diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst index 0365154d..90e873df 100644 --- a/doc/v2/documentation_data_format.rst +++ b/doc/v2/documentation_data_format.rst @@ -521,6 +521,8 @@ Detailed field description - ``measurement`` [NUMERIC, REQUIRED] The measured value in the same units/scale as the model output. + If the corresponding ``noiseDistribution`` specifies a discrete distribution, + this value must be integral. - ``time`` [NUMERIC OR ``inf``, REQUIRED] @@ -746,11 +748,25 @@ Detailed field description Noise distributions ~~~~~~~~~~~~~~~~~~~ -Denote by :math:`m` the measured value, +The supported continuous and discrete probability distributions to model +measurement noise are listed below. +Those distributions 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` +and noise parameters :math:`\Sigma=\{\sigma_i\}_i`, +the current specification assumes independence, i.e. the full distribution is + +.. math:: + \pi(D|Y,\Sigma) = \prod_i\pi(m_i|y_i,\sigma_i) + +Continuous distributions +++++++++++++++++++++++++ + +Denote by :math:`m:=\text{measurement}` 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, +and :math:`\sigma := \text{noiseFormula}` the scale parameter of the noise +distribution (e.g., the standard deviation of a normal, or the scale parameter of a Laplace model). Then we have the following effective noise distributions: @@ -780,14 +796,40 @@ Then we have the following effective noise distributions: - .. math:: \pi(m|y,\sigma) = \frac{1}{2\sigma m}\exp\left(-\frac{|\log m - \log y|}{\sigma}\right) -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` -and noise parameters :math:`\Sigma=\{\sigma_i\}_i`, -the current specification assumes independence, i.e. the full distribution is +Discrete distributions +++++++++++++++++++++++ -.. math:: - \pi(D|Y,\Sigma) = \prod_i\pi(m_i|y_i,\sigma_i) +Denote by :math:`m` the ``measurement`` in the measurement table, +then we have the following effective noise distributions: + +.. list-table:: + :header-rows: 1 + :widths: 10 10 80 + + * - Type + - ``noiseDistribution`` + - Probability density function (PDF) + * - Poisson distribution + - ``poisson`` + - | :math:`\pi(m|\lambda) = \frac{\lambda^m\exp(-\lambda)}{m!}` + | where the rate :math:`\lambda` is given via ``observableFormula``. + | ``noiseFormula`` must be empty in this case. + | The measurement :math:`m` is the number of observed events + | and must be a non-negative integer. + * - Binomial distribution + - ``binomial`` + - | :math:`\pi(m|n,p) = \binom{n}{m}p^m(1-p)^{n-m}` + | where :math:`n` is the number of trials given via ``observableFormula`` + | and :math:`p` the probability of success given via ``noiseFormula``. + | The measurement :math:`m` is the number of observed successes + | and must be an integer between 0 and :math:`n`. + * - Negative binomial distribution + - ``negative-binomial`` + - | :math:`\pi(m|r,p) = \binom{m+r-1}{m}p^r(1-p)^m` + | where :math:`r` is the number of successes given via ``observableFormula`` + | and :math:`p` the probability of success given via ``noiseFormula``. + | The measurement :math:`m` is the number of observed failures + | and must be a non-negative integer. .. _v2_parameter_table: