uga-configuration.yml

# ---------------------------------------------------------------
#
# Boni Lab
#
# Reference UGANDA model configuration data
#
# WARNING This configuration is not intended to be run by the 
# simulation, but to be used as an aggregate of reference data
# for the various configuration parameter. The configuration in
# PfPR Decline/uga-pfpr-constant.yml is the canonical baseline.
# ---------------------------------------------------------------

# ---------------------------------------------------------------
# Items controlling execution of the model
# ---------------------------------------------------------------
# The number of model days between updates to the user
days_between_notifications: 30

# The number to use as the default seed value, comment out or set
# to zero (0) to use random seed.
initial_seed_number: 0

# Connection string for the PostgreSQL database
connection_string: "host=masimdb.vmhost.psu.edu dbname=uganda user=sim password=sim connect_timeout=60"

# Record the genomic data
record_genome_db: false

# Report to GUI and console every 30 days
report_frequency: 30

# ---------------------------------------------------------------
# Items controlling the behavior of the model
# ---------------------------------------------------------------
# Starting date is calibration year minus 11 years of burn-in
starting_date: 2009/1/1

# 2020 is the target calibration date based upon DHS MIS surveys
start_of_comparison_period: 2020/1/1

# Ending date is start of recording period plus 20 years, this
# will change depending upon the actual studies
ending_date: 2045/1/1

# Discard the first five years worth of data
start_collect_data_day: 1826

# Number of days to keep track total number of parasites in population
number_of_tracking_days: 11

# Transmission parameter based upon MMC data, adjusts the odds that
# an individual will be infected when challenged by sporozoites
transmission_parameter: 0.55

# Age classes used for reporting age-specific mortality calculations
number_of_age_classes: 15
age_structure: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 20, 60, 100]

# 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 of the population in the model
artificial_rescaling_of_population_size: 0.15

# ---------------------------------------------------------------
# Rasters to be used in conjunction with the location_db, note 
# that the paths are relative to the binary file for the simulation
# ---------------------------------------------------------------
raster_db:
  # Adjusted population to account for burn-in up to 2009 start 
  population_raster: "uga_init_pop.asc"
    
  # Raster files defining the country
  district_raster: "uga_district.asc"
  
  # Raster files defining treatments
  pr_treatment_under5: "uga_treatment.asc"
  pr_treatment_over5: "uga_treatment.asc" 

  # Raster file containing the calibrated beta value
  beta_raster: "uga_beta.asc"
  
  # Raster file containing the travel time / friction surface
  travel_raster: "uga_travel.asc"

  # Set the cell size used by raster, in sq.km
  cell_size: 5

  # Approximate national age distribution for Uganda
  age_distribution_by_location: [[0.0423, 0.0423, 0.0423, 0.0423, 0.0349, 0.0349, 0.0349, 0.0349, 0.0349, 0.0317, 0.0317, 0.0317, 0.0317, 0.0317, 0.1743, 0.1132, 0.0832, 0.0601, 0.0341, 0.0331, 0.0]]

  # Probability that an infected an symptomatic person receives treatment, 
  # note that a single value is being used for the entire country
  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 ]

# Seasonality of malaria in Uganda
seasonal_info:
  enable: true
  mode: rainfall
  rainfall:
    filename: "uga_adjustment.csv"
    period: 365

# Country specific movement model and calibration  
# TODO Generic movement model that needs to be updated for Uganda at some point
spatial_model:
  name: "WesolowskiSurface"
  WesolowskiSurface:
    kappa: 0.01093251
    alpha: 0.22268982
    beta: 0.14319618
    gamma: 0.83741484

# Crude Birth Rate: 38 (UN 2019)
birth_rate: 0.038

# Malaria adjusted, all-causes death rate for Uganda
death_rate_by_age_class: [ 0.04286, 0.02918, 0.01955, 0.01470, 0.01178, 0.00067, 0.00067, 0.00068, 0.00071, 0.00071, 0.00072, 0.00078, 0.00649, 0.00717, 0.06115 ]


# probability of death for patients who are not treated or patients who experience a treatment failure (due to drug resistance, or otherwise)
# when received treatment, this rate drop by factor of 10 in 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]

