Parameters
Parameter classes.
AssayParams
Bases: BaseModel
Parameters for assay generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
baseline
|
float
|
Baseline reading value |
1.0
|
degrade
|
float
|
Rate at which sample responses decrease per day after first day (0..1) |
0.05
|
delay
|
int
|
Maximum number of days between specimen collection and assay |
5
|
mutant
|
float
|
Mutant reading value (must be positive) |
5.0
|
reading_noise
|
float
|
Noise level for readings (must be positive) |
0.2
|
plate_size
|
int
|
Size of assay plate (must be positive) |
4
|
image_noise
|
int
|
Plate image noise (grayscale 0-255) |
32
|
p_duplicate_assay
|
float
|
Probably that an assay is repeated |
0.05
|
Source code in src/snailz/parameters.py
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validate_fields()
Validate requirements on fields.
Source code in src/snailz/parameters.py
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MachineParams
Bases: BaseModel
Parameters for machine generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
number
|
int
|
Number of machines |
5
|
variation
|
float
|
Camera variation |
0.15
|
Source code in src/snailz/parameters.py
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PersonParams
Bases: BaseModel
Parameters for people generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
locale
|
str
|
Locale for names |
'et_EE'
|
number
|
int
|
Number of people |
5
|
Source code in src/snailz/parameters.py
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|
validate_fields(v)
Validate that the locale is available in faker.
Source code in src/snailz/parameters.py
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SpecimenParams
Bases: BaseModel
Parameters for specimen generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
length
|
int
|
Length of specimen genomes (must be positive) |
20
|
start_date
|
date
|
Start date for specimen collection |
datetime.date(2024, 3, 1)
|
max_mass
|
float
|
Maximum mass for specimens (must be positive) |
10.0
|
mut_mass_scale
|
float
|
Scaling factor for mutant snail mass |
2.0
|
num_mutations
|
int
|
Number of mutations in specimens (must be between 0 and length) |
5
|
spacing
|
float
|
Inter-specimen spacing |
3.75
|
daily_growth
|
float
|
Mass increase per day |
0.01
|
p_missing_location
|
float
|
Probability that location is missing |
0.05
|
Source code in src/snailz/parameters.py
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SurveyParams
Bases: BaseModel
Parameters for survey generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
number
|
int
|
Number of surveys |
3
|
size
|
int
|
Survey size |
15
|
start_date
|
date
|
Start date for specimen collection |
datetime.date(2024, 3, 1)
|
max_interval
|
int
|
Maximum interval between samples |
7
|
Source code in src/snailz/parameters.py
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|
ScenarioParams
Bases: BaseModel
Represent all parameters combined.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
seed
|
int
|
RNG seed |
7493418
|
assay
|
AssayParams
|
parameters for assay generation |
AssayParams(baseline=1.0, degrade=0.05, delay=5, mutant=5.0, reading_noise=0.2, plate_size=4, image_noise=32, p_duplicate_assay=0.05)
|
machine
|
MachineParams
|
parameters for machine generation |
MachineParams(number=5, variation=0.15)
|
person
|
PersonParams
|
parameters for people generation |
PersonParams(locale='et_EE', number=5)
|
specimen
|
SpecimenParams
|
parameters for specimen generation |
SpecimenParams(length=20, start_date=datetime.date(2024, 3, 1), max_mass=10.0, mut_mass_scale=2.0, num_mutations=5, spacing=3.75, daily_growth=0.01, p_missing_location=0.05)
|
survey
|
SurveyParams
|
parameters for survey generation |
SurveyParams(number=3, size=15, start_date=datetime.date(2024, 3, 1), max_interval=7)
|
Source code in src/snailz/parameters.py
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|