR}}},
+  author = {Meyer, Derek and Vega Yon, George G},
+  year = {2023},
+  month = oct,
+  journal = {Journal of Open Source Software},
+  volume = {8},
+  number = {90},
+  pages = {5781},
+  issn = {2475-9066},
+  doi = {10.21105/joss.05781},
+  urldate = {2023-10-04}
+}