From 32f76ac677f770e250c750cc923f8f9dc78caaa9 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 28 Feb 2020 17:40:15 +0100 Subject: [PATCH] Clarify types in doc + fixups (Closes #304) --- doc/documentation_data_format.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/doc/documentation_data_format.md b/doc/documentation_data_format.md index 674f8a54..ecc2687d 100644 --- a/doc/documentation_data_format.md +++ b/doc/documentation_data_format.md @@ -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)] @@ -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 @@ -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. @@ -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. @@ -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 | | ... | ... | ... | ... | ... | @@ -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