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Update default params, optimized for sero, dt=2, trajectory deltasse

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sidneymbell
sidneymbell committed Feb 20, 2019
1 parent 707e96f commit ad31b815c2fc71ccde079b5a535f3c24d9db176c
Showing with 6 additions and 6 deletions.
  1. +6 −6 fitness_model/antigenic_fitness.py
@@ -557,12 +557,12 @@ 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=0.86)
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=0.43)
args.add_argument('--beta', type=float, help='Value or value range for beta. antigenic fitness = -1.*beta*population_immunity', default=2.57)
args.add_argument('--DENV1_f0', type=float, help='Relative intrinsic fitness value for DENV1', default = 2.0)
args.add_argument('--DENV2_f0', type=float, help='Relative intrinsic fitness value for DENV2', default = 2.0)
args.add_argument('--DENV3_f0', type=float, help='Relative intrinsic fitness value for DENV3', default = 1.0)
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('--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')

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