Bumping version and creating citation file

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
-Version: 0.0-9999
+Version: 0.1-0
 Date: 2024-04-07
 Authors@R: c(
   person("Derek", "Meyer", role=c("aut","cre"), 

Makefile

@@ -15,7 +15,7 @@ install-dev: clean
 	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldRdev/g' R/epiworldR-package.R
 	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldRdev/g' NAMESPACE
 	sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION 
-	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldRdev)/g' README.*
+	sed -i -E 's/^library\(epiworldR\)/library(epiworldRdev)/g' README.*
 	Rscript --vanilla -e 'roxygen2::roxygenize()'
 	EPI_DEV=yes R CMD INSTALL .& $(MAKE) clean
 
@@ -42,7 +42,7 @@ clean:
 	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldR/g' NAMESPACE
 	sed -i -E 's/^Package:.+/Package: epiworldR/g' DESCRIPTION 
 	# sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' man/epiworldR-package.Rd
-	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldR)/g' README.*
+	sed -i -E 's/^library\(epiworldRdev\)/library(epiworldR)/g' README.*
 
 docs:
 	Rscript --vanilla -e 'devtools::document()'

NEWS.md

@@ -1,4 +1,4 @@
-# epiworldR 0.0-9999 (development version)
+# epiworldR 0.1-0`
 
 * Force model to update agents' states when running a simulation.
   This was causing issues when calling `run_multiple()` after a single

README.Rmd

@@ -244,6 +244,14 @@ plot(ans$reproductive)
 https://github.com/UofUEpiBio/epiworldR-workshop/tree/sunbetl2023-inperson
 
 
+# Citation
+
+If you use `epiworldR` in your research, please cite it as follows:
+
+```{r}
+citation("epiworldR")
+```
+
 # Existing Alternatives
 
 Several alternatives to `epiworldR` exist and provide researchers with a range of options, each with its own unique features and strengths, enabling the exploration and analysis of infectious disease dynamics through agent-based modeling. Below is a manually curated table of existing alternatives including ABM [@ABM], abmR [@abmR], cystiSim [@cystiSim], villager [@villager], and RNetLogo [@RNetLogo].

README.md

@@ -119,8 +119,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 155.00ms
-#> Last run speed      : 32.12 million agents x day / second
+#> Last run elapsed t  : 141.00ms
+#> Last run speed      : 35.22 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global events:
@@ -412,6 +412,28 @@ plot(ans$reproductive)
 - The in-person INSNA Sunbelt 2023 session can be found here:
   <https://github.com/UofUEpiBio/epiworldR-workshop/tree/sunbetl2023-inperson>
 
+# Citation
+
+If you use `epiworldR` in your research, please cite it as follows:
+
+``` r
+citation("epiworldR")
+#> To cite epiworldR in publications use:
+#> 
+#>   Meyer, Derek and Vega Yon, George (2023). epiworldR: Fast Agent-Based
+#>   Epi Models. Journal of Open Source Software, 8(90), 5781,
+#>   https://doi.org/10.21105/joss.05781
+#> 
+#> And the actual R package:
+#> 
+#>   Meyer D, Vega Yon G (2024). _epiworldR: Fast Agent-Based Epi Models_.
+#>   R package version 0.1-0, <https://github.com/UofUEpiBio/epiworldR>.
+#> 
+#> To see these entries in BibTeX format, use 'print(<citation>,
+#> bibtex=TRUE)', 'toBibtex(.)', or set
+#> 'options(citation.bibtex.max=999)'.
+```
+
 # Existing Alternatives
 
 Several alternatives to `epiworldR` exist and provide researchers with a

inst/CITATION

@@ -0,0 +1,36 @@
+year <- sub("-.*", "", meta$Date)
+note <- sprintf("R package version %s", meta$Version)
+
+bibentry(
+  header = "To cite epiworldR in publications use:",
+  bibtype = "Article",
+  entry  = "Article",
+  title = "epiworldR: Fast Agent-Based Epi Models",
+  author = c(
+    person("Derek", "Meyer", role=c("aut","cre"), email="[email protected]", comment = c(ORCID = "0009-0005-1350-6988")),
+    person("George", "Vega Yon", role=c("aut"), email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844"))
+    ),
+  journal = "The Journal of Open Source Software",
+  year    = 2023,
+  month   = "oct",
+  volume  = 8,
+  number  = 90,
+  doi     = "10.21105/joss.05781",
+  url     = "https://joss.theoj.org/papers/10.21105/joss.05781",
+  textVersion = paste(
+    "Meyer, Derek and Vega Yon, George (2023). epiworldR: Fast Agent-Based Epi Models.",
+    "Journal of Open Source Software, 8(90), 5781,",
+    "https://doi.org/10.21105/joss.05781"
+  )
+)
+
+bibentry(bibtype = "Manual",
+         title = "{{epiworldR: Fast Agent-Based Epi Models}}",
+         author = c(
+          person("Derek", "Meyer", comment = c(ORCID = "0009-0005-1350-6988")),
+          person("George", "Vega Yon", comment = c(ORCID = "0000-0002-3171-0844"))
+          ),
+         year = year,
+         note = note,
+         url = "https://github.com/UofUEpiBio/epiworldR", 
+         header = "And the actual R package:")