Update README.md

README.md

@@ -44,7 +44,7 @@ The function `pair.sets.filter ` selects the sequences to be used in the analysi
 
 *Simulation analysis* consists of (a) simulating phylogenetic trees for a transmission pair using the epidemiological timelines for that pair for a range of transmission models, (b) computing the likelihood associated with each transmission model by combining both the empirical and simulation outcomes for a transmission pair (Model calibration), (c) calculating the probability of one founder strain for each transmission pair’s maximum likelihood model, and (d) calculating the relative risk that one founder strain initiates infection in acute pair transmissions than in chronic pair transmissions (across all pairs)
 
-pair.simulator generates the transmission timelines for a transmission pair based on their epidemiological data, simulates sequences using VirusTreeSimulator (xxxx) and for each simulation, calculates a maximum likelihood tree for the pair; using these ML trees, we then calculate the number of topology classifications (i.e. PP, PM, MM) for each pair across all the simulations.  
+pair.simulator generates the transmission timelines for a transmission pair based on their epidemiological data, simulates sequences using VirusTreeSimulator and for each simulation, calculates a maximum likelihood tree for the pair; using these ML trees, we then calculate the number of topology classifications (i.e. PP, PM, MM) for each pair across all the simulations.  
 
 `pair.founder.p.R` uses maximum likelihood to calculate the best fit model for each transmission pair and then, for this model, calculates the probability that one variant was transmitted. Finally, we calculate the relative risk of acute transmissions vs. chronic transmissions initiating infections with one founder strain across pairs.