############################# # names of results ############################# #### # within host models ##### MINIMAL_FIXED_NAME = minimal_fixed MINIMAL_VISVAR_NAME = minimal_visvar MINIMAL_STERILIZING_NAME = minimal_sterilizing MINIMAL_DELETERIOUS_FIXED_NAME = minimal_deleterious_fixed MINIMAL_DELETERIOUS_VAR_NAME = minimal_deleterious_var MINIMAL_COMP_NAIVE_NAME = minimal_comp_naive MINIMAL_TEST_NAME = minimal_test MINIMAL_VISVAR_NAME = minimal_visvar MINIMAL_BN_NAMES = $(MINIMAL_STERILIZING_NAME) MINIMAL_VB_NAMES = $(MINIMAL_VISVAR_NAME) $(MINIMAL_FIXED_NAME) SENSITIVITY_NAMES = $(MINIMAL_FIXED_NAME) $(MINIMAL_VISVAR_NAME) ############################# # Default parameter values - mimimal model ############################# DEFAULT_MWH_BOTTLENECKS = 1 3 10 50 100 200 DEFAULT_MWH_VB_RATIOS = 1 3 10 50 100 200 DEFAULT_T_M = 2 DEFAULT_T_N = 6 DEFAULT_P_C = 0 DEFAULT_C_MAX = 4e8 DEFAULT_R0_WH = 5 DEFAULT_D_V = 4 DEFAULT_Z_WT = 0.95 DEFAULT_Z_MUT = 0 DEFAULT_MUT_WT_NEUT_RATIO = 0 DEFAULT_MU = 0.33e-5 DEFAULT_K = 6 DEFAULT_F = 1 DEFAULT_CROSS_IMM = 0 DEFAULT_R_W = 100 DEFAULT_R_M = 100 DEFAULT_E_W = 0 DEFAULT_E_M = 0 DEFAULT_TRANS_THRESHOLD = 1e7 # value of the max instantaneous transmission # probability below which we # say "wasn't ever transmissible" DEFAULT_TRANS_CUTOFF = 5e-2 # viral load at which transmission # given contact with a naive host # occurs with 50% probability DEFAULT_TD50 = 1e8 DEFAULT_DETECTION_THRESHOLD = 1e-2 DEFAULT_DETECTION_LIMIT = 1e5 DEFAULT_T_FINAL = 50 DEFAULT_LEAP_TIMESTEP = 0.01 DEFAULT_INOCULATOR_LEAP_TIMESTEP = 0.01 DEFAULT_BOTTLENECK = 1 DEFAULT_RNG_SEED = 33252 DEFAULT_VB_RATIO = 10 # ratio of bottleneck to n encounters iga DEFAULT_EMERGENCE_THRESHOLD = 4 # number of virions to count as an emergence near-certain to survive stochastic loss DEFAULT_F_MUT = 9e-5 DEFAULT_USE_Z_MUT = -1 MINIMAL_NITER = 250000 MINIMAL_TEST_LEAP_TIMESTEP = 0.01 MINIMAL_TEST_T_FINAL = 50 ############# # minimal within host model variants: # parameter definitions ############## MINIMAL_FIXED_T_M = 0 MINIMAL_VISVAR_RNG_SEED = 12 MINIMAL_FIXED_RNG_SEED = 14 MINIMAL_STERILIZING_RNG_SEED = 212 MINIMAL_STERILIZING_NITER = 100000 MINIMAL_STERILIZING_K = 20 MINIMAL_STERILIZING_T_M = 0 MINIMAL_STERILIZING_Z_WT = 0 MINIMAL_STERILIZING_CROSS_IMM = 0 MINIMAL_STERILIZING_LEAP_TIMESTEP = 0.001 MINIMAL_STERILIZING_INOCULATOR_LEAP_TIMESTEP = 0.01 MINIMAL_COMPROMISED_RNG_SEED = 23587 MINIMAL_COMPROMISED_NITER = 1000 MINIMAL_COMPROMISED_P_C = 