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Update Stan syntax to version 2.33 #3859

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merged 2 commits into from Sep 12, 2023
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Update Stan syntax to version 2.33 #3859

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6322ca4
Update Stan syntax to version 2.33
WardBrian Sep 11, 2023
8994b79
Update CHANGES.md
WardBrian Sep 11, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -40,6 +40,7 @@ Core Grammars:
- fix(reasonml) simplify syntax and align it with ocaml [jchavarri][]
- fix(swift) `warn_unqualified_access` is an attribute [Bradley Mackey][]
- enh(swift) macro attributes are highlighted as keywords [Bradley Mackey][]
- enh(stan) updated for version 2.33 (#3859) [Brian Ward][]

Dev tool:

Expand All @@ -62,6 +63,7 @@ Dev tool:
[aana-h2]: https://github.com/aana-h2
[Nicholas Thompson]: https://github.com/NAThompson
[Yasith Deelaka]: https://github.com/YasithD
[Brian Ward]: https://github.com/WardBrian


## Version 11.8.0
Expand Down
58 changes: 43 additions & 15 deletions src/languages/stan.js
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Expand Up @@ -32,16 +32,20 @@ export default function(hljs) {

const TYPES = [
'array',
'tuple',
'complex',
'int',
'real',
'vector',
'complex_vector',
'ordered',
'positive_ordered',
'simplex',
'unit_vector',
'row_vector',
'complex_row_vector',
'matrix',
'complex_matrix',
'cholesky_factor_corr|10',
'cholesky_factor_cov|10',
'corr_matrix|10',
Expand All @@ -58,8 +62,6 @@ export default function(hljs) {
// functions_quoted.txt

const FUNCTIONS = [
'Phi',
'Phi_approx',
'abs',
'acos',
'acosh',
Expand All @@ -77,7 +79,6 @@ export default function(hljs) {
'bessel_first_kind',
'bessel_second_kind',
'binary_log_loss',
'binomial_coefficient_log',
'block',
'cbrt',
'ceil',
Expand All @@ -88,37 +89,48 @@ export default function(hljs) {
'cols',
'columns_dot_product',
'columns_dot_self',
'complex_schur_decompose',
'complex_schur_decompose_t',
'complex_schur_decompose_u',
'conj',
'cos',
'cosh',
'cov_exp_quad',
'crossprod',
'csr_extract',
'csr_extract_u',
'csr_extract_v',
'csr_extract_w',
'csr_matrix_times_vector',
'csr_to_dense_matrix',
'cumulative_sum',
'dae',
'dae_tol',
'determinant',
'diag_matrix',
'diagonal',
'diag_post_multiply',
'diag_pre_multiply',
'diagonal',
'digamma',
'dims',
'distance',
'dot_product',
'dot_self',
'eigendecompose',
'eigendecompose_sym',
'eigenvalues',
'eigenvalues_sym',
'eigenvectors',
'eigenvectors_sym',
'erf',
'erfc',
'exp',
'exp2',
'expm1',
'fabs',
'falling_factorial',
'fdim',
'fft',
'fft2',
'floor',
'fma',
'fmax',
Expand All @@ -128,28 +140,31 @@ export default function(hljs) {
'gamma_q',
'generalized_inverse',
'get_imag',
'get_lp',
'get_real',
'head',
'hmm_hidden_state_prob',
'hmm_marginal',
'hypot',
'identity_matrix',
'inc_beta',
'int_step',
'integrate_1d',
'integrate_ode',
'integrate_ode_adams',
'integrate_ode_bdf',
'integrate_ode_rk45',
'int_step',
'inv',
'inv_Phi',
'inv_cloglog',
'inv_erfc',
'inverse',
'inverse_spd',
'inv_fft',
'inv_fft2',
'inv_inc_beta',
'inv_logit',
'inv_Phi',
'inv_sqrt',
'inv_square',
'inverse',
'inverse_spd',
'is_inf',
'is_nan',
'lambert_w0',
Expand All @@ -175,12 +190,12 @@ export default function(hljs) {
'log_falling_factorial',
'log_inv_logit',
'log_inv_logit_diff',
'logit',
'log_mix',
'log_modified_bessel_first_kind',
'log_rising_factorial',
'log_softmax',
'log_sum_exp',
'logit',
'machine_precision',
'map_rect',
'matrix_exp',
Expand All @@ -195,10 +210,11 @@ export default function(hljs) {
'min',
'modified_bessel_first_kind',
'modified_bessel_second_kind',
'multiply_log',
'multiply_lower_tri_self_transpose',
'negative_infinity',
'norm',
'norm1',
'norm2',
'not_a_number',
'num_elements',
'ode_adams',
Expand All @@ -219,14 +235,18 @@ export default function(hljs) {
'ones_row_vector',
'ones_vector',
'owens_t',
'Phi',
'Phi_approx',
'polar',
'positive_infinity',
'pow',
'print',
'prod',
'proj',
'qr',
'qr_Q',
'qr_R',
'qr_thin',
'qr_thin_Q',
'qr_thin_R',
'quad_form',
Expand Down Expand Up @@ -266,6 +286,7 @@ export default function(hljs) {
'sub_col',
'sub_row',
'sum',
'svd',
'svd_U',
'svd_V',
'symmetrize_from_lower_tri',
Expand All @@ -278,6 +299,7 @@ export default function(hljs) {
'to_array_1d',
'to_array_2d',
'to_complex',
'to_int',
'to_matrix',
'to_row_vector',
'to_vector',
Expand Down Expand Up @@ -321,18 +343,22 @@ export default function(hljs) {
'inv_chi_square',
'inv_gamma',
'inv_wishart',
'inv_wishart_cholesky',
'lkj_corr',
'lkj_corr_cholesky',
'logistic',
'loglogistic',
'lognormal',
'multi_gp',
'multi_gp_cholesky',
'multinomial',
'multinomial_logit',
'multi_normal',
'multi_normal_cholesky',
'multi_normal_prec',
'multi_student_cholesky_t',
'multi_student_t',
'multinomial',
'multinomial_logit',
'multi_student_t_cholesky',
'neg_binomial',
'neg_binomial_2',
'neg_binomial_2_log',
Expand All @@ -352,12 +378,14 @@ export default function(hljs) {
'skew_double_exponential',
'skew_normal',
'std_normal',
'std_normal_log',
'student_t',
'uniform',
'von_mises',
'weibull',
'wiener',
'wishart'
'wishart',
'wishart_cholesky'
];

const BLOCK_COMMENT = hljs.COMMENT(
Expand Down
6 changes: 4 additions & 2 deletions test/detect/stan/default.txt
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Expand Up @@ -5,6 +5,7 @@ data {
int<lower=0> N;
int K;
matrix[N, K] x;
complex_row_vector[K] z;
}
transformed data {
complex zi = 1+3.14i;
Expand All @@ -16,13 +17,14 @@ parameters {
array[K - 1] real mu;
array[K + 1] real<lower=0> sigma;
cholesky_factor_corr[K] L;
tuple(real, tuple(real, real)) t;
}
model {
target += normal_lpdf(x[ : , 1] | mu[1], sigma[1]);
target += gumbel_lpdf(x[ : , 2] | mu[2], sigma[2]);
target += lognormal_lpdf(x[ : , 3] | mu[3], sigma[3]);
target += weibull_lpdf(x[ : , 4] | sigma[4], sigma[5]);

