diff --git a/src/functions-reference/binary_distributions.qmd b/src/functions-reference/binary_distributions.qmd index 58777b158..85c603c99 100644 --- a/src/functions-reference/binary_distributions.qmd +++ b/src/functions-reference/binary_distributions.qmd @@ -29,7 +29,7 @@ Increment target log probability density with `bernoulli_lupmf(y | theta)`. {{< since 2.0 >}} -\index{{\tt \bfseries bernoulli }!sampling statement|hyperpage} +\index{{\tt \bfseries bernoulli }!distribution statement|hyperpage} ### Stan Functions @@ -109,7 +109,7 @@ Increment target log probability density with `bernoulli_logit_lupmf(y | alpha)` {{< since 2.0 >}} -\index{{\tt \bfseries bernoulli\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries bernoulli\_logit }!distribution statement|hyperpage} ### Stan Functions @@ -168,7 +168,7 @@ Increment target log probability density with `bernoulli_logit_glm_lupmf(y | x, {{< since 2.25 >}} -\index{{\tt \bfseries bernoulli\_logit\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries bernoulli\_logit\_glm }!distribution statement|hyperpage} ### Stan Functions diff --git a/src/functions-reference/bounded_continuous_distributions.qmd b/src/functions-reference/bounded_continuous_distributions.qmd index 9f568cee2..b7afcfaea 100644 --- a/src/functions-reference/bounded_continuous_distributions.qmd +++ b/src/functions-reference/bounded_continuous_distributions.qmd @@ -25,7 +25,7 @@ $y \in [\alpha,\beta]$, \begin{equation*} \text{Uniform}(y|\alpha,\beta) = Increment target log probability density with `uniform_lupdf(y | alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries uniform }!sampling statement|hyperpage} +\index{{\tt \bfseries uniform }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/bounded_discrete_distributions.qmd b/src/functions-reference/bounded_discrete_distributions.qmd index a2cd3a064..209671602 100644 --- a/src/functions-reference/bounded_discrete_distributions.qmd +++ b/src/functions-reference/bounded_discrete_distributions.qmd @@ -37,7 +37,7 @@ Increment target log probability density with `binomial_lupmf(n | N, theta)`. {{< since 2.0 >}} -\index{{\tt \bfseries binomial }!sampling statement|hyperpage} +\index{{\tt \bfseries binomial }!distribution statement|hyperpage} ### Stan functions @@ -127,7 +127,7 @@ n}{\text{logit}^{-1}(\alpha)} \end{equation*} Increment target log probability density with `binomial_logit_lupmf(n | N, alpha)`. {{< since 2.0 >}} -\index{{\tt \bfseries binomial\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries binomial\_logit }!distribution statement|hyperpage} ### Stan functions @@ -173,7 +173,7 @@ Increment target log probability density with `binomial_logit_glm_lupmf(n | N, x {{< since 2.34 >}} -\index{{\tt \bfseries binomial\_logit\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries binomial\_logit\_glm }!distribution statement|hyperpage} ### Stan Functions @@ -293,7 +293,7 @@ If $N \in \mathbb{N}$, $\alpha \in \mathbb{R}^+$, and $\beta \in Increment target log probability density with `beta_binomial_lupmf(n | N, alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries beta\_binomial }!sampling statement|hyperpage} +\index{{\tt \bfseries beta\_binomial }!distribution statement|hyperpage} ### Stan functions @@ -369,7 +369,7 @@ If $a \in \mathbb{N}$, $b \in \mathbb{N}$, and $N \in Increment target log probability density with `hypergeometric_lupmf(n | N, a, b)`. {{< since 2.0 >}} -\index{{\tt \bfseries hypergeometric }!sampling statement|hyperpage} +\index{{\tt \bfseries hypergeometric }!distribution statement|hyperpage} ### Stan functions @@ -419,7 +419,7 @@ Increment target log probability density with `categorical_lupmf(y | theta)` dropping constant additive terms. {{< since 2.0 >}} -\index{{\tt \bfseries categorical }!sampling statement|hyperpage} +\index{{\tt \bfseries categorical }!distribution statement|hyperpage} ### Distribution statement @@ -428,7 +428,7 @@ dropping constant additive terms. Increment target log probability density with `categorical_logit_lupmf(y | beta)`. {{< since 2.4 >}} -\index{{\tt \bfseries categorical\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries categorical\_logit }!distribution statement|hyperpage} ### Stan functions @@ -522,7 +522,7 @@ See [the definition of softmax](matrix_operations.qmd#softmax) for the definitio Increment target log probability density with `categorical_logit_glm_lupmf(y | x, alpha, beta)`. {{< since 2.23 >}} -\index{{\tt \bfseries categorical\_logit\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries categorical\_logit\_glm }!distribution statement|hyperpage} ### Stan functions @@ -612,7 +612,7 @@ Increment the target log probability density with `discrete_range_lupmf(y | l, u dropping constant additive terms. {{< since 2.26 >}} -\index{{\tt \bfseries discrete\_range }!sampling statement|hyperpage} +\index{{\tt \bfseries discrete\_range }!distribution statement|hyperpage} ### Stan functions @@ -695,7 +695,7 @@ $\text{logit}^{-1}(\infty) = 1$. Increment target log probability density with `ordered_logistic_lupmf(k | eta, c)`. {{< since 2.0 >}} -\index{{\tt \bfseries ordered\_logistic }!sampling statement|hyperpage} +\index{{\tt \bfseries ordered\_logistic }!distribution statement|hyperpage} ### Stan functions @@ -754,7 +754,7 @@ $\text{logit}^{-1}(\infty) = 1$. Increment target log probability density with `ordered_logistic_lupmf(y | x, beta, c)`. {{< since 2.23 >}} -\index{{\tt \bfseries ordered\_logistic\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries ordered\_logistic\_glm }!distribution statement|hyperpage} ### Stan functions @@ -851,7 +851,7 @@ $\Phi(\infty) = 1$. Increment target log probability density with `ordered_probit_lupmf(k | eta, c)`. {{< since 2.19 >}} -\index{{\tt \bfseries ordered\_probit }!sampling statement|hyperpage} +\index{{\tt \bfseries ordered\_probit }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/circular_distributions.qmd b/src/functions-reference/circular_distributions.qmd index 495358485..6658d16c5 100644 --- a/src/functions-reference/circular_distributions.qmd +++ b/src/functions-reference/circular_distributions.qmd @@ -43,7 +43,7 @@ of the values of $y$ or $\mu$). Increment target log probability density with `von_mises_lupdf(y | mu, kappa)`. {{< since 2.0 >}} -\index{{\tt \bfseries von\_mises }!sampling statement|hyperpage} +\index{{\tt \bfseries von\_mises }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/continuous_distributions_on_0_1.qmd b/src/functions-reference/continuous_distributions_on_0_1.qmd index 45575e474..c6934e19a 100644 --- a/src/functions-reference/continuous_distributions_on_0_1.qmd +++ b/src/functions-reference/continuous_distributions_on_0_1.qmd @@ -30,7 +30,7 @@ distribution requires strictly positive parameters, $\alpha, \beta > Increment target log probability density with `beta_lupdf(theta | alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries beta }!sampling statement|hyperpage} +\index{{\tt \bfseries beta }!distribution statement|hyperpage} ### Stan functions @@ -111,7 +111,7 @@ parameter, $\kappa > 0$. Increment target log probability density with `beta_proportion_lupdf(theta | mu, kappa)`. {{< since 2.19 >}} -\index{{\tt \bfseries beta\_proportion }!sampling statement|hyperpage} +\index{{\tt \bfseries beta\_proportion }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/conventions_for_probability_functions.qmd b/src/functions-reference/conventions_for_probability_functions.qmd index edc4034ff..daa33f4e1 100644 --- a/src/functions-reference/conventions_for_probability_functions.qmd +++ b/src/functions-reference/conventions_for_probability_functions.qmd @@ -224,7 +224,7 @@ is just a more efficient way to write } ``` -With the same arguments, the vectorized sampling statement +With the same arguments, the vectorized distribution statement ```stan y ~ normal(mu, sigma); diff --git a/src/functions-reference/correlation_matrix_distributions.qmd b/src/functions-reference/correlation_matrix_distributions.qmd index 3ecea54d5..75b0ac4a4 100644 --- a/src/functions-reference/correlation_matrix_distributions.qmd +++ b/src/functions-reference/correlation_matrix_distributions.qmd @@ -61,7 +61,7 @@ practice. Increment target log probability density with `lkj_corr_lupdf(y | eta)`. {{< since 2.3 >}} -\index{{\tt \bfseries lkj\_corr }!sampling statement|hyperpage} +\index{{\tt \bfseries lkj\_corr }!distribution statement|hyperpage} ### Stan functions @@ -139,7 +139,7 @@ unit Euclidean length. Increment target log probability density with `lkj_corr_cholesky_lupdf(L | eta)`. {{< since 2.4 >}} -\index{{\tt \bfseries lkj\_corr\_cholesky }!sampling statement|hyperpage} +\index{{\tt \bfseries lkj\_corr\_cholesky }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/covariance_matrix_distributions.qmd b/src/functions-reference/covariance_matrix_distributions.qmd index 787daebbb..10dad60dc 100644 --- a/src/functions-reference/covariance_matrix_distributions.qmd +++ b/src/functions-reference/covariance_matrix_distributions.qmd @@ -36,7 +36,7 @@ Gamma function, Increment target log probability density with `wishart_lupdf(W | nu, Sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries wishart }!sampling statement|hyperpage} +\index{{\tt \bfseries wishart }!distribution statement|hyperpage} ### Stan functions @@ -150,7 +150,7 @@ for symmetric and positive-definite $W \in \mathbb{R}^{K \times K}$, Increment target log probability density with `inv_wishart_lupdf(W | nu, Sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries inv\_wishart }!sampling statement|hyperpage} +\index{{\tt \bfseries inv\_wishart }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/distributions_over_unbounded_vectors.qmd b/src/functions-reference/distributions_over_unbounded_vectors.qmd index 730f7bc9a..1f696197b 100644 --- a/src/functions-reference/distributions_over_unbounded_vectors.qmd +++ b/src/functions-reference/distributions_over_unbounded_vectors.qmd @@ -31,7 +31,7 @@ where $|\Sigma|$ is the absolute determinant of $\Sigma$. Increment target log probability density with `multi_normal_lupdf(y | mu, Sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries multi\_normal }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_normal }!distribution statement|hyperpage} ### Stan functions @@ -165,7 +165,7 @@ for $y \in \mathbb{R}^K$, \begin{equation*} \text{MultiNormalPrecision}(y|\mu,\O Increment target log probability density with `multi_normal_prec_lupdf(y | mu, Omega)`. {{< since 2.3 >}} -\index{{\tt \bfseries multi\_normal\_prec }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_normal\_prec }!distribution statement|hyperpage} ### Stan functions @@ -258,7 +258,7 @@ probability functions will raise errors. Increment target log probability density with `multi_normal_cholesky_lupdf(y | mu, L)`. {{< since 2.0 >}} -\index{{\tt \bfseries multi\_normal\_cholesky }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_normal\_cholesky }!distribution statement|hyperpage} ### Stan functions @@ -391,7 +391,7 @@ function does not take into account the mean prediction. Increment target log probability density with `multi_gp_lupdf(y | Sigma, w)`. {{< since 2.3 >}} -\index{{\tt \bfseries multi\_gp }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_gp }!distribution statement|hyperpage} ### Stan functions @@ -436,7 +436,7 @@ account the mean prediction. Increment target log probability density with `multi_gp_cholesky_lupdf(y | L, w)`. {{< since 2.5 >}} -\index{{\tt \bfseries multi\_gp\_cholesky }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_gp\_cholesky }!distribution statement|hyperpage} ### Stan functions @@ -479,7 +479,7 @@ K)/2\right)} {\Gamma(\nu/2)} \ \frac{1}{\sqrt{\left| \Sigma Increment target log probability density with `multi_student_t_lupdf(y | nu, mu, Sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries multi\_student\_t }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_student\_t }!distribution statement|hyperpage} ### Stan functions @@ -615,7 +615,7 @@ L^{-T}L^{-1} \, \left(y - \mu\right) \right)^{-(\nu + K)/2} \! . Increment target log probability density with `multi_student_t_cholesky_lupdf(y | nu, mu, L)`. {{< since 2.30 >}} -\index{{\tt \bfseries multi\_student\_t\_cholesky }!sampling statement|hyperpage} +\index{{\tt \bfseries multi\_student\_t\_cholesky }!distribution statement|hyperpage} ### Stan functions @@ -696,14 +696,14 @@ processes observations and avoids a matrix inversions can be used Increment target log probability density with `gaussian_dlm_obs_lupdf(y | F, G, V, W, m0, C0)`. {{< since 2.0 >}} -\index{{\tt \bfseries gaussian\_dlm\_obs }!sampling statement|hyperpage} +\index{{\tt \bfseries gaussian\_dlm\_obs }!distribution statement|hyperpage} ### Stan functions The following two functions differ in the type of their V, the first taking a full observation covariance matrix V\ and the second a vector V\ representing the diagonal of the observation covariance matrix. -The sampling statement defined in the previous section works with +The distribution statement defined in the previous section works with either type of observation V. diff --git a/src/functions-reference/embedded_laplace.qmd b/src/functions-reference/embedded_laplace.qmd index 75a9e1b7d..5ae411062 100644 --- a/src/functions-reference/embedded_laplace.qmd +++ b/src/functions-reference/embedded_laplace.qmd @@ -366,7 +366,7 @@ group the $i^\text{th}$ observation belongs to. * `m`: a vector of offsets or prior means for $\theta$. -\index{{\tt \bfseries laplace\_marginal\_poisson\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_poisson\_log }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_poisson_log`**`(y_index, m, hessian_block_size, covariance_function, covariance_arguments)`
