From 386fc258e6ff130f8ace485a48a178e9fb5b0c7b Mon Sep 17 00:00:00 2001 From: KienTTran Date: Mon, 30 Sep 2024 15:05:03 -0400 Subject: [PATCH] 1. Added merged input file in input/input.yml --- input/input.yml | 829 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 829 insertions(+) create mode 100644 input/input.yml diff --git a/input/input.yml b/input/input.yml new file mode 100644 index 0000000..ac6c222 --- /dev/null +++ b/input/input.yml @@ -0,0 +1,829 @@ +# --------------------------------------------------------------- +# Boni Lab Malaria Simulation Configuration +# --------------------------------------------------------------- +# This configuration file runs the malaria simulation from year 2000 to year 2030. +# The drug is deployed in year 2010. + +# --------------------------------------------------------------- +# 1. Execution Settings +# --------------------------------------------------------------- +execution_settings: + # Number of model days between updates to the user + days_between_notifications: 30 + + # Initial seed number for random number generator; set to 0 or comment out to use a random seed + initial_seed_number: 0 + + # Record the genomic data (set to true for a real run) + record_genome_db: true + + # Frequency (in days) to report to GUI and console + report_frequency: 30 + +# --------------------------------------------------------------- +# 2. Simulation Timeframe +# --------------------------------------------------------------- +simulation_timeframe: + # Simulation starting date (calibration year minus 11 years of burn-in) + starting_date: 2000/1/1 + + # Start of comparison period (mutations start in 2010) + start_of_comparison_period: 2010/1/1 + + # Simulation ending date + ending_date: 2030/1/1 + + # Day to start collecting data (discard the first five years of data) + start_collect_data_day: 0 + + # Number of days to keep track of the total number of parasites in the population + number_of_tracking_days: 11 + +# --------------------------------------------------------------- +# 3. Transmission Settings +# --------------------------------------------------------------- +transmission_settings: + # Transmission parameter based on data; adjusts the odds that an individual will be infected when challenged by sporozoites + transmission_parameter: 0.55 + + # Probability that an infectious bite on a human causes a blood-stage malaria infection + p_infection_from_an_infectious_bite: 0.1 + +# --------------------------------------------------------------- +# 4. Population Structure +# --------------------------------------------------------------- +population_structure: + # Number of age classes used for reporting age-specific mortality calculations + number_of_age_classes: 15 + + # Age structure used for reporting (in years) + age_structure: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 20, 60, 100] + + # Initial age structure used when initializing the model at T=0 + initial_age_structure: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 35, 45, 55, 65, 100] + + # Scaling factor for the population in the model (based on data) + artificial_rescaling_of_population_size: 0.25 + +# --------------------------------------------------------------- +# 5. Raster and Geographic Settings +# --------------------------------------------------------------- +raster_settings: + # Adjusted population raster to account for burn-in up to 2009 start + population_raster: "../input/kag_init_pop.asc" + + # Raster files defining the country districts + district_raster: "../input/kag_district.asc" + + # Raster files defining treatment probabilities (comment these out for beta calibration) + pr_treatment_under5: "../input/kag_treatment.asc" + pr_treatment_over5: "../input/kag_treatment.asc" + + # Raster file containing the calibrated beta value + beta_raster: "../input/kag_beta_r1.asc" + + # Cell size used by raster, in square kilometers + cell_size: 5 + + # Approximate national age distribution (to be updated with specific country