search

maxbiostat / FMDV_AMERICA

Tracking the spread of Foot-and-Mouth Disease virus in South America
1 stars 0 forks source link

R2MC12 #96

Closed maxbiostat closed 4 years ago

maxbiostat commented 9 years ago

Page 6 Line 9: Sensitivity analysis. The sub-samples (as referred in table S4 and S5) is excluding the over-represented countries, i.e. Argentina and Colombia. However, if you exclude Argentina from the type A data, you have now Venezuela that is over-represented (the same holds true for type O, for which Colombia is the over-represented after the exclusion of Ecuador). Since both the Argentinian and Ecuador samples are, let’s say, monophyletic (collected for the majority within epidemics), this are not really changing the global picture. In addition, you claim (Page 24 Line 37) that removing Argentina from the type A analysis move the MRCA estimate of ~6 years. Is this because you eliminate one of the oldest sequences present in your data, thus leaving only the Brazil ’58 and, therefore, introduce a more substantial sampling bias/uncertainty? For type O, considering that the oldest samples are from Colombia, removing Ecuador has no impact in the results. I am getting confused to understand which methodology is behind your random sampling approach used for the 5 sub-sampling. Is this a proportional random sampling (with a temporal sub-sampling as well) of each country?

maxbiostat commented 9 years ago

Will make the sensitivity analysis cleverer. After the new analyses are out.