config-simulation.yaml

# Integer for N, the number of individuals to simulate
"N": 500

# List of real numbers for g0, the initial viral trait value at the root
g0:
  - 4.5

# List of real numbers for alpha, the selection strength parameter
alpha:
  - 0.1
  - 0.5
  - 1
  - 5
  - 10
  - 20
  - 30
  - 40
  - 50
  - 60

# List of real numbers for theta, the evolutionarily optimal viral trait value
theta:
  - 4.5

# Integer for M, the number of human SNPs with direct effect on trait
M: 20

# Integer for K, the total number of human SNPs to simulate
K: 100

# Integer for d, human ploidy
d: 2

# Real number for delta, the per-copy effect size on the trait for human SNPs
delta:
  - 0.2

# List of real numbers for H2, the heritability of the trait due to the virus
H2:
  - 0.15
  - 0.25
  - 0.35
  - 0.45
  - 0.55
  - 0.65
  - 0.75

# Real number for H2.h, the fraction of the total trait variance due to human SNPs; H2.h + max(H2) must be <= 1
H2.h: 0.25

# Real number for var.z, the total trait variance
var.z:
  - 0.73

# Integer for N.reps, the number of simulated data sets to generate for each unique combination of parameters
N.reps: 20

# Boolean for whether (True) to infer POUMM parameters from simulated data or (False) use true values
is.MLE: True

is.HIVTree: True