# Standard values used in other models
parasite_density_level:
  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 1000 parasites per microliter of blood
  log_parasite_density_clinical:        4.301    # corresponds to 20,000 parasites per microliter of blood (total 10^11)
  log_parasite_density_clinical_from:   3.301    # corresponds to 2000 parasites per microliter of blood (total 10^10)
  log_parasite_density_clinical_to:     5.301    # corresponds to 200,000 parasites per microliter of blood (total 10^12)
  log_parasite_density_detectable:      1.000    # corresponds to 10 parasites per microliter of blood
  log_parasite_density_detectable_pfpr: 1.699    # corresponds to 50 parasites per microliter of blood
  log_parasite_density_pyrogenic:       3.398    # corresponds to 2500 parasites per microliter of blood

immune_system_information:
  #rate at which antimalarial immune function increases when a host is parasitaemic
  b1: 0.00125

  #rate at which antimalarial immune function decreases when a host is parasitaemic
  b2: 0.0025

  # durations of infection of naive and fully-immune hosts. 
  # these parameters are used to calculate max and min killing rate by immune system
  duration_for_naive: 300
  duration_for_fully_immune: 60

  # initial conditions for the immune function of the population at time zero
  mean_initial_condition: 0.1
  sd_initial_condition: 0.1

  # (per year) age-dependent faster acquisition of immunity from age 1 to age 10
  immune_inflation_rate: 0.01

  # Max probabilities of experiencing symptoms as a result of a new infection
  # the actual probability will depend on the host's immunity
  max_clinical_probability: 0.99

  # slope of sigmoidal prob-v-immunity function (parameter z in supplement of 2015 LGH paper) 
  immune_effect_on_progression_to_clinical: 4

  # age at which immune function is mature
  age_mature_immunity: 10

  # parameter kappa in supplement of 2015 LGH paper
  factor_effect_age_mature_immunity: 1

  # Adjust the infliction point in the curve
  midpoint: 0.4

# 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
    Exponential:
      scale: 0.17
    Gamma:
      mean: 5
      sd: 10
  # Percentage of the population selected for movement outside of their cell each timestep
  # TODO Circulation is currently based upon BFA and needs to be updated
  circulation_percent: 0.00336
  length_of_stay:
    mean: 5
    sd: 10

# Definition for initial parasite
#
# 1. loc 
# 2. id (this is the resistance type of the parasite) 
# 3. prevalence unweighted by biting rate
#
# location id is -1 results in all locations having the same initial parasites
initial_parasite_info:
  - location_id: -1
    parasite_info:
      # TNY--R1 / 
      # T - CQ resistance (everywhere)
      # NY-- - N (diversity at 86 locus), Y (184 locus)
      # R - Artemisinin (ART) sensitive
      # 1 - PPQ sensitive
      - parasite_type_id: 32
        prevalence: 0.05

      # TYY--R1
      - parasite_type_id: 36
        prevalence: 0.05
        
# Events for Uganda
events:
  - name: turn_off_mutation
    info:
      - day: 2009/1/1


# Drug Information
#
# maximum_parasite_killing_rate: 
#       e.g. 0.999 means the drug can kill 99.9% of parasites in 1 day if a person has 
#       the highest possible drug concentration
#
# n: 
#       the slope of the linear portion of the concentration-effect curve
#
# EC50: 
#       the drug concentration which produces 50% of the parasite killing achieved at maximum-concentration
#       ( the expected starting concentration is 1.0 )
#
# age_specific_drug_concentration_sd: 
#       the actual drug concentration, per individual, will be drawn from a normal distribution with mean=1 and this sd.
#
# k: 
#       parameter that describes the change in the mutation probability when drug levels are intermediate
#       - set k=0.5 for a simple linear model where mutation probability decreases linearly with drug concentration
#       - set k=2 or k=4 for a piecewise-linear model where mutation probability increases from high concentrations
#               to intermediate concentrations, and then decreases linearly from intermediate concentrations to zero
#
drug_db:
  # Uganda treatments
  0:
    name: "ART"       # 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]
    mutation_probability: 0.005
    affecting_loci: [2]
    selecting_alleles: [[1]]
    k: 4
    EC50:
      ..0..: 0.75
      ..1..: 1.2
      ..2..: 1.2
  1:
    name: "LUM"       # 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]
    mutation_probability: 0.005
    affecting_loci: [0,1]
    selecting_alleles: [[0],[0,2,3,4,6,7]]
    k: 4
    EC50:
      #KNY--
      00...: 0.8
      #KYY--
      01...: 0.67
      #KNF--
      02...: 0.9
      #KYF--
      03...: 0.8
      #KNYNY
      04...: 1.0
      #KYYYY
      05...: 0.87
      #KNFNF
      06...: 1.1
      #KYFYF
      07...: 1.0
      #TNY--
      10...: 0.75
      #TYY--
      11...: 0.6
      #TNF--
      12...: 0.85
      #TYF--
      13...: 0.75
      #TNYNY
      14...: 0.95
      #TYYNY
      15...: 0.8
      #TNFNF
      16...: 1.05
      #TYFYF
      17...: 0.95       
  2:
    name: "ADQ"       # 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]
    mutation_probability: 0.005
    affecting_loci: [0,1]
    selecting_alleles: [[1],[0,1,3,4,5,7]]
    k: 4
    EC50:
      #KNY--
      00...: 0.62
      #KYY--
      01...: 0.85
      #KNF--
      02...: 0.5
      #KYF--
      03...: 0.775
      #KNYNY
      04...: 0.62
      #KYYYY
      05...: 0.85
      #KNFNF
      06...: 0.5
      #KYFYF
      07...: 0.775
      #TNY--
      10...: 0.7
      #TYY--
      11...: 0.9
      #TNF--
      12...: 0.65
      #TYF--
      13...: 0.82
      #TNYNY
      14...: 0.7
      #TYYYY
      15...: 0.9
      #TNFNF
      16...: 0.65
      #TYFYF
      17...: 0.82   
  3:
    name: "PQ"        # 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]
    mutation_probability: 0.005
    affecting_loci: [3]
    selecting_alleles: [[1]]
    resistant_factor: [[1]]
    k: 4
    EC50:
      ...0.: 0.58
      ...1.: 1.4       
  4:
    name: "QUIN"       # Quinine
    half_life: 18
    maximum_parasite_killing_rate: 0.9
    n: 3                              
    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]
    mutation_probability: 0.0
    affecting_loci: []
    selecting_alleles: []
    k: 4
    EC50:
      # K----
      0....: 1.41
      # T----
      1....: 1.41      
         
