Skip to content
Permalink
Browse files

Plug in rmse optimized parameters

  • Loading branch information...
sidneymbell
sidneymbell committed Mar 31, 2019
1 parent 56a7c5e commit d3a5b565305b8cae063a3007ffca187b10019d39
Showing with 6 additions and 6 deletions.
  1. +6 −6 fitness_model/antigenic_fitness.py
@@ -566,12 +566,12 @@ def plot_trajectory_multiples(af, starting_timepoints=None, n_clades_per_plot=4)
args.add_argument('--date_range', nargs=2, type=float, help='which dates to look at', default=[1970., 2015.])
args.add_argument('--years_back', type=int, help='how many years of past immunity to include in fitness estimates', default=2)
args.add_argument('--years_forward', type=int, help='how many years into the future to predict', default=2)
args.add_argument('--gamma', type=float, help='Value or value range for the proportion of titers that wane per year post-exposure (slope of years vs. p(titers remaining))', default=0.2)
args.add_argument('--sigma', type=float, help='Value or value range for -1*probability of protection from i conferred by each log2 titer unit against i', default=0.78)
args.add_argument('--beta', type=float, help='Value or value range for beta. antigenic fitness = -1.*beta*population_immunity', default=0.2)
args.add_argument('--DENV1_f0', type=float, help='Relative intrinsic fitness value for DENV1', default = 0.45)
args.add_argument('--DENV2_f0', type=float, help='Relative intrinsic fitness value for DENV2', default = 0.45)
args.add_argument('--DENV3_f0', type=float, help='Relative intrinsic fitness value for DENV3', default = 0.3)
args.add_argument('--gamma', type=float, help='Value or value range for the proportion of titers that wane per year post-exposure (slope of years vs. p(titers remaining))', default=0.55)
args.add_argument('--sigma', type=float, help='Value or value range for -1*probability of protection from i conferred by each log2 titer unit against i', default=2.35)
args.add_argument('--beta', type=float, help='Value or value range for beta. antigenic fitness = -1.*beta*population_immunity', default=0.7)
args.add_argument('--DENV1_f0', type=float, help='Relative intrinsic fitness value for DENV1', default = 0.7)
args.add_argument('--DENV2_f0', type=float, help='Relative intrinsic fitness value for DENV2', default = 0.85)
args.add_argument('--DENV3_f0', type=float, help='Relative intrinsic fitness value for DENV3', default = 0.4)
args.add_argument('--DENV4_f0', type=float, help='Relative intrinsic fitness value for DENV4', default = 0.)
args.add_argument('--trajectory', type=float, nargs='*', help='timepoint(s) to compute trajectories for')
args.add_argument('--plot', help='make plots?', action='store_true')

0 comments on commit d3a5b56

Please sign in to comment.
You can’t perform that action at this time.