\newline @@ -374,7 +374,7 @@ Increment target log probability density with `laplace_marginal_poisson_log_lupm {{< since 2.39 >}} -\index{{\tt \bfseries laplace\_marginal\_tol\_poisson\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_tol\_poisson\_log }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_tol_poisson_log`**`(y_index, m, hessian_block_size, covariance_function, covariance_arguments, tolerances)`
\newline @@ -464,7 +464,7 @@ group the $i^\text{th}$ observation belongs to. * `m`: a vector of offsets or prior means for $\theta$. -\index{{\tt \bfseries laplace\_marginal\_neg\_binomial\_2\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_neg\_binomial\_2\_log }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_neg_binomial_2_log`**`(y_index, eta, m, hessian_block_size, covariance_function, covariance_arguments)`
\newline @@ -472,7 +472,7 @@ Increment target log probability density with `laplace_marginal_neg_binomial_2_l {{< since 2.39 >}} -\index{{\tt \bfseries laplace\_marginal\_tol\_neg\_binomial\_2\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_tol\_neg\_binomial\_2\_log }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_tol_neg_binomial_2_log`**`(y_index, eta, m, hessian_block_size, covariance_function, covariance_arguments, tolerances)`
\newline @@ -560,7 +560,7 @@ group the $i^\text{th}$ observation belongs to. * `m`: a vector of offsets or prior means for $\theta$. -\index{{\tt \bfseries laplace\_marginal\_bernoulli\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_bernoulli\_logit }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_bernoulli_logit`**`(y_index, m, hessian_block_size, covariance_function, covariance_arguments)`
\newline @@ -568,7 +568,7 @@ Increment target log probability density with `laplace_marginal_bernoulli_logit_ {{< since 2.39 >}} -\index{{\tt \bfseries laplace\_marginal\_tol\_bernoulli\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries laplace\_marginal\_tol\_bernoulli\_logit }!distribution statement|hyperpage} `y ~ ` **`laplace_marginal_tol_bernoulli_logit`**`(y_index, m, hessian_block_size, covariance_function, covariance_arguments, tolerances)`
\newline diff --git a/src/functions-reference/multivariate_discrete_distributions.qmd b/src/functions-reference/multivariate_discrete_distributions.qmd index 8a993feac..b49353363 100644 --- a/src/functions-reference/multivariate_discrete_distributions.qmd +++ b/src/functions-reference/multivariate_discrete_distributions.qmd @@ -31,7 +31,7 @@ where the multinomial coefficient is defined by Increment target log probability density with `multinomial_lupmf(y | theta)`. {{< since 2.0 >}} -\index{{\tt \bfseries multinomial }!sampling statement|hyperpage} +\index{{\tt \bfseries multinomial }!distribution statement|hyperpage} ### Stan functions @@ -92,7 +92,7 @@ where the multinomial coefficient is defined by Increment target log probability density with `multinomial_logit_lupmf(y | gamma)`. {{< since 2.24 >}} -\index{{\tt \bfseries multinomial\_logit }!sampling statement|hyperpage} +\index{{\tt \bfseries multinomial\_logit }!distribution statement|hyperpage} ### Stan functions @@ -148,7 +148,7 @@ where $\alpha_0$ is defined as $\alpha_0 = \sum_{k=1}^K \alpha_k$. Increment target log probability density with `dirichlet_multinomial_lupmf(y | alpha)`. {{< since 2.34 >}} -\index{{\tt \bfseries dirichlet\_multinomial }!sampling statement|hyperpage} +\index{{\tt \bfseries dirichlet\_multinomial }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/positive_continuous_distributions.qmd b/src/functions-reference/positive_continuous_distributions.qmd index 5f3761809..379944204 100644 --- a/src/functions-reference/positive_continuous_distributions.qmd +++ b/src/functions-reference/positive_continuous_distributions.qmd @@ -26,7 +26,7 @@ If $\mu \in \mathbb{R}$ and $\sigma \in \mathbb{R}^+$, then for $y \in Increment target log probability density with `lognormal_lupdf(y | mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries lognormal }!sampling statement|hyperpage} +\index{{\tt \bfseries lognormal }!distribution statement|hyperpage} ### Stan functions @@ -95,7 +95,7 @@ y^{\nu/2 - 1} \, \exp \! \left( -\, \frac{1}{2} \, y \right) . \end{equation*} Increment target log probability density with `chi_square_lupdf(y | nu)`. {{< since 2.0 >}} -\index{{\tt \bfseries chi\_square }!sampling statement|hyperpage} +\index{{\tt \bfseries chi\_square }!distribution statement|hyperpage} ### Stan functions @@ -164,7 +164,7 @@ If $\nu \in \mathbb{R}^+$, then for $y \in \mathbb{R}^+$, \begin{equation*} Increment target log probability density with `inv_chi_square_lupdf(y | nu)`. {{< since 2.0 >}} -\index{{\tt \bfseries inv\_chi\_square }!sampling statement|hyperpage} +\index{{\tt \bfseries inv\_chi\_square }!distribution statement|hyperpage} ### Stan functions @@ -235,7 +235,7 @@ y^{-(\nu/2 + 1)} \, \exp \! \left( \! - \, \frac{1}{2} \, \nu \, Increment target log probability density with `scaled_inv_chi_square_lupdf(y | nu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries scaled\_inv\_chi\_square }!sampling statement|hyperpage} +\index{{\tt \bfseries scaled\_inv\_chi\_square }!distribution statement|hyperpage} ### Stan functions @@ -303,7 +303,7 @@ If inverse scale (rate) $\beta \in \mathbb{R}^+$, then for $y \in \mathbb{R}^+$, Increment target log probability density with `exponential_lupdf(y | beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries exponential }!sampling statement|hyperpage} +\index{{\tt \bfseries exponential }!distribution statement|hyperpage} ### Stan functions @@ -374,7 +374,7 @@ Under the shape and rate formulation of the Gamma distribution, $\mathbb{E}[y] = Increment target log probability density with `gamma_lupdf(y | alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries gamma }!sampling statement|hyperpage} +\index{{\tt \bfseries gamma }!distribution statement|hyperpage} ### Stan functions @@ -444,7 +444,7 @@ If $\alpha \in \mathbb{R}^+$ and $\beta \in \mathbb{R}^+$, then for $y Increment target log probability density with `inv_gamma_lupdf(y | alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries inv\_gamma }!sampling statement|hyperpage} +\index{{\tt \bfseries inv\_gamma }!distribution statement|hyperpage} ### Stan functions @@ -518,7 +518,7 @@ Note that if $Y \propto \text{Weibull}(\alpha,\sigma)$, then $Y^{-1} Increment target log probability density with `weibull_lupdf(y | alpha, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries weibull }!sampling statement|hyperpage} +\index{{\tt \bfseries weibull }!distribution statement|hyperpage} ### Stan functions @@ -591,7 +591,7 @@ Note that if $Y \propto \text{Frechet}(\alpha,\sigma)$, then $Y^{-1} Increment target log probability density with `frechet_lupdf(y | alpha, sigma)`. {{< since 2.5 >}} -\index{{\tt \bfseries frechet }!sampling statement|hyperpage} +\index{{\tt \bfseries frechet }!distribution statement|hyperpage} ### Stan functions @@ -659,7 +659,7 @@ If $\sigma \in \mathbb{R}^+$, then for $y \in [0,\infty)$, \begin{equation*} Increment target log probability density with `rayleigh_lupdf(y | sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries rayleigh }!sampling statement|hyperpage} +\index{{\tt \bfseries rayleigh }!distribution statement|hyperpage} ### Stan functions @@ -729,7 +729,7 @@ version of `loglogistic_lpdf(y | alpha, beta)` {{< since 2.29 >}} -\index{{\tt \bfseries loglogistic }!sampling statement|hyperpage} +\index{{\tt \bfseries loglogistic }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/positive_lower-bounded_distributions.qmd b/src/functions-reference/positive_lower-bounded_distributions.qmd index 9919e8245..8cf54af18 100644 --- a/src/functions-reference/positive_lower-bounded_distributions.qmd +++ b/src/functions-reference/positive_lower-bounded_distributions.qmd @@ -26,7 +26,7 @@ then for $y \in \mathbb{R}^+$ with $y \geq y_{\text{min}}$, Increment target log probability density with `pareto_lupdf(y | y_min, alpha)`. {{< since 2.0 >}} -\index{{\tt \bfseries pareto }!sampling statement|hyperpage} +\index{{\tt \bfseries pareto }!distribution statement|hyperpage} ### Stan functions @@ -101,7 +101,7 @@ $\mu=0$. Increment target log probability density with `pareto_type_2_lupdf(y | mu, lambda, alpha)`. {{< since 2.5 >}} -\index{{\tt \bfseries pareto\_type\_2 }!sampling statement|hyperpage} +\index{{\tt \bfseries pareto\_type\_2 }!distribution statement|hyperpage} ### Stan functions @@ -284,7 +284,7 @@ Increment target log probability density with `wiener_lupdf(y | alpha, tau, beta {{< since 2.35 >}} -\index{{\tt \bfseries wiener }!sampling statement|hyperpage} +\index{{\tt \bfseries wiener }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/real-valued_basic_functions.qmd b/src/functions-reference/real-valued_basic_functions.qmd index 2ce19f6cc..e574d7c2e 100644 --- a/src/functions-reference/real-valued_basic_functions.qmd +++ b/src/functions-reference/real-valued_basic_functions.qmd @@ -359,7 +359,7 @@ probability accumulator starts at zero and is then incremented in various ways by a Stan program. The variables are first transformed from unconstrained to constrained, and the log Jacobian determinant added to the log probability accumulator. Then the model block is -executed on the constrained parameters, with each sampling statement +executed on the constrained parameters, with each distribution statement (`~`) and log probability increment statement (`increment_log_prob`) adding to the accumulator. At the end of the model block execution, the value of the log probability accumulator is the log probability diff --git a/src/functions-reference/simplex_distributions.qmd b/src/functions-reference/simplex_distributions.qmd index 1d484c050..ee1546e52 100644 --- a/src/functions-reference/simplex_distributions.qmd +++ b/src/functions-reference/simplex_distributions.qmd @@ -98,7 +98,7 @@ $\alpha = 1000$, Increment target log probability density with `dirichlet_lupdf(theta | alpha)`. {{< since 2.0 >}} -\index{{\tt \bfseries dirichlet }!sampling statement|hyperpage} +\index{{\tt \bfseries dirichlet }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/unbounded_continuous_distributions.qmd b/src/functions-reference/unbounded_continuous_distributions.qmd index d88ad45cd..41cae61a3 100644 --- a/src/functions-reference/unbounded_continuous_distributions.qmd +++ b/src/functions-reference/unbounded_continuous_distributions.qmd @@ -28,7 +28,7 @@ If $\mu \in \mathbb{R}$ and $\sigma \in \mathbb{R}^+$, then for $y \in Increment target log probability density with `normal_lupdf(y | mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries normal }!sampling statement|hyperpage} +\index{{\tt \bfseries normal }!distribution statement|hyperpage} ### Stan functions @@ -117,7 +117,7 @@ normal log density with constant location $0$ and scale $1$. Increment target log probability density with `std_normal_lupdf(y)`. {{< since 2.19 >}} -\index{{\tt \bfseries std\_normal }!sampling statement|hyperpage} +\index{{\tt \bfseries std\_normal }!distribution statement|hyperpage} ### Stan functions @@ -214,7 +214,7 @@ If $x\in \mathbb{R}^{n\cdot m}, \alpha \in \mathbb{R}^n, \beta\in Increment target log probability density with `normal_id_glm_lupdf(y | x, alpha, beta, sigma)`. {{< since 2.19 >}} -\index{{\tt \bfseries normal\_id\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries normal\_id\_glm }!distribution statement|hyperpage} ### Stan functions @@ -398,7 +398,7 @@ y}{\sqrt{2}\sigma}\right) . \end{equation*} Increment target log probability density with `exp_mod_normal_lupdf(y | mu, sigma, lambda)`. {{< since 2.0 >}} -\index{{\tt \bfseries exp\_mod\_normal }!sampling statement|hyperpage} +\index{{\tt \bfseries exp\_mod\_normal }!distribution statement|hyperpage} ### Stan functions @@ -471,7 +471,7 @@ If $\xi \in \mathbb{R}$, $\omega \in \mathbb{R}^+$, and $\alpha \in Increment target log probability density with `skew_normal_lupdf(y | xi, omega, alpha)`. {{< since 2.0 >}} -\index{{\tt \bfseries skew\_normal }!sampling statement|hyperpage} +\index{{\tt \bfseries skew\_normal }!distribution statement|hyperpage} ### Stan functions @@ -543,7 +543,7 @@ If $\nu \in \mathbb{R}^+$, $\mu \in \mathbb{R}$, and $\sigma \in Increment target log probability density with `student_t_lupdf(y | nu, mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries student\_t }!sampling statement|hyperpage} +\index{{\tt \bfseries student\_t }!distribution statement|hyperpage} ### Stan functions @@ -614,7 +614,7 @@ If $\mu \in \mathbb{R}$ and $\sigma \in \mathbb{R}^+$, then for $y \in \mathbb{R Increment target log probability density with `cauchy_lupdf(y | mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries cauchy }!sampling statement|hyperpage} +\index{{\tt \bfseries cauchy }!distribution statement|hyperpage} ### Stan functions @@ -698,7 +698,7 @@ a non-centered parameterization by taking \begin{equation*} \beta^{\text{raw}} \ Increment target log probability density