diff --git a/doc/documentation_data_format.rst b/doc/documentation_data_format.rst index 97795dfb..fa3bfc2b 100644 --- a/doc/documentation_data_format.rst +++ b/doc/documentation_data_format.rst @@ -212,7 +212,7 @@ Detailed field description - ``observableId`` [STRING, NOT NULL, REFERENCES(observables.observableID)] - Observable ID as defined in the observables table described below. + Observable ID as defined in the observable table described below. - ``preequilibrationConditionId`` [STRING OR NULL, REFERENCES(conditionsTable.conditionID), OPTIONAL] @@ -277,8 +277,8 @@ Detailed field description ``datasetId``, which is helpful for plotting e.g. error bars. -Observables table ------------------ +Observable table +---------------- Parameter estimation requires linking experimental observations to the model of interest. Therefore, one needs to define observables (model outputs) and diff --git a/doc/tutorial.rst b/doc/tutorial.rst index b95908b5..e02c76e5 100644 --- a/doc/tutorial.rst +++ b/doc/tutorial.rst @@ -130,7 +130,7 @@ functions. Additionally, a noise model can be introduced to account for the measurement errors. In PEtab, this can be encoded in the observable file: -.. list-table:: Observables table ``observables.tsv``. +.. list-table:: Observable table ``observables.tsv``. :header-rows: 1 * - observableId @@ -146,7 +146,7 @@ file: - Rel. STAT5A abundance [%] - ... -.. list-table:: Observables table ``observables.tsv`` (continued). +.. list-table:: Observable table ``observables.tsv`` (continued). :header-rows: 1 * - ... @@ -162,7 +162,7 @@ file: - 100*(STAT5A + pApB + 2*pApA) / (2 \* pApB + 2\* pApA + STAT5A + STAT5B + 2*pBpB) - ... -.. list-table:: Observables table ``observables.tsv`` (continued). +.. list-table:: Observable table ``observables.tsv`` (continued). :header-rows: 1 * - ... @@ -235,8 +235,8 @@ PEtab measurement file: brevity, only the first and last time point of the example are shown here (the omitted measurements are indicated by “...” in the example). -* *noiseParameters* relates to the *noiseParameters* in the observables - file. In our example, the measurement noise is unknown. Therefore we +* *noiseParameters* relates to the *noiseParameters* in the observable table. + In our example, the measurement noise is unknown. Therefore we define parameters here which have to be estimated (see parameters sheet below). If the noise is known, e.g. from multiple replicates, numeric values can be used in this column.