0.6 MINIMAL_COMPROMISED_CROSS_IMM = 0.75 MINIMAL_COMPROMISED_K = 0.5 MINIMAL_COMPROMISED_T_FINAL = 100 MINIMAL_COMPROMISED_T_N = 101 MINIMAL_COMP_NAIVE_RNG_SEED = 23587 MINIMAL_COMP_NAIVE_NITER = 1000 MINIMAL_COMP_NAIVE_P_C = 0.6 MINIMAL_COMP_NAIVE_CROSS_IMM = 0.75 MINIMAL_COMP_NAIVE_K = 0.5 MINIMAL_COMP_NAIVE_T_FINAL = 100 MINIMAL_COMP_NAIVE_T_N = 101 MINIMAL_COMP_NAIVE_T_M = 6 MINIMAL_TEST_RNG_SEED = 325 MINIMAL_TEST_R0_WH = 5 #4.04551 MINIMAL_TEST_R_W = 2914.81 MINIMAL_TEST_R_M = 2914.81 MINIMAL_TEST_MU = 0 #8.82457e-06 MINIMAL_TEST_D_V= 7.34099 MINIMAL_TEST_K = 7.60462 MINIMAL_TEST_T_M = 2.27212 MINIMAL_TEST_T_N = 8.1794 MINIMAL_TEST_CROSS_IMM = 0.166546 MINIMAL_TEST_Z_WT = 0.860967 MINIMAL_TEST_MUT_WT_NEUT_RATIO = 0.0298177 MINIMAL_TEST_C_MAX = 4e8 #4.7677e+09 #################################### # params for sensitivity analysis #################################### SENSITIVITY_BOTTLENECKS = 1 3 10 50 SENSITIVITY_NITER = 50000 SENSITIVITY_N_PARAMSETS = 10 # parameter ranges for sensitivity DEFAULT_R0_WH_MIN = 5 DEFAULT_R0_WH_MAX = 15 DEFAULT_R_W_MIN = 50 DEFAULT_R_W_MAX = 500 DEFAULT_MU_MIN = 0.33e-6 DEFAULT_MU_MAX = 0.33e-4 DEFAULT_D_V_MIN = 2 DEFAULT_D_V_MAX = 8 DEFAULT_K_MIN = 0 DEFAULT_K_MAX = 20 DEFAULT_CROSS_IMM_MIN = 0.5 DEFAULT_CROSS_IMM_MAX = .99 DEFAULT_T_M_MIN = 2 DEFAULT_T_M_MAX = 4.5 DEFAULT_T_N_MIN = 6 DEFAULT_T_N_MAX = 9 DEFAULT_C_MAX_MIN = 4e7 DEFAULT_C_MAX_MAX = 4e9 DEFAULT_Z_WT_MIN = 0.70 DEFAULT_Z_WT_MAX = 0.99 DEFAULT_VB_RATIO_MIN = 1 DEFAULT_VB_RATIO_MAX = 1 DEFAULT_TRANS_THRESHOLD_MIN = 1e6 DEFAULT_TRANS_THRESHOLD_MAX = 1e8 DEFAULT_TD50_MIN = 1e7 DEFAULT_TD50_MAX = 1e9 DEFAULT_Z_MUT_Z_WT_RATIO_MIN = 0.5 DEFAULT_Z_MUT_Z_WT_RATIO_MAX = 0.9 # visvar sensitivity analysis MINIMAL_VISVAR_R0_WH_MIN = 5 MINIMAL_VISVAR_R0_WH_MAX = 15 MINIMAL_VISVAR_R_W_MIN = 10 MINIMAL_VISVAR_R_W_MAX = 500 MINIMAL_VISVAR_MU_MIN = 0.33e-6 MINIMAL_VISVAR_MU_MAX = 0.33e-4 MINIMAL_VISVAR_D_V_MIN = 2 MINIMAL_VISVAR_D_V_MAX = 8 MINIMAL_VISVAR_K_MIN = 3 MINIMAL_VISVAR_K_MAX = 20 MINIMAL_VISVAR_CROSS_IMM_MIN = 0.5 MINIMAL_VISVAR_CROSS_IMM_MAX = 1 MINIMAL_VISVAR_T_M_MIN = 2 MINIMAL_VISVAR_T_M_MAX = 4.5 MINIMAL_VISVAR_T_N_MIN = 6 MINIMAL_VISVAR_T_N_MAX = 9 MINIMAL_VISVAR_C_MAX_MIN = 4e7 MINIMAL_VISVAR_C_MAX_MAX = 4e9 MINIMAL_VISVAR_Z_WT_MIN = 0.70 MINIMAL_VISVAR_Z_WT_MAX = 0.99 MINIMAL_VISVAR_Z_MUT_Z_WT_RATIO_MIN = 0.5 MINIMAL_VISVAR_Z_MUT_Z_WT_RATIO_MAX = 0.9 MINIMAL_VISVAR_VB_RATIO_MIN = 1 MINIMAL_VISVAR_VB_RATIO_MAX= 50 # fixed immunity