Update rooting to minimal deviation, update numbers for R0 graph
@@ -174,7 +174,7 @@ rule refine:
tree = "results/tree.nwk",
node_data = "results/branch_lengths.json"
params:
- root = "Wuhan/WIV04/2019 Wuhan/WIV06/2019",
+ root = "min_dev",
clock_rate = 0.00035,
clock_std_dev = 0.00015,
coalescent = "skyline",
@@ -380,7 +380,7 @@ rule poisson_tmrca:
rule branching_process_R0:
params:
infectious_period = 10, # days
- population = [600, 3000, 15000],
+ population = [6000, 30000, 150000],
start_recent = "2019-12-01",
start_early = "2019-11-01"
output:
