Merge pull request #336 from hyanwong/docs-typos

Extra doc corrections

docs/historical_samples.md

@@ -24,7 +24,7 @@ data which includes *historical samples*,
 whose time is older that the current generation (i.e. sample nodes with
 times > 0).
 
-The output of {ref}`tsinfer:sec_introduction` is valid regardless
+The output of [`tsinfer`](tsinfer:sec_introduction) is valid regardless
 of the inclusion of historical samples, but *dating* such a tree sequence
 is more complicated. This is because the time scale of a tsinferred
 tree sequence is uncalibrated, so it is unclear where in time to

docs/introduction.md

@@ -18,8 +18,10 @@ kernelspec:
 
 # Introduction
 
-`Tsdate` {cite}`wohns2022unified` infers dates for nodes in a genetic genealogy. More precisely, it takes a
-[tree sequence](https://tskit.dev/tutorials/what_is.html) as input
+`Tsdate` {cite}`wohns2022unified` infers dates for nodes in a genetic genealogy,
+sometimes loosely known as an ancestral recombination graph or ARG
+{cite}`wong2023general`. More precisely, it takes a genealogy in 
+[tree sequence](https://tskit.dev/tutorials/what_is.html) format as an input
 and returns a copy of that tree sequence with altered node times. These
 times have been estimated on the basis of the number of mutations
 along the edges connecting genomes in the genealogy (i.e. using the "molecular clock").

docs/references.bib

@@ -26,7 +26,7 @@ @article{wohns2022unified
 
 @inproceedings{minka2001expectation,
     author = {Minka, Thomas P.},
-    title = {Expectation Propagation for Approximate Bayesian Inference},
+    title = {Expectation Propagation for Approximate {Bayesian} Inference},
     year = {2001},
     isbn = {1558608001},
     publisher = {Morgan Kaufmann Publishers Inc.},
@@ -35,5 +35,25 @@ @inproceedings{minka2001expectation
     pages = {362–369},
     numpages = {8},
     location = {Seattle, Washington},
-    series = {UAI'01}
+    series = {UAI'01},
+    doi = {10.48550/arXiv.1301.2294},
 }
+
+@article{schweiger2023ultra,
+  title={Ultra-fast genome-wide inference of pairwise coalescence times},
+  author={Schweiger, Regev and Durbin, Richard},
+  journal={Genome research},
+  volume={33},
+  pages={1023-1031},
+  year={2023},
+  doi={10.1101/gr.277665.123},
+}
+
+@article {wong2023general,
+	author = {Yan Wong and Anastasia Ignatieva and Jere Koskela and Gregor Gorjanc and Anthony W. Wohns and Jerome Kelleher},
+	title = {A general and efficient representation of ancestral recombination graphs},
+	year = {2023},
+	doi = {10.1101/2023.11.03.565466},
+	publisher = {Cold Spring Harbor Laboratory},
+	journal = {bioRxiv}
+}