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JuliaPhylo · Jun 19, 2023 · ce4dec4 · ce4dec4
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diff --git a/CITATION.bib b/CITATION.bib
@@ -1,5 +1,15 @@
 % reference for the package, and for the correlated inheritance model
 @article{2023fogg_phylocoalsimulations,
+  author = {Fogg, John and Allman, Elizabeth S and An{\'e}, C{\'e}cile},
+  title = {{PhyloCoalSimulations}: A simulator for network multispecies coalescent
+        models, including a new extension for the inheritance of gene flow},
+  journal = {Systematic Biology},
+  year = {2023},
+  volume = {in press},
+  doi = {10.1093/sysbio/syad030},
+}
+% older bioRxiv preprint
+@article{2023fogg_phylocoalsimulations_bioRxiv,
   author = {Fogg, John and Allman, Elizabeth S and An{\'e}, C{\'e}cile},
   title = {{PhyloCoalSimulations}: A simulator for network multispecies coalescent
         models, including a new extension for the inheritance of gene flow},

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -14,7 +14,7 @@ References:
 please see [bibtex entries here](https://github.com/cecileane/PhyloCoalSimulations.jl/blob/main/CITATION.bib).
 
 - for this package and the network coalescent model with inheritance correlation:\
-  [Fogg, Allman & Ané (2023)](https://doi.org/10.1101/2023.01.11.523690)
+  [Fogg, Allman & Ané (2023)](https://doi.org/10.1093/sysbio/syad030)
   PhyloCoalSimulations: A simulator for network multispecies coalescent models,
   including a new extension for the inheritance of gene flow.
 

diff --git a/docs/src/man/correlated_inheritance.md b/docs/src/man/correlated_inheritance.md
@@ -29,7 +29,7 @@ with independent lineages.
 
 It also has an option to simulate lineage inheritance with positive correlation,
 under a coalescent model described in
-[Fogg, Allman & Ané (2023)](https://doi.org/10.1101/2023.01.11.523690).
+[Fogg, Allman & Ané (2023)](https://doi.org/10.1093/sysbio/syad030).
 For this, lineages' parents are drawn according to a Dirichlet process with
 base distribution determined by the γ values, and with concentration parameter
 α = (1-r)/r, that is, r = 1/(1+α), where r is the input inheritance correlation.

diff --git a/src/simulatecoalescent_network.jl b/src/simulatecoalescent_network.jl
@@ -56,7 +56,7 @@ are simulated according to a Dirichlet process with base distribution determined
 by the γ values, and with concentration parameter α = (1-r)/r, that is, r = 1/(1+α),
 where `r` is the input inheritance correlation.
 For more details about this model, please read the package manual or refer
-to [Fogg, Allman & Ané (2023)](https://doi.org/10.1101/2023.01.11.523690).
+to [Fogg, Allman & Ané (2023)](https://doi.org/10.1093/sysbio/syad030).
 
 Assumptions:
 - `net` must have non-missing edge lengths and γ values.