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Clarify types in doc + fixups (Closes #304)
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dweindl committed Feb 28, 2020
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Showing 1 changed file with 6 additions and 8 deletions.
14 changes: 6 additions & 8 deletions doc/documentation_data_format.md
Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ REFERENCES(conditionsTable.conditionID), OPTIONAL]

The `conditionId` to be used for preequilibration. E.g. for drug
treatments the model would be preequilibrated with the no-drug condition.
Empty for no preequlibration.
Empty for no preequilibration.

- `simulationConditionId` [STRING, NOT NULL,
REFERENCES(conditionsTable.conditionID)]
Expand All @@ -180,7 +180,7 @@ condition-specific parameters used for simulation.
Time point of the measurement in the time unit specified in the SBML model,
numeric value or `inf` (lower-case) for steady-state measurements.

- `observableParameters` [STRING OR NULL, OPTIONAL]
- `observableParameters` [NUMERIC, STRING OR NULL, OPTIONAL]

This field allows overriding or introducing condition-specific versions of
output parameters defined in the observation model. The model can define
Expand All @@ -202,7 +202,7 @@ numeric value or `inf` (lower-case) for steady-state measurements.
All placeholders defined in the observation model must be overwritten here.
If there are no placeholders used, this column may be omitted.

- `noiseParameters` [STRING, OPTIONAL]
- `noiseParameters` [NUMERIC, STRING OR NULL, OPTIONAL]

The measurement standard deviation or `NaN` if the corresponding sigma is a
model parameter.
Expand All @@ -215,7 +215,7 @@ numeric value or `inf` (lower-case) for steady-state measurements.
The datasetId is used to group certain measurements to datasets. This is
typically the case for data points which belong to the same observable,
the same simulation and preequilibration condition, the same noise model,
the same observable tranformation and the same observable parameters.
the same observable transformation and the same observable parameters.
This grouping makes it possible to use the plotting routines which are
provided in the PEtab repository.

Expand All @@ -241,7 +241,7 @@ The observable table has the following columns:

| observableId | [observableName] | observableFormula | [observableTransformation] | noiseFormula | [noiseDistribution] |
| --- | --- | --- | --- | --- | --- |
| [String] | [String] | [String] | ['lin'(default)|'log'|'log10'] | [String'log'|Number] | ['laplace'|'normal'] |
| [String] | [String] | [String] | ['lin'(default)|'log'|'log10'] | [String|Number] | ['laplace'|'normal'] |
| e.g. | | | | | |
| relativeTotalProtein1 | Relative abundance of Protein1 | observableParameter1 * (protein1 + phospho_protein1 ) | lin | noiseParameter1 | normal |
| ... | ... | ... | ... | ... |
Expand Down Expand Up @@ -276,9 +276,7 @@ The observable table has the following columns:
The measurements and model outputs are both assumed to be provided in linear
space.

* `noiseFormula` [STRING]

Noise model parameters as plain text formula expression.
* `noiseFormula` [NUMERIC|STRING]

Measurement noise can be specified as a numerical value which will
default to a Gaussian noise model if not specified differently in
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