diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst index 0365154d..dbdd44d9 100644 --- a/doc/v2/documentation_data_format.rst +++ b/doc/v2/documentation_data_format.rst @@ -746,13 +746,12 @@ Detailed field description Noise distributions ~~~~~~~~~~~~~~~~~~~ -Denote by :math:`m` the measured value, -:math:`y:=\text{observableFormula}` the simulated value -(the location parameter of the noise distribution), -and :math:`\sigma` the scale parameter of the noise distribution -as given via the ``noiseFormula`` field (the standard deviation of a normal, -or the scale parameter of a Laplace model). -Then we have the following effective noise distributions: +Let :math:`m` denote the measured value, +:math:`y := \text{observableFormula}` the simulated value (the median of +the noise distribution), and :math:`\sigma := \text{noiseFormula}` the +noise parameter (the standard deviation and the scale parameter for the +Normal and Laplace distributions, respectively). Then we have the following +effective noise distributions: .. list-table:: :header-rows: 1 @@ -761,25 +760,31 @@ Then we have the following effective noise distributions: * - Type - ``noiseDistribution`` - Probability density function (PDF) - * - Gaussian distribution + * - | Gaussian distribution + | (i.e., :math:`m \sim \mathcal{N}(y, \sigma^2)`) - ``normal`` - .. math:: \pi(m|y,\sigma) = \frac{1}{\sqrt{2\pi}\sigma}\exp\left(-\frac{(m-y)^2}{2\sigma^2}\right) * - | Log-normal distribution - | (i.e., :math:`\log(m)` is normally distributed) + | (i.e., :math:`\log(m) \sim \mathcal{N}(\log(y), \sigma^2)`) - ``log-normal`` - .. math:: \pi(m|y,\sigma) = \frac{1}{\sqrt{2\pi}\sigma m}\exp\left(-\frac{(\log m - \log y)^2}{2\sigma^2}\right) - * - Laplace distribution + * - | Laplace distribution + | (i.e., :math:`m \sim \mathrm{Laplace}(y, \sigma)`) - ``laplace`` - .. math:: \pi(m|y,\sigma) = \frac{1}{2\sigma}\exp\left(-\frac{|m-y|}{\sigma}\right) * - | Log-Laplace distribution - | (i.e., :math:`\log(m)` is Laplace distributed) + | (i.e., :math:`\log(m) \sim \mathrm{Laplace}(\log(y), \sigma)`) - ``log-laplace`` - .. math:: \pi(m|y,\sigma) = \frac{1}{2\sigma m}\exp\left(-\frac{|\log m - \log y|}{\sigma}\right) +Note that, for all PEtab noise distributions, the simulated value is modeled +as the median of the noise distribution; i.e., measurements are assumed to +be equally likely to lie above or below the model output. + The distributions above are for a single data point. For a collection :math:`D=\{m_i\}_i` of data points and corresponding simulations :math:`Y=\{y_i\}_i`