with `double_exponential_lupdf(y | mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries double\_exponential }!sampling statement|hyperpage} +\index{{\tt \bfseries double\_exponential }!distribution statement|hyperpage} ### Stan functions @@ -769,7 +769,7 @@ If $\mu \in \mathbb{R}$ and $\sigma \in \mathbb{R}^+$, then for $y \in \mathbb{R Increment target log probability density with `logistic_lupdf(y | mu, sigma)`. {{< since 2.0 >}} -\index{{\tt \bfseries logistic }!sampling statement|hyperpage} +\index{{\tt \bfseries logistic }!distribution statement|hyperpage} ### Stan functions @@ -838,7 +838,7 @@ If $\mu \in \mathbb{R}$ and $\beta \in \mathbb{R}^+$, then for $y \in \mathbb{R} Increment target log probability density with `gumbel_lupdf(y | mu, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries gumbel }!sampling statement|hyperpage} +\index{{\tt \bfseries gumbel }!distribution statement|hyperpage} ### Stan functions @@ -910,7 +910,7 @@ $$\begin{aligned} Increment target log probability density with `skew_double_exponential(y | mu, sigma, tau)` {{< since 2.28 >}} -\index{{\tt \bfseries skew\_double\_exponential }!sampling statement|hyperpage} +\index{{\tt \bfseries skew\_double\_exponential }!distribution statement|hyperpage} ### Stan functions diff --git a/src/functions-reference/unbounded_discrete_distributions.qmd b/src/functions-reference/unbounded_discrete_distributions.qmd index 1f6329ca4..0864d4db2 100644 --- a/src/functions-reference/unbounded_discrete_distributions.qmd +++ b/src/functions-reference/unbounded_discrete_distributions.qmd @@ -34,7 +34,7 @@ The mean and variance of a random variable $n \sim Increment target log probability density with `neg_binomial_lupmf(n | alpha, beta)`. {{< since 2.0 >}} -\index{{\tt \bfseries neg\_binomial }!sampling statement|hyperpage} +\index{{\tt \bfseries neg\_binomial }!distribution statement|hyperpage} ### Stan functions @@ -122,7 +122,7 @@ the overdispersion, scaled by the square of the mean, $\mu^2$. Increment target log probability density with `neg_binomial_2_lupmf(n | mu, phi)`. {{< since 2.3 >}} -\index{{\tt \bfseries neg\_binomial\_2 }!sampling statement|hyperpage} +\index{{\tt \bfseries neg\_binomial\_2 }!distribution statement|hyperpage} ### Stan functions @@ -194,7 +194,7 @@ for log-linear negative binomial regressions. Increment target log probability density with `neg_binomial_2_log_lupmf(n | eta, phi)`. {{< since 2.3 >}} -\index{{\tt \bfseries neg\_binomial\_2\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries neg\_binomial\_2\_log }!distribution statement|hyperpage} ### Stan functions @@ -248,7 +248,7 @@ If $x\in \mathbb{R}^{n\cdot m}, \alpha \in \mathbb{R}^n, \beta\in Increment target log probability density with `neg_binomial_2_log_glm_lupmf(y | x, alpha, beta, phi)`. {{< since 2.19 >}} -\index{{\tt \bfseries neg\_binomial\_2\_log\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries neg\_binomial\_2\_log\_glm }!distribution statement|hyperpage} ### Stan functions @@ -369,7 +369,7 @@ If $\lambda \in \mathbb{R}^+$, then for $n \in \mathbb{N}$, \begin{equation*} Increment target log probability density with `poisson_lupmf(n | lambda)`. {{< since 2.0 >}} -\index{{\tt \bfseries poisson }!sampling statement|hyperpage} +\index{{\tt \bfseries poisson }!distribution statement|hyperpage} ### Stan functions @@ -442,7 +442,7 @@ If $\alpha \in \mathbb{R}$, then for $n \in \mathbb{N}$, \begin{equation*} Increment target log probability density with `poisson_log_lupmf(n | alpha)`. {{< since 2.0 >}} -\index{{\tt \bfseries poisson\_log }!sampling statement|hyperpage} +\index{{\tt \bfseries poisson\_log }!distribution statement|hyperpage} ### Stan functions @@ -493,7 +493,7 @@ n}\text{Poisson}(y_i|\exp(\alpha_i + x_i\cdot \beta)). \end{equation*} Increment target log probability density with `poisson_log_glm_lupmf(y | x, alpha, beta)`. {{< since 2.19 >}} -\index{{\tt \bfseries poisson\_log\_glm }!sampling statement|hyperpage} +\index{{\tt \bfseries poisson\_log\_glm }!distribution statement|hyperpage} ### Stan functions @@ -602,7 +602,7 @@ If $r \in \mathbb{R}^+$, $\alpha \in \mathbb{R}^+$, and $\beta \in \mathbb{R}^+$ Increment target log probability density with `beta_neg_binomial_lupmf(n | r, alpha, beta)`. {{< since 2.36 >}} -\index{{\tt \bfseries beta\_neg\_binomial }!sampling statement|hyperpage} +\index{{\tt \bfseries beta\_neg\_binomial }!distribution statement|hyperpage} ### Stan functions @@ -666,7 +666,7 @@ If $\alpha \in \mathbb{R}^+$, then for $n \in \mathbb{N}^+=\{1,2,...