# Drug IDs for the model
artemisinin_drug_id: 0
lumefantrine_drug_id: 4

# Therapies that are used in Uganda
tf_testing_day: 28
therapy_db:
  # ACT - artemether–lumefantrine (AL) / first-line therapy
  0:
    drug_id: [0, 1]
    dosing_days: [3]
  # ACT - artesunate-amodiaquine (ASAQ) / alternative first-line therapy
  1:
    drug_id: [0, 2]
    dosing_days: [3]
  # ACT - dihydroartemisinin-piperaquine (DHAPPQ) / second-line therapy
  2:
    drug_id: [0, 3]
    dosing_days: [3]
  # MONO - Quinine (QUIN)
  3:
    drug_id: [4]
    dosing_days: [7]    
  
# Drug-deployment strategy - baseline represents the survey data for Uganda
# 
# NOTE severe treatments are not included in the strategy
strategy_db:
  0:
    name: Uganda-Baseline
    type: MFT
    therapy_ids: [ 0, 1, 2, 3 ]
    distribution: [ 0.806, 0.046, 0.055, 0.093 ]
initial_strategy_id: 0

# Days from end of liver-stage infection to appearance of symptoms
days_to_clinical_under_five: 4
days_to_clinical_over_five: 6

# Days that parasites develop mature gametocyte after exiting liver stage
days_mature_gametocyte_under_five: 4
days_mature_gametocyte_over_five: 6

# Probability of patient compliance
p_compliance: 1

# Minimum dosing days if patient compliance is < 1 - EFFECTIVELY DISABLED 
min_dosing_days: 1

# relative biting rates for individuals; uncomment "distribution: Exponential" to use an
# exponentially distributed biting rate
relative_bitting_info:
  max_relative_biting_value: 35
  number_of_biting_levels: 100
  biting_level_distribution:
    #  distribution: Exponential
    distribution: Gamma
    Exponential:
      scale: 0.17
    Gamma:
      mean: 5
      sd: 10

gametocyte_level_under_artemisinin_action: 1.0
gametocyte_level_full: 1.0

# these values are based on Ross 2006 - these parameters determine the probability a mosquito
# becomes infected based on the host's asexual parasitaemia level
relative_infectivity:
  sigma: 3.91
  ro: 0.00031
  # on average 1 mosquito take 3 microliters of blood per bloodeal
  blood_meal_volume: 3

# probability to relapse after no treatment, or a treatment failure due to drug resistance
p_relapse: 0.01

# number of days before a relapse can occur
relapse_duration: 30

# relapse rate - used to increase the parasite density after a treatment failure (at the drug clearance day)
# multiply by sqrt(20) per day
relapseRate: 4.4721