sensitivity analysis MINIMAL_FIXED_R0_WH_MIN = 5 MINIMAL_FIXED_R0_WH_MAX = 15 MINIMAL_FIXED_R_W_MIN = 10 MINIMAL_FIXED_R_W_MAX = 500 MINIMAL_FIXED_MU_MIN = 0.33e-6 MINIMAL_FIXED_MU_MAX = 0.33e-4 MINIMAL_FIXED_D_V_MIN = 2 MINIMAL_FIXED_D_V_MAX = 8 MINIMAL_FIXED_K_MIN = 3 MINIMAL_FIXED_K_MAX = 16 MINIMAL_FIXED_CROSS_IMM_MIN = 0.5 MINIMAL_FIXED_CROSS_IMM_MAX = 1 MINIMAL_FIXED_T_M_MIN = 0 MINIMAL_FIXED_T_M_MAX = 1 MINIMAL_FIXED_T_N_MIN = 6 MINIMAL_FIXED_T_N_MAX = 9 MINIMAL_FIXED_C_MAX_MIN = 1e8 MINIMAL_FIXED_C_MAX_MAX = 1e9 MINIMAL_FIXED_Z_WT_MIN = 0.70 MINIMAL_FIXED_Z_WT_MAX = 0.99 MINIMAL_FIXED_Z_MUT_Z_WT_RATIO_MIN = 0.5 MINIMAL_FIXED_Z_MUT_Z_WT_RATIO_MAX = 0.9 MINIMAL_FIXED_VB_RATIO_MIN = 1 MINIMAL_FIXED_VB_RATIO_MAX = 50 ###################################### # replication selection probability # simulation parameters ###################################### REPL_NITER = 250000 REPL_T_FINAL = 3 REPL_T_MS = 0 0.25 0.5 1 1.5 2 2.5 3 REPL_KS = 0.5 1 2 4 8 ###################################### # chain model parameters ###################################### N_CHAINS = 1000 SPLIT_N_CHAINS = 250 # parallelize chain simulations for four cores DEFAULT_CHAIN_BOTTLENECK = 1 DEFAULT_CHAIN_LENGTH = 60000 DEFAULT_IMMUNE_HISTORIES = -0.8 -0.5 0 DEFAULT_IMMUNE_HISTORY_DISTRIBUTION = 0.2 0.2 0.2 0.4 DEFAULT_CHAIN_CONTACT_RATE = 1 DEFAULT_CHAIN_MUT_MEAN = 0.0 DEFAULT_CHAIN_MUT_SD = 0.08 DEFAULT_CHAIN_INIT_PHEN = 0.0 DEFAULT_CHAIN_ANTIGENIC_SCALE = 0.01 DRIFT_CHAIN_Z_WT = 0 DRIFT_CHAIN_VB_RATIO = 10 DRIFT_CHAIN_K = 25 DRIFT_CHAIN_LEAP_TIMESTEP = 0.01 DRIFT_CHAIN_IMMUNE_HISTORIES = 0 DRIFT_CHAIN_IMMUNE_HISTORY_DISTRIBUTION = 0 1.0 DRIFT_CHAIN_RNG_SEED = 3245 CONSTANT_CHAIN_Z_WT = 0 CONSTANT_CHAIN_VB_RATIO = 1 CONSTANT_CHAIN_BOTTLENECK = 10 CONSTANT_CHAIN_K = 25 CONSTANT_CHAIN_T_M = 0 CONSTANT_CHAIN_LEAP_TIMESTEP = 0.01 CONSTANT_CHAIN_RNG_SEED = 23492852 CONSTANT_CHAIN_T_FINAL = 200 ## long infections when R_WH ~= 1 PT_CHAIN_Z_WT = 0.95 PT_CHAIN_VB_RATIO = 10 PT_CHAIN_K = 25 PT_CHAIN_T_M = 2 PT_CHAIN_LEAP_TIMESTEP = 0.01 PT_CHAIN_RNG_SEED = 938238 BETTER_TOGETHER_CHAIN_Z_WT = 0.95 BETTER_TOGETHER_CHAIN_K = 25 BETTER_TOGETHER_CHAIN_T_M = 0 BETTER_TOGETHER_CHAIN_LEAP_TIMESTEP = 0.01 BETTER_TOGETHER_RNG_SEED = 4034 BETTER_TOGETHER_CHAIN_VB_RATIO = 10 ############################### # other generic info ############################### PUBLIC_REPO_URL = https://github.com/dylanhmorris/asynchrony-influenza PUBLIC_DATA_URL = https://doi.org/10.17605/OSF.IO/jdsbp/