fixes #114

Author: maxbiostat

FMDV_AMERICA.bib

@@ -706,6 +706,15 @@ @article{Gill2016
  year={2016},
  publisher={Oxford University Press}
 }
+@article{Hall2016,
+ title={The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study},
+ author={Hall, Matthew D and Woolhouse, Mark EJ and Rambaut, Andrew},
+ journal={Virus evolution},
+ volume={2},
+ number={1},
+ year={2016},
+ publisher={Oxford University Press}
+}
 @article{Holmes2016,
  title={The evolution of {E}bola virus: Insights from the 2013--2016 epidemic},
  author={Holmes, Edward C and Dudas, Gytis and Rambaut, Andrew and Andersen, Kristian G},
@@ -736,16 +745,6 @@ @article{Rambaut2016
  year={2016},
  publisher={The Oxford University Press}
 }
-@article{Dudas2017,
- title={Virus genomes reveal factors that spread and sustained the Ebola epidemic},
- author={Dudas, Gytis and Carvalho, Luiz Max and Bedford, Trevor and Tatem, Andrew J and Baele, Guy and Faria, Nuno R and Park, Daniel J and Ladner, Jason T and Arias, Armando and Asogun, Danny and others},
- journal={Nature},
- volume={544},
- number={7650},
- pages={309--315},
- year={2017},
- publisher={Nature Research}
-}
 @article{Clavijo2017,
  title={Current Status and Future Prospects to Achieve Foot-and-Mouth Disease Eradication in South America},
  author={Clavijo, A and Sanchez-Vazquez, MJ and Buzanovsky, LP and Martini, M and Pompei, JC and Cosivi, O},
@@ -756,6 +755,25 @@ @article{Clavijo2017
  year={2017},
  publisher={Wiley Online Library}
 }
+@article{Dearlove2017,
+ title={Biased phylodynamic inferences from analysing clusters of viral sequences},
+ author={Dearlove, Bethany L and Xiang, Fei and Frost, Simon DW},
+ journal={Virus evolution},
+ volume={3},
+ number={2},
+ year={2017},
+ publisher={Oxford University Press}
+}
+@article{Dudas2017,
+ title={Virus genomes reveal factors that spread and sustained the Ebola epidemic},
+ author={Dudas, Gytis and Carvalho, Luiz Max and Bedford, Trevor and Tatem, Andrew J and Baele, Guy and Faria, Nuno R and Park, Daniel J and Ladner, Jason T and Arias, Armando and Asogun, Danny and others},
+ journal={Nature},
+ volume={544},
+ number={7650},
+ pages={309--315},
+ year={2017},
+ publisher={Nature Research}
+}
 @article{Karcher2017,
  title = {{phylodyn}: an {R} package for phylodynamic simulation and inference},
  author = {Karcher, M and Palacios, JA and Lan, S and Minin, VN},

FMDV_AMERICA.tex

@@ -229,6 +229,7 @@ \section*{Discussion}
 
 \subsection*{Limitations of this study}
 
+Sampling-related effects have the potential to lead to incorrect inferences about temporal and spatial patterns in phylodynamic studies~\citep{Hall2016,Dearlove2017}.
 As discussed above, we have employed modern statistical methods to quantify and mitigate spatial and temporal preferential sampling in the data analysed in this study.
 Despite this, however, we feel it is important to clarify its limitations as they relate to the nature of the sampling process.
 We highlight three key limitations, which in our view cannot be completely circumvented by the use of state-of-the-art statistical methods.