From 81bd1c1ad2652793e2a08d415cbdbe82a78467a6 Mon Sep 17 00:00:00 2001 From: gowerc Date: Mon, 3 Feb 2025 12:01:44 +0000 Subject: [PATCH] fix rcmdcheck --- R/Prior.R | 10 +++-- tests/testthat/_snaps/JointModel.md | 38 +++++++++---------- .../_snaps/LongitudinalClaretBruno.md | 20 +++++----- tests/testthat/_snaps/LongitudinalGSF.md | 20 +++++----- .../_snaps/LongitudinalRandomSlope.md | 8 ++-- .../testthat/_snaps/LongitudinalSteinFojo.md | 16 ++++---- tests/testthat/_snaps/SurvivalGamma.md | 8 ++-- tests/testthat/_snaps/SurvivalWeibullPH.md | 8 ++-- tests/testthat/test-Prior.R | 3 ++ tests/testthat/test-stan_functions.R | 2 + 10 files changed, 71 insertions(+), 62 deletions(-) diff --git a/R/Prior.R b/R/Prior.R index 9b305cd05..0974e9919 100755 --- a/R/Prior.R +++ b/R/Prior.R @@ -141,7 +141,11 @@ as.character.Prior <- function(x, ...) { glue::glue, append(x@display, parameters_rounded) ) - paste0(display_string, " ", render_stan_limits(x@limits)) + display_limits <- render_stan_limits(x@limits) + if (display_limits != "" && display_string != "" && display_string != "") { + display_string <- paste0(display_string, display_limits) + } + return(display_string) } @@ -155,7 +159,7 @@ render_stan_limits <- function(limits) { u_bound <- if (limits[[2]] < Inf) limits[[2]] else "" string <- "" if (l_bound != "" || u_bound != "") { - string <- glue::glue("T[{l_bound}, {u_bound}]", l_bound = l_bound, u_bound = u_bound) + string <- glue::glue(" T[{l_bound}, {u_bound}]", l_bound = l_bound, u_bound = u_bound) } return(string) } @@ -185,7 +189,7 @@ setMethod( #' @export as.StanModule.Prior <- function(object, name, ...) { trunctation <- if (object@repr_model != "") { - paste0(" ", render_stan_limits(object@limits), ";") + paste0(render_stan_limits(object@limits), ";") } else { "" } diff --git a/tests/testthat/_snaps/JointModel.md b/tests/testthat/_snaps/JointModel.md index 6c7378568..4f663f7e7 100644 --- a/tests/testthat/_snaps/JointModel.md +++ b/tests/testthat/_snaps/JointModel.md @@ -10,16 +10,16 @@ Survival: Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) Longitudinal: Random Slope Longitudinal Model with parameters: lm_rs_intercept ~ normal(mu = 30, sigma = 10) lm_rs_slope_mu ~ normal(mu = 1, sigma = 3) - lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) - lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) + lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] + lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] lm_rs_ind_rnd_slope ~ Link: @@ -38,16 +38,16 @@ Survival: Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) Longitudinal: Random Slope Longitudinal Model with parameters: lm_rs_intercept ~ normal(mu = 30, sigma = 10) lm_rs_slope_mu ~ normal(mu = 1, sigma = 3) - lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) - lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) + lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] + lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] lm_rs_ind_rnd_slope ~ Link: @@ -66,8 +66,8 @@ Survival: Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) Longitudinal: @@ -94,11 +94,11 @@ lm_gsf_mu_ks ~ normal(mu = -0.69315, sigma = 1) lm_gsf_mu_kg ~ normal(mu = -1.20397, sigma = 1) lm_gsf_mu_phi ~ normal(mu = 0, sigma = 1) - lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_sigma ~ lognormal(mu = -2.30259, sigma = 1) + lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_sigma ~ lognormal(mu = -2.30259, sigma = 1) T[0, ] lm_gsf_eta_tilde_bsld ~ std_normal() lm_gsf_eta_tilde_ks ~ std_normal() lm_gsf_eta_tilde_kg ~ std_normal() @@ -119,16 +119,16 @@ Survival: Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) Longitudinal: Random Slope Longitudinal Model with parameters: lm_rs_intercept ~ normal(mu = 30, sigma = 10) lm_rs_slope_mu ~ normal(mu = 1, sigma = 3) - lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) - lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) + lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] + lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] lm_rs_ind_rnd_slope ~ Link: diff --git a/tests/testthat/_snaps/LongitudinalClaretBruno.md b/tests/testthat/_snaps/LongitudinalClaretBruno.md index 079beb539..d0d3d7f