\}$, \begin{ Increment target log probability density with `yule_simon_lupmf(n | alpha)`. {{< since 2.39 >}} -\index{{\tt \bfseries yule\_simon }!sampling statement|hyperpage} +\index{{\tt \bfseries yule\_simon }!distribution statement|hyperpage} ### Stan functions diff --git a/src/reference-manual/statements.qmd b/src/reference-manual/statements.qmd index 2779d637a..2eb7d2c8f 100644 --- a/src/reference-manual/statements.qmd +++ b/src/reference-manual/statements.qmd @@ -404,11 +404,6 @@ model { To access the accumulated log density up to the current execution point, the function `target()` may be used. -## Sampling statements {#sampling-statements.section} - -The term "sampling statement" has been replaced with -[distribution statement](#distribution-statements.section). - ## Distribution statements {#distribution-statements.section} Stan supports writing probability statements also using distribution diff --git a/src/reference-manual/syntax.qmd b/src/reference-manual/syntax.qmd index cbf626249..e5e0e356c 100644 --- a/src/reference-manual/syntax.qmd +++ b/src/reference-manual/syntax.qmd @@ -479,7 +479,7 @@ User defined functions which end in `_lp` and the `target()` function can only be used in the `model` block, `transformed parameters` block, and in the bodies of other user defined functions which end in `_lp`. -Sampling statements (using `~`) can only be used in the `model` block or in the +Distribution statements (using `~`) can only be used in the `model` block or in the bodies of user-defined functions which end in `_lp`. `jacobian +=` statements can only be used inside of the `transformed parameters` block diff --git a/src/stan-users-guide/efficiency-tuning.qmd b/src/stan-users-guide/efficiency-tuning.qmd index 97c4ecfb5..f7b440c80 100644 --- a/src/stan-users-guide/efficiency-tuning.qmd +++ b/src/stan-users-guide/efficiency-tuning.qmd @@ -1158,7 +1158,7 @@ vectorization, but can be put into such shape with some munging (either inside Stan's transformed data block or outside). John Hall provided a simple example on the Stan users group. -Simplifying notation a bit, the original model had a sampling +Simplifying notation a bit, the original model had a distribution statement in a loop, as follows. ```stan diff --git a/src/stan-users-guide/reparameterization.qmd b/src/stan-users-guide/reparameterization.qmd index 64060286f..37a2222ba 100644 --- a/src/stan-users-guide/reparameterization.qmd +++ b/src/stan-users-guide/reparameterization.qmd @@ -348,7 +348,7 @@ $$ \log \textsf{normal}(\log y \mid \mu, \sigma) - \log y. $$ -In Stan, the change of variables can be applied in the sampling +In Stan, the change of variables can be applied in the distribution statement. To adjust for the curvature, the log probability accumulator is incremented with the log absolute derivative of the transform. The lognormal distribution can thus be implemented diff --git a/src/stan-users-guide/simulation-based-calibration.qmd b/src/stan-users-guide/simulation-based-calibration.qmd index fc28b74c8..963dadc58 100644 --- a/src/stan-users-guide/simulation-based-calibration.qmd +++ b/src/stan-users-guide/simulation-based-calibration.qmd @@ -513,7 +513,7 @@ encodes the data-generating process using random number generators. Here, the population parameters $\mu$ and $\tau$ are first simulated, then the school-level effects $\theta$, and then finally the observed data $\sigma_j$ and $y_j.$ The parameters and model are a direct -encoding of the mathematical presentation using vectorized sampling +encoding of the mathematical presentation using vectorized distribution statements. The generated quantities block includes indicators for parameter comparisons, saving only $\theta_1$ because the schools are exchangeable in the simulation. diff --git a/src/stan-users-guide/user-functions.qmd b/src/stan-users-guide/user-functions.qmd index 93b273bc7..423960f5c 100644 --- a/src/stan-users-guide/user-functions.qmd +++ b/src/stan-users-guide/user-functions.qmd @@ -252,7 +252,7 @@ transformed parameters { ## Functions accessing the log probability accumulator -Functions whose names end in `_lp` are allowed to use sampling +Functions whose names end in `_lp` are allowed to use distribution statements and `target +=` statements; other functions are not. Because of this access, their use is restricted to the transformed parameters and model blocks.