From 6f2d1adc16faf057dcf7d7d0d0ce21f01d9d7d90 Mon Sep 17 00:00:00 2001 From: gowerc Date: Thu, 20 Jun 2024 17:53:15 +0100 Subject: [PATCH] fixed breakages from main update --- inst/stan/base/functions.stan | 2 +- inst/stan/lm-claret-bruno/functions.stan | 2 +- inst/stan/lm-claret-bruno/link_dsld.stan | 2 +- .../_snaps/LongitudinalClaretBruno.md | 47 +++++++++++++++++++ .../_snaps/SimLongitudinalClaretBruno.md | 9 ++++ 5 files changed, 59 insertions(+), 3 deletions(-) create mode 100644 tests/testthat/_snaps/LongitudinalClaretBruno.md create mode 100644 tests/testthat/_snaps/SimLongitudinalClaretBruno.md diff --git a/inst/stan/base/functions.stan b/inst/stan/base/functions.stan index 5083f5c0a..380aa5073 100644 --- a/inst/stan/base/functions.stan +++ b/inst/stan/base/functions.stan @@ -101,7 +101,7 @@ functions { return result; } - matrix if_lt0_else(matrix x, matrix y, matrix replacement) { + matrix if_gte0_else(matrix x, matrix y, matrix replacement) { int nrow = rows(x); int ncol = cols(x); matrix[nrow, ncol] result; diff --git a/inst/stan/lm-claret-bruno/functions.stan b/inst/stan/lm-claret-bruno/functions.stan index 1479b36f6..9390258f5 100644 --- a/inst/stan/lm-claret-bruno/functions.stan +++ b/inst/stan/lm-claret-bruno/functions.stan @@ -12,7 +12,7 @@ functions { vector ind_p ) { int nrow = rows(time); - vector[nrow] ind_p_mod = if_lt0_else(time, ind_p, 0); + vector[nrow] ind_p_mod = if_gte0_else(time, ind_p, 0); vector[nrow] result = fmin( 8000.0, diff --git a/inst/stan/lm-claret-bruno/link_dsld.stan b/inst/stan/lm-claret-bruno/link_dsld.stan index f193b36db..749b06b6e 100644 --- a/inst/stan/lm-claret-bruno/link_dsld.stan +++ b/inst/stan/lm-claret-bruno/link_dsld.stan @@ -37,6 +37,6 @@ functions { (1 - exp(- ind_c_matrix .* time)) ) ); - return if_lt0_else(time, result_gt0, result_lt0); + return if_gte0_else(time, result_gt0, result_lt0); } } diff --git a/tests/testthat/_snaps/LongitudinalClaretBruno.md b/tests/testthat/_snaps/LongitudinalClaretBruno.md new file mode 100644 index 000000000..079beb539 --- /dev/null +++ b/tests/testthat/_snaps/LongitudinalClaretBruno.md @@ -0,0 +1,47 @@ +# Print method for LongitudinalClaretBruno works as expected + + Code + x <- LongitudinalClaretBruno() + print(x) + Output + + Claret-Bruno Longitudinal Model with parameters: + lm_clbr_mu_b ~ normal(mu = 4.09434, sigma = 0.5) + lm_clbr_mu_g ~ normal(mu = 0, sigma = 0.5) + lm_clbr_mu_c ~ normal(mu = -0.91629, sigma = 0.5) + lm_clbr_mu_p ~ normal(mu = 0.69315, sigma = 0.5) + lm_clbr_omega_b ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_g ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_c ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_p ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_sigma ~ lognormal(mu = -2.30259, sigma = 0.5) + lm_clbr_eta_b ~ std_normal() + lm_clbr_eta_g ~ std_normal() + lm_clbr_eta_c ~ std_normal() + lm_clbr_eta_p ~ std_normal() + + +--- + + Code + x <- LongitudinalClaretBruno(sigma = prior_normal(0, 1), mu_g = prior_gamma(2, + 1)) + print(x) + Output + + Claret-Bruno Longitudinal Model with parameters: + lm_clbr_mu_b ~ normal(mu = 4.09434, sigma = 0.5) + lm_clbr_mu_g ~ gamma(alpha = 2, beta = 1) + lm_clbr_mu_c ~ normal(mu = -0.91629, sigma = 0.5) + lm_clbr_mu_p ~ normal(mu = 0.69315, sigma = 0.5) + lm_clbr_omega_b ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_g ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_c ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_omega_p ~ lognormal(mu = -1.60944, sigma = 0.5) + lm_clbr_sigma ~ normal(mu = 0, sigma = 1) + lm_clbr_eta_b ~ std_normal() + lm_clbr_eta_g ~ std_normal() + lm_clbr_eta_c ~ std_normal() + lm_clbr_eta_p ~ std_normal() + + diff --git a/tests/testthat/_snaps/SimLongitudinalClaretBruno.md b/tests/testthat/_snaps/SimLongitudinalClaretBruno.md new file mode 100644 index 000000000..c228ea527 --- /dev/null +++ b/tests/testthat/_snaps/SimLongitudinalClaretBruno.md @@ -0,0 +1,9 @@ +# print methods work as expected + + Code + print(SimLongitudinalClaretBruno()) + Output + + A SimLongitudinalClaretBruno Object + +