{
matrix[K, N] y;
for (n in 1 : N) {
Expand All @@ -37,4 +39,4 @@ model {
}
generated quantities {
matrix[K, K] Sigma = multiply_lower_tri_self_transpose(L);
}
}
6 changes: 4 additions & 2 deletions test/markup/stan/default.expect.txt
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Expand Up @@ -5,6 +5,7 @@
<span class="hljs-type">int</span>&lt;<span class="hljs-keyword">lower</span>=<span class="hljs-number">0</span>&gt; N;
<span class="hljs-type">int</span> K;
<span class="hljs-type">matrix</span>[N, K] x;
<span class="hljs-type">complex_row_vector</span>[K] z;
}
<span class="hljs-title">transformed</span> <span class="hljs-title">data</span> {
<span class="hljs-type">complex</span> zi = <span class="hljs-number">1</span>+<span class="hljs-number">3.14i</span>;
Expand All @@ -16,13 +17,14 @@
<span class="hljs-type">array</span>[K - <span class="hljs-number">1</span>] <span class="hljs-type">real</span> mu;
<span class="hljs-type">array</span>[K + <span class="hljs-number">1</span>] <span class="hljs-type">real</span>&lt;<span class="hljs-keyword">lower</span>=<span class="hljs-number">0</span>&gt; sigma;
<span class="hljs-type">cholesky_factor_corr</span>[K] L;
<span class="hljs-type">tuple</span>(<span class="hljs-type">real</span>, <span class="hljs-type">tuple</span>(<span class="hljs-type">real</span>, <span class="hljs-type">real</span>)) t;
}
<span class="hljs-title">model</span> {
<span class="hljs-keyword">target</span> += <span class="hljs-built_in">normal_lpdf</span>(x[ : , <span class="hljs-number">1</span>] | mu[<span class="hljs-number">1</span>], sigma[<span class="hljs-number">1</span>]);
<span class="hljs-keyword">target</span> += <span class="hljs-built_in">gumbel_lpdf</span>(x[ : , <span class="hljs-number">2</span>] | mu[<span class="hljs-number">2</span>], sigma[<span class="hljs-number">2</span>]);
<span class="hljs-keyword">target</span> += <span class="hljs-built_in">lognormal_lpdf</span>(x[ : , <span class="hljs-number">3</span>] | mu[<span class="hljs-number">3</span>], sigma[<span class="hljs-number">3</span>]);
<span class="hljs-keyword">target</span> += <span class="hljs-built_in">weibull_lpdf</span>(x[ : , <span class="hljs-number">4</span>] | sigma[<span class="hljs-number">4</span>], sigma[<span class="hljs-number">5</span>]);

{
<span class="hljs-type">matrix</span>[K, N] y;
<span class="hljs-keyword">for</span> (n <span class="hljs-keyword">in</span> <span class="hljs-number">1</span> : N) {
Expand All @@ -37,4 +39,4 @@
}
<span class="hljs-title">generated</span> <span class="hljs-title">quantities</span> {
<span class="hljs-type">matrix</span>[K, K] Sigma = <span class="hljs-built_in">multiply_lower_tri_self_transpose</span>(L);
}
}
6 changes: 4 additions & 2 deletions test/markup/stan/default.txt
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Expand Up @@ -5,6 +5,7 @@ data {
int<lower=0> N;
int K;
matrix[N, K] x;
complex_row_vector[K] z;
}
transformed data {
complex zi = 1+3.14i;
Expand All @@ -16,13 +17,14 @@ parameters {
array[K - 1] real mu;
array[K + 1] real<lower=0> sigma;
cholesky_factor_corr[K] L;
tuple(real, tuple(real, real)) t;
}
model {
target += normal_lpdf(x[ : , 1] | mu[1], sigma[1]);
target += gumbel_lpdf(x[ : , 2] | mu[2], sigma[2]);
target += lognormal_lpdf(x[ : , 3] | mu[3], sigma[3]);
target += weibull_lpdf(x[ : , 4] | sigma[4], sigma[5]);

{
matrix[K, N] y;
for (n in 1 : N) {
Expand All @@ -37,4 +39,4 @@ model {
}
generated quantities {
matrix[K, K] Sigma = multiply_lower_tri_self_transpose(L);
}
}