data) + age_distribution_by_location: + - [0.0378, 0.0378, 0.0378, 0.0378, 0.0282, 0.0282, 0.0282, 0.0282, 0.0282, 0.029, 0.029, 0.029, 0.029, 0.029, 0.169, 0.134, 0.106, 0.066, 0.053, 0.035, 0.0] + + # Probability that an infected and symptomatic person receives treatment; single value for the entire country + # If set to '-1', these values are read from 'pr_treatment_under5' and 'pr_treatment_over5' above + p_treatment_for_less_than_5_by_location: [-1] + p_treatment_for_more_than_5_by_location: [-1] + + # Will be overridden by beta_raster + beta_by_location: [-1] + +# --------------------------------------------------------------- +# 6. Seasonality Settings +# --------------------------------------------------------------- +seasonality_settings: + # Seasonality of malaria (to be updated with specific country data) + enable: false + mode: rainfall + rainfall: + filename: "rwa_adjustment.csv" + period: 365 + +# --------------------------------------------------------------- +# 7. Movement and Spatial Model +# --------------------------------------------------------------- +movement_settings: + # Country-specific movement model and calibration + spatial_model: + name: "Wesolowski" + Wesolowski: + kappa: 0.01093251 + alpha: 0.22268982 + beta: 0.14319618 + gamma: 0.83741484 + + # Settings that determine how long an individual stays in a given location + circulation_info: + max_relative_moving_value: 35 + number_of_moving_levels: 100 + moving_level_distribution: + distribution: Gamma + Gamma: + mean: 5 + sd: 10 + + # Percentage of the population selected for movement outside of their cell each timestep + circulation_percent: 0.0 + length_of_stay: + mean: 5 + sd: 10 + +# --------------------------------------------------------------- +# 8. Demographic Parameters +# --------------------------------------------------------------- +demographic_parameters: + # Crude birth rate (to be updated with specific country data) + birth_rate: 0.0288 + + # Malaria-adjusted all-cause death rate by age class (to be updated with specific country data) + death_rate_by_age_class: + - [0.02641, 0.00202, 0.00202, 0.00202, 0.00198, 0.00247, 0.00247, 0.00247, 0.00247, 0.00247, 0.00247, 0.00247, 0.00455, 0.00455, 0.05348] + + # Probability of death for patients who are not treated or experience a treatment failure + # When receiving treatment, this rate drops by a factor of 10 in the code + mortality_when_treatment_fail_by_age_class: + - [0.040, 0.020, 0.020, 0.020, 0.020, 0.004, 0.004, 0.004, 0.004, 0.004, 0.004, 0.001, 0.001, 0.001, 0.001] + +# --------------------------------------------------------------- +# 9. Parasite Parameters +# --------------------------------------------------------------- +parasite_parameters: + parasite_density_levels: + # Standard values used in other models + log_parasite_density_cured: -4.699 # Corresponds to 100 total parasites (0.00002 per μl) + log_parasite_density_from_liver: -2.000 # Corresponds to 50,000 total parasites (0.01 per μl) + log_parasite_density_asymptomatic: 3 # Corresponds to 1,000 parasites per μl of blood + log_parasite_density_clinical: 4.301 # Corresponds to 20,000 parasites per μl of blood + log_parasite_density_clinical_from: 3.301 # Corresponds to 2,000 parasites per μl of blood + log_parasite_density_clinical_to: 5.301 # Corresponds to 200,000 parasites per μl of blood + log_parasite_density_detectable: 1.000 # Corresponds to 10 parasites per μl of blood + log_parasite_density_detectable_pfpr: 1.699 # Corresponds to 100 parasites per μl of blood + log_parasite_density_pyrogenic: 3.398 # Corresponds to 2,500 parasites per μl of blood + + recombination_parameters: + # Within-chromosome recombination rate + within_chromosome_recombination_rate: 0.1 + + # Free recombination among the drug resistance loci + using_free_recombination: true + +# --------------------------------------------------------------- +# 10. Immune System Parameters +# --------------------------------------------------------------- +immune_system_parameters: + # Parameters governing the immune response + b1: 0.00125 # Rate at which antimalarial immune function increases when a host is parasitemic + b2: 0.0025 # Rate at which antimalarial immune function decreases when a host is parasitemic + duration_for_naive: 300 # Duration of infection for naive hosts + duration_for_fully_immune: 60 # Duration of infection for fully immune hosts + mean_initial_condition: 0.1 # Initial immune function mean at time zero + sd_initial_condition: 0.1 # Initial immune function standard deviation at time zero + immune_inflation_rate: 0.01 # Age-dependent faster acquisition of immunity from age 1 to age 10 (per year) + min_clinical_probability: 0.05 # Minimum probability of experiencing symptoms from a new infection + max_clinical_probability: 0.99 # Maximum probability of experiencing symptoms from a new infection + immune_effect_on_progression_to_clinical: 5.4 # Slope of the sigmoidal probability vs. immunity function + age_mature_immunity: 10 # Age at which immune function is mature + factor_effect_age_mature_immunity: 0.3 # Adjusts the inflection point in the curve + midpoint: 0.4 # Midpoint for the immunity curve + +# --------------------------------------------------------------- +# 11. Mutation and Genotype Parameters +# --------------------------------------------------------------- +mutation_and_genotype_parameters: + # Mutation mask indicating positions of genetic mutations + mutation_mask: "||||111||1111111,0||||||000000000010|1" + + # Daily probability that a parasite will mutate at a given locus when drug concentration is not zero + mutation_probability_by_locus: 0.001 + + pf_genotype_info: + - chromosome: 5 + genes: + - name: "Pfmdr1" + max_copies: 2 + # copy number variation cost of resistances + cnv_daily_crs: [ 0, 0.0005 ] + cnv_multiplicative_effect_on_EC50: + - drug_id: 4 + factors: [ 1, 2.44444444 ] + - drug_id: 1 + factors: [ 1, 1.3 ] + multiplicative_effect_on_EC50_for_2_or_more_mutations: + - drug_id: 1 + factor: 1.05 + aa_positions: + - position: 86 + amino_acids: [ 'N', 'Y' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 6 + factors: [ 1, 1.25 ] + - drug_id: 1 + factors: [ 1.25, 1 ] + - drug_id: 2 + factors: [ 1, 1.42 ] + - position: 184 + amino_acids: [ 'Y', 'F' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 1 + factors: [ 1, 1.25 ] # base*1.25*1.25 0.9375 > 0.8xxx (old value) + - drug_id: 2 + factors: [ 1.2, 1 ] + - chromosome: 7 + genes: + - name: "Pfcrt" + multiplicative_effect_on_EC50_for_2_or_more_mutations: + - drug_id: 3 + factor: 1.0 + average_daily_crs: 0.1290 + # 0.1290 is average of (0.1169,0.0081,0.2621 - converted from fitness (2.19,2.46,1.83)) from Small-Sander PLOS 2019 paper (Mar 1 23 slides) + aa_positions: + - position: 76 + amino_acids: [ 'K', 'T' ] + daily_crs: [ 0, 0.003875969 ] + multiplicative_effect_on_EC50: + - drug_id: 6 + factors: [ 1, 1.6 ] + - drug_id: 1å + factors: [ 1.1, 1 ] + - drug_id: 2 + factors: [ 1, 1.2 ] + - position: 93 + amino_acids: [ 'T', 'S' ] + daily_crs: [ 0, 0.0002433748 ] #0.0000313953492 = (0.0081/0.1290)*0.0005 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 1.6648 ] + - position: 97 + amino_acids: [ 'H', 'Y' ] + daily_crs: [ 0, 0.003875969 ] #0.000500000001 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 1.6648 ] + - position: 145 + amino_acids: [ 'F', 'I' ] + daily_crs: [ 0, 0.0078751277 ] #0.0010158914733 = (0.2621/0.1290)*0.0005 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 2.2226 ] + - position: 218 + amino_acids: [ 'I', 'F' ] + daily_crs: [ 0, 0.0035124091 ] #0.0004531007739 = (0.1169/0.1290)*0.0005 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 1.6648 ] + - position: 343 + amino_acids: [ 'M', 'L' ] + daily_crs: [ 0, 0.003875969 ] #0.000500000001 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 1.0 ] + - position: 353 + amino_acids: [ 'G', 'V' ] + daily_crs: [ 0, 0.003875969 ] #0.000500000001 + multiplicative_effect_on_EC50: + - drug_id: 3 + factors: [ 1, 1.0 ] + - name: "Pfkaf" + aa_positions: + - position: 500 + amino_acids: [ 'x', 'X' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 7 + factors: [ 1, 1.6 ] + - chromosome: 13 + genes: + - name: "Pfkelch13" + multiplicative_effect_on_EC50_for_2_or_more_mutations: + - drug_id: 0 + factor: 1.1 + aa_positions: + - position: 446 + amino_acids: [ 'F', 'I' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 458 + amino_acids: [ 'N', 'Y' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 469 + amino_acids: [ 'C', 'Y' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 476 + amino_acids: [ 'M', 'I' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 493 + amino_acids: [ 'Y', 'H' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 539 + amino_acids: [ 'R', 'T' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 543 + amino_acids: [ 'I', 'T' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 553 + amino_acids: [ 'P', 'L' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 561 + amino_acids: [ 'R', 'H' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 574 + amino_acids: [ 'P', 'L' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 580 + amino_acids: [ 'C', 'Y' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - position: 675 + amino_acids: [ 'A', 'V' ] + daily_crs: [ 0, 0.0005 ] + multiplicative_effect_on_EC50: + - drug_id: 0 + factors: [ 1, 1.6 ] + - chromosome: 14 + genes: + - name: "Pfplasmepsin" + max_copies: 2 + cnv_daily_crs: [ 0, 0.0005 ] + cnv_multiplicative_effect_on_EC50: + - drug_id: 3 + # factors: [ 1, 2.4137931 ] + factors: [ 1, 1.37 ] + aa_positions: [ ] + + override_ec50_patterns: + - pattern: "||||NY1||K......,.||||||............|." + drug_id: 1 + ec50: 0.8 + - pattern: "||||YY1||K......,.||||||............|." + drug_id: 1 + ec50: 0.67 + - pattern: "||||NF1||K......,.||||||............|." + drug_id: 1 + ec50: 0.9 + - pattern: "||||YF1||K......,.||||||............|." + drug_id: 1 + ec50: 0.8 + - pattern: "||||NY2||K......,.||||||............|." + drug_id: 1 + ec50: 1.0 + - pattern: "||||YY2||K......,.||||||............|." + drug_id: 1 + ec50: 0.87 + - pattern: "||||NF2||K......,.||||||............|." + drug_id: 1 + ec50: 1.1 + - pattern: "||||YF2||K......,.||||||............|." + drug_id: 1 + ec50: 1.0 + - pattern: "||||NY1||T......,.||||||............|." + drug_id: 1 + ec50: 0.75 + - pattern: "||||YY1||T......,.||||||............|." + drug_id: 1 + ec50: 0.6 + - pattern: "||||NF1||T......,.||||||............|." + drug_id: 1 + ec50: 0.85 + - pattern: "||||YF1||T......,.||||||............|." + drug_id: 1 + ec50: 0.75 + - pattern: "||||NY2||T......,.||||||............|." + drug_id: 1 + ec50: 0.95 + - pattern: "||||YY2||T......,.||||||............|." + drug_id: 1 + ec50: 0.8 + - pattern: "||||NF2||T......,.||||||............|." + drug_id: 1 + ec50: 1.05 + - pattern: "||||YF2||T......,.||||||............|." + drug_id: 1 + ec50: 0.95 + - pattern: "||||NY.||K......,.||||||............|." + drug_id: 2 + ec50: 0.62 + - pattern: "||||YY.||K......,.||||||............|." + drug_id: 2 + ec50: 0.85 + - pattern: "||||NF.||K......,.||||||............|." + drug_id: 2 + ec50: 0.5 + - pattern: "||||YF.||K......,.||||||............|." + drug_id: 2 + ec50: 0.775 + - pattern: "||||NY.||T......,.||||||............|." + drug_id: 2 + ec50: 0.7 + - pattern: "||||YY.||T......,.||||||............|." + drug_id: 2 + ec50: 0.9 + - pattern: "||||NF.||T......,.||||||............|." + drug_id: 2 + ec50: 0.65 + - pattern: "||||YF.||T......,.||||||............