How-to upload a virtual population?
You can upload your population in jinkō with two different formats (JSON and CSV). This can be done using the create VPOP feature
Requirements
In both cases (JSON and CSV), you need the following information per patient:
A patientIndex: Text - a unique value identifying the patient
A set of patientAttributes where each attribute has:
An identifier
A value
An optional unit
This translates as follows for each format:
CSV format
The separator is the standard comma: “,”
The header follows the pattern patientIndex,id1(unit1), id2, ..., idn(unitn) . The unit can be specified in brackets (unit) after the id. In this example id2 does not have a unit specified
Body follows the following pattern: patient1, val11, val12, ..., val1n
patientIndex column: Text, should be unique for each row
Patient descriptors columns: Float is mandatory
Example (presented in tabular format for readability):
patientIndex |
age(year) |
sizeHelper |
isMale |
patient1 |
60.7 |
0.294 |
1 |
patient2 |
55.2 |
0.407 |
0 |
patient3 |
70.3 |
0.822 |
0 |
JSON format
The virtual population object is a list of patients
Each Patient has:
A "patientIndex": Text
A "patientAttributes": Object
"id": Text
"val": Float
"unit": Text (optional)
Example:
{
"patients": [{
"patientIndex": "patient1",
"patientAttributes": [{
"id": "age",
"val": 60.7,
"unit": "year"
},
{
"id": "sizeHelper",
"val": 0.294,
"unit": "dimensionless"
},
{
"id": "isMale",
"val": 1,
"unit": "dimensionless"
}
],
"patientIndex": "patient1"
},
{
"patientIndex": "patient2",
"patientAttributes": [{
"id": "age",
"val": 55.2,
"unit": "year"
},
{
"id": "sizeHelper",
"val": 0.407,
"unit": "dimensionless"
},
{
"id": "isMale",
"val": 0,
"unit": "dimensionless"
}
]
},
{
"patientIndex": "patient3",
"patientAttributes": [{
"id": "age",
"val": 70.3,
"unit": "year"
},
{
"id": "sizeHelper",
"val": 0.822,
"unit": "dimensionless"
},
{
"id": "isMale",
"val": 0,
"unit": "dimensionless"
}
]
}
]
}A note on Units
The base units used in the platform are:
[length] : "meter = m = metre"
[time] : "second = s = sec"
[current] : "ampere = A = amp"
[luminosity] : "candela = cd = candle"
[mass] : "gram = g"
[substance] : "mole = mol"
[temperature ] : "degK = K = kelvin"
[] : "dimensionless”
You can use prefix in the units combination, below is a non-exhaustive of accepted prefix:
"nano- = 1e-9 = n-"
"micro- = 1e-6 = u-"
"milli- = 1e-3 = m-"
"centi- = 1e-2 = c-"
"deci- = 1e-1 = d-"
"deca- = 1e+1 = da-"
"hecto- = 1e2 = h-"
"kilo- = 1e3 = k-"
"mega- = 1e6 = M-"
"giga- = 1e9 = G-"
You can combine and exponent units as follow: kilogram * meter / second ** 2
