forked from trvrb/antigen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathparameters.yml
90 lines (81 loc) · 6.59 KB
/
parameters.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
# This contains all the parameters used in the model.
# These values correspond to defaults.
# Leaving an entry out is fine, the value will remain at its default.
# simulation parameters
burnin: 0 # days to wait before logging output
endDay: 600 # number of days to simulate
deltaT: 0.1 # number of days to move forward in a single timestep
printStep: 50 # print to out.timeseries every X days
fitnessSampleSize: 100 # number of random hosts to sample for average infection risk
tipSamplingRate: 0.0002 # store X samples per deme per day
tipSamplesPerDeme: 2000 # cap number of samples per deme
tipSamplingProportional: true # whether to sample proportional to prevalence
treeProportion: 0.1 # proportion of tips to use in tree reconstruction
diversitySamplingCount: 1000 # how many samples to draw to calculate diversity, netau and serial interval
netauWindow: 100 # window in days to calculate Ne*tau
repeatSim: true # repeat simulation until endDay is reached?
immunityReconstruction: false # whether to print immunity reconstruction to out.immunity
memoryProfiling: false # requires -javaagent:classmexer.jar to run
yearsFromMK: 1.0 # how many years to consider present when calculating MK
pcaSamples: false # whether to rotate and flip virus tree
reducedOutput: false # whether to output only out.summary and out.timeseries
detailedOutput: false # whether to output out.hosts and out.viruses files enabling checkpointing
restartFromCheckpoint: false # whether to load population from out.hosts
outPath: "output/"
outPrefix: 'run-out'
inPath: "input/"
sampleHostImmunity: true # whether to sample host immunity throughout the simulation
printHostImmunityStep: 50 # how often to print host immunity (ever X days)
# metapopulation parameters
demeCount: 3 # number of demes
demeNames: ["north", "tropics", "south"] # deme names
initialNs: [1000000, 1000000, 1000000] # inital deme population sizes
hostImmunitySamplesPerDeme: [10, 10, 10] # how many hosts to sample for host immunity
# host parameters
birthRate: 0.000091 # in births per individual per day, 1/30 years = 0.000091
deathRate: 0.000091 # in deaths per individual per day, 1/30 years = 0.000091
swapDemography: true # whether to keep overall population size constant
# epidemiological parameters
initialI: 10 # in individuals
initialDeme: 2 # index of deme where infection starts, 1..n
initialPrR: 0.5 # as proportion of population
beta: 0.36 # in contacts per individual per day
nu: 0.2 # in recoveries per individual per day
betweenDemePro: 0.0005 # relative to within-deme beta
# transcendental parameters
transcendental: false # whether to include a general recovered class
immunityLoss: 0.01 # in R->S per individual per day
initialPrT: 0.1 # initial faction in general recovered class
# seasonal parameters
demeBaselines: [1., 1., 1.] # baseline of seasonality
demeAmplitudes: [0.1, 0., 0.1] # amplitude of seasonality
demeOffsets: [0., 0., 0.5] # seasonal offset relative to the year
# immune parameters
phenotypeSpace: "geometricSeq" # options include: geometric, geometric3d, geometric10d, sequence, geometricSeq
muPhenotype: 0.05 # in mutations per individual per day
waning: false # whether to allow waning of host immunity
waningRate: 0.01 # rate per day of a host removing a random phenotype from their immune history
smithConversion: 0.1 # multiplier to distance to give cross-immunity
homologousImmunity: 0.95 # immunity raised to antigenically identical virus
initialTraitA: -6. # value in dimension 1 for initial host immunity
meanStep: 0.00001 # mean mutation size for non-epitopes
sdStep: 0.00001 # standard deviation of mutation size for non-epitopes
mut2D: false # whether to mutate in a full 360 degree arc
fixedStep: false # whether to fix step size, i.e. ignore sdStep
# sequence-specific parameters
startingSequence: "startingSequence.fasta" # the fasta file of the starting sequence of a Virus (must be divisible by 3 and cannot contain stop codon)
epitopeSites: "epitopeSites.txt" # the txt file of the epitope sites in the sequence
# epitopeSitesLow: "epitopeSitesLow.txt" # the txt file of the epitope sites in the sequence
# epitopeSitesHigh: "epitopeSitesHigh.txt" # the txt file of the epitope sites in the sequence
# proportionHighSites: 0.1 # the proportion of epitope sites that are placed into the "high" distribution
predefinedVectors: false # whether to use predefined vectors for mutations
meanStepEpitope: 0.3 # mean mutation size for epitopes
sdStepEpitope: 0.3 # standard deviation of mutation size for epitopes
meanStepEpitopeLow: 0.3 # mean mutation size for epitopes
sdStepEpitopeLow: 0.3 # standard deviation of mutation size for epitopes
meanStepEpitopeHigh: 0.3 # mean mutation size for epitopes
sdStepEpitopeHigh: 0.3 # standard deviation of mutation size for epitopes
transitionTransversionRatio: 5.0 # transition/transversion rate ratio, k
nonEpitopeAcceptance: 1.0 # probability of accepting a non-epitope mutation
epitopeAcceptance: 1.0 # probability of accepting an epitope mutation
DMSFile: # name of DMS csv file: must have 21 columns (site number and amino acid preferences ordered alphabetically) and rows must be in sequential order and equal the number of amino acid sites in the virus sequence