# minimum update frequency for a host's attributes (esp. parasite density) is every 7 days, or
# more frequently if other events are occurring at this time
update_frequency: 7

# if an infected and asymptomatic host is bitten and infected by a new 
# parasite clone, this setting allows the new infection to cause symptoms
allow_new_coinfection_to_cause_symtoms: true

# free recombination among the drug resistance loci
using_free_recombination: true

# the current treatment failure rate as observed in the population is not really
# today's treatment failure rate, as these data are never assembled that quickly in
# real life; rather, it is the average treatment failure rate observed over the 
# past 60 days
tf_window_size: 60

# Mosquitoes always finish their blood meal
fraction_mosquitoes_interrupted_feeding: 0.0

# TODO - What's this do?
inflation_factor: 0.01

# Define locations of drug resistant genes
genotype_info:
  loci:
    - locus_name: "pfcrt"
      position: 0
      alleles:
        - value: 0
          allele_name: "K76"
          short_name: "K"
          can_mutate_to: [1]
          mutation_level: 0
          daily_cost_of_resistance: 0.0
        - value: 1
          allele_name: "76T"
          short_name: "T"
          can_mutate_to: [0]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005
    - locus_name: "pfmdr1"
      position: 1
      alleles:
        - value: 0
          allele_name: "N86 Y184 one copy of pfmdr1"
          short_name: "NY--"
          can_mutate_to: [1,2,4]
          mutation_level: 0
          daily_cost_of_resistance: 0.0
        - value: 1
          allele_name: "86Y Y184 one copy of pfmdr1"
          short_name: "YY--"
          can_mutate_to: [3,0,5]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005
        - value: 2
          allele_name: "N86 184F one copy of pfmdr1"
          short_name: "NF--"
          can_mutate_to: [3,0,6]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005
        - value: 3
          allele_name: "86Y 184F one copy of pfmdr1"
          short_name: "YF--"
          can_mutate_to: [1,2,7]
          mutation_level: 2
          daily_cost_of_resistance: 0.00099975
        - value: 4
          allele_name: "N86 Y184 2 copies of pfmdr1"
          short_name: "NYNY"
          can_mutate_to: [0]
          mutation_level: 1
          daily_cost_of_resistance: 0.005
        - value: 5
          allele_name: "86Y Y184 2 copies of pfmdr1"
          short_name: "YYYY"
          can_mutate_to: [1]
          mutation_level: 2
          daily_cost_of_resistance: 0.0055
        - value: 6
          allele_name: "N86 184F 2 copies of pfmdr1"
          short_name: "NFNF"
          can_mutate_to: [2]
          mutation_level: 2
          daily_cost_of_resistance: 0.0055
        - value: 7
          allele_name: "86Y 184F 2 copies of pfmdr1"
          short_name: "YFYF"
          can_mutate_to: [3]
          mutation_level: 3
          daily_cost_of_resistance: 0.006
    - locus_name: "K13 Propeller"
      position: 2
      # NOTE This is proxy data for C469Y and A675V based upon C580Y
      alleles:
        # Wild type
        - value: 0
          allele_name: "C469-A675"
          short_name: "CA"
          can_mutate_to: [1,2]
          mutation_level: 0
          daily_cost_of_resistance: 0.0

        # Single mutants
        - value: 1
          allele_name: "469Y-A675"
          short_name: "YA"
          can_mutate_to: [0]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005
        - value: 2
          allele_name: "C469-675V"
          short_name: "CV"
          can_mutate_to: [0]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005
        
    - locus_name: "Plasmepsin 2-3"
      position: 3
      alleles:
        - value: 0
          allele_name: "Plasmepsin 2-3 one copy"
          short_name: "1"
          can_mutate_to: [1]
          mutation_level: 0
          daily_cost_of_resistance: 0.0
        - value: 1
          allele_name: "Plasmepsin 2-3 2 copies"
          short_name: "2"
          can_mutate_to: [0]
          mutation_level: 1
          daily_cost_of_resistance: 0.0005

# --- DISABLED FEATURES ---

# special function to make the mean biting rate (across hosts) depend on age
using_age_dependent_bitting_level: false

# special function which makes the probability of an infection (resulting 
# from an infectious mosquito bite) age-dependent
using_variable_probability_infectious_bites_cause_infection: false

# Settings for MDAs - NOT USED
mda_therapy_id: 8
age_bracket_prob_individual_present_at_mda: [10, 40]
mean_prob_individual_present_at_mda: [0.85, 0.75, 0.85]
sd_prob_individual_present_at_mda: [0.3, 0.3, 0.3]