|." + drug_id: 2 + ec50: 0.82 + + initial_parasite_info: + - location_id: -1 # -1 indicates all locations + parasite_info: + - aa_sequence: "||||YY1||TTHFIMG,x||||||FNCMYRIPRPCA|1" + prevalence: 0.05 + - aa_sequence: "||||NY1||TTHFIMG,x||||||FNCMYRIPRPCA|1" + prevalence: 0.05 + +# --------------------------------------------------------------- +# 12. Drug Parameters +# --------------------------------------------------------------- +drug_parameters: + # IDs for specific drugs + artemisinin_drug_id: 0 + lumefantrine_drug_id: 4 + + drug_db: + 0: + name: "artemisinin" + half_life: 0.0 + maximum_parasite_killing_rate: 0.999 + n: 25 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.75 + 1: + name: "lumefantrine" + half_life: 4.5 + maximum_parasite_killing_rate: 0.99 + n: 20 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + age_specific_drug_absorption: [ 0.7,0.7,0.85,0.85,0.85,0.85,0.85,0.85,0.85,0.85,1.0,1.0,1.0,1.0,1.0 ] + k: 4 + base_EC50: 0.6 + 2: + name: "amodiaquine" + half_life: 9.0 + maximum_parasite_killing_rate: 0.95 + n: 19 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.5 + 3: + name: "piperaquine" + half_life: 28.0 + maximum_parasite_killing_rate: 0.9 + n: 15 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.58 + #MQ + 4: + name: "Mefloquine" + half_life: 21.0 + maximum_parasite_killing_rate: 0.9 + n: 15 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.45 + resistant_genes: [ "Pfmdr1" ] + 5: + name: "SP" + half_life: 6.5 + maximum_parasite_killing_rate: 0.9 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + n: 15 + k: 4 + base_EC50: 1.08 + resistant_genes: [ ] + 6: + name: "CQ" + half_life: 10 + maximum_parasite_killing_rate: 0.95 + n: 19 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.72 + 7: + name: "KAF156" + half_life: 1.6 + maximum_parasite_killing_rate: 0.99 + n: 15 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.55 + 8: + name: "generic" + half_life: 7 + maximum_parasite_killing_rate: 0.8 + n: 15 + age_specific_drug_concentration_sd: [ 0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 ] + k: 4 + base_EC50: 0.68 + +# --------------------------------------------------------------- +# 13. Therapy Parameters +# --------------------------------------------------------------- +therapy_parameters: + # Testing day for determining if treatment failed + tf_testing_day: 28 + + # Treatment failure rate used to determine whether a therapy is "useful" + tf_rate: 0.1 + + therapy_db: + #mono as + 0: + drug_id: [0] + dosing_days: [3] + #mono Lumefaltrine + 1: + drug_id: [1] + dosing_days: [3] + #mono AQ + 2: + drug_id: [2] + dosing_days: [3] + #mono PPQ + 3: + drug_id: [3] + dosing_days: [3] + #mono MQ + 4: + drug_id: [4] + dosing_days: [3] + #mono SP + 5: + drug_id: [5] + dosing_days: [3] + #AL + 6: + drug_id: [0,1] + dosing_days: [3] + #AS-AQ + 7: + drug_id: [0,2] + dosing_days: [3] + # DHA-PPQ + 8: + drug_id: [0,3] + dosing_days: [3] + #AS-MQ + 9: + drug_id: [0,4] + dosing_days: [3] + #TACT DHA-PPQ-MQ + 10: + drug_id: [0,3,4] + dosing_days: [3] + #TACT AL-AQ + 11: + drug_id: [0,1,2] + dosing_days: [3] + #CQ + 12: + drug_id: [6] + dosing_days: [3] + #Generic for Burn-in + 13: + drug_id: [8] + dosing_days: [3] + +# --------------------------------------------------------------- +# 14. Treatment Strategy Parameters +# --------------------------------------------------------------- +strategy_parameters: + # Initial treatment strategy ID + initial_strategy_id: 15 + + strategy_db: + 0: + name: SP-AQ-CQ-AL-MFTStrategy + type: MFT + therapy_ids: [5,2,12,6] + distribution: [0.3,0.3,0.3,0.1] + 1: + name: AL-SFTStrategy + type: SFT + therapy_id: 6 + 2: + name: ASAQ-SFTStrategy + type: SFT + therapy_id: 7 + 3: + name: CyclingStrategy + type: Cycling + therapy_ids: [8,7,6] + cycling_time: 1825 + 4: + name: AdaptiveCyclingStrategy + type: AdaptiveCycling + therapy_ids: [8,7,6] + trigger_value: 0.1 + delay_until_actual_trigger: 365 + turn_off_days: 365 + 5: + name: MFTStrategy + type: MFT + therapy_ids: [8,7,6] + distribution: [0.333333,0.333333,0.333334] + 6: + name: AL-ASAQ-DP-MFTRebalancingStrategy1 + type: MFTRebalancing + therapy_ids: [8,7,6] + distribution: [0.333333,0.333333,0.333334] + delay_until_actual_trigger: 365 + update_duration_after_rebalancing: 365 + 7: + name: AL-ASAQ-DP-MFTRebalancingStrategy2 + type: MFTRebalancing + therapy_ids: [8,7,6] + distribution: [0.333333,0.333333,0.333334] + delay_until_actual_trigger: 365 + update_duration_after_rebalancing: 730 + 8: + name: AL-ASAQ-DP-MFTRebalancingStrategy4 + type: MFTRebalancing + therapy_ids: [8,7,6] + distribution: [0.333333,0.333333,0.333334] + delay_until_actual_trigger: 365 + update_duration_after_rebalancing: 1460 + 9: + name: DPM-SFTStrategy + type: SFT + therapy_id: 10 + 10: + name: AL-AQ-SFTStrategy + type: SFT + therapy_id: 11 + 11: + name: AL-BaseLineStrategy + type: NestedMFT + strategy_ids: [1,0] + start_distribution: [0.05, 0.95] + peak_distribution: [0.8,0.2] + peak_after: 3650 + 12: + name: ASAQ-BaseLineStrategy + type: NestedMFT + strategy_ids: [2,0] + start_distribution: [0.05, 0.95] + peak_distribution: [0.8,0.2] + peak_after: 3650 + 13: + name: BaseLineStrategy + type: NestedMFTMultiLocation + strategy_ids: [0,1] + start_distribution: [[0.05, 0.95]] + peak_distribution: [[0.8,0.2]] + peak_after: 3650 + 14: + name: DHAPPQ-SFTStrategy + type: SFT + therapy_id: 8 + 15: + name: Burnin-SFTStrategy + type: SFT + therapy_id: 13 + +# --------------------------------------------------------------- +# 15. Epidemiological Parameters +# --------------------------------------------------------------- +epidemiological_parameters: + # Days from end of liver-stage infection to appearance of symptoms + days_to_clinical_under_five: 4 + days_to_clinical_over_five: 6 + + # Days for parasites to develop mature gametocytes after exiting liver stage + # Note: There are no explicit gametocytes in version 3.0.2 of the simulation + days_mature_gametocyte_under_five: 4 + days_mature_gametocyte_over_five: 6 + + # Probability that a patient completes a course of treatment + p_compliance: 1 + + # Guarantees that the minimum number of dosing days for a poorly complying patient is still 1 + min_dosing_days: 1 + + # Relative biting rates for individuals + relative_biting_info: + max_relative_biting_value: 35 + min_relative_biting_value: 1.0 + number_of_biting_levels: 100 + biting_level_distribution: + distribution: Gamma + Gamma: + mean: 5 + sd: 10 + + # Gametocyte levels under artemisinin action and when full + gametocyte_level_under_artemisinin_action: 1.0 + gametocyte_level_full: 1.0 + + # Parameters determining the probability a mosquito becomes infected based on the host's parasitemia level + relative_infectivity: + sigma: 3.91 + ro: 0.00031 + blood_meal_volume: 3 # Average blood meal volume in microliters + + # Probability of relapse after no treatment or treatment failure + p_relapse: 0.01 + + # Number of days before a relapse can occur + relapse_duration: 30 + + # Relapse rate used to increase parasite density after treatment failure + # Multiply by sqrt(20) per day + relapseRate: 4.4721 + + # Minimum update frequency for a host's attributes (especially parasite density) + update_frequency: 7 + + # Allows new co-infections to cause symptoms in infected but asymptomatic hosts + allow_new_coinfection_to_cause_symptoms: true + + # Window size for observing treatment failure rates + tf_window_size: 60 + + # Fraction of mosquitoes experiencing interrupted feeding + fraction_mosquitoes_interrupted_feeding: 0.0 + + # Inflation factor for certain calculations + inflation_factor: 0.01 + +# --------------------------------------------------------------- +# 16. Mosquito Parameters +# --------------------------------------------------------------- +mosquito_parameters: + mosquito_config: + interrupted_feeding_rate: [0.19] + prmc_size: 100 + + # Within-host induced free recombination + within_host_induced_free_recombination: true + +# --------------------------------------------------------------- +# 17. Events +# --------------------------------------------------------------- +events: + - name: "turn_off_mutation" + info: + - day: 2000/1/1 + - name: "turn_on_mutation" + info: + - day: 2010/1/1 + - name: "change_treatment_strategy" + info: + - day: 2010/1/1 + strategy_id: 3 + - name: "change_treatment_coverage" + info: + - type: "SteadyTCM" + day: 2010/1/1 + p_treatment_for_less_than_5_by_location: [0.750000] + p_treatment_for_more_than_5_by_location: [0.750000] + - name: "change_mutation_probability_by_locus" + info: + - day: 2000/1/1 + value: 0.0 + - day: 2010/1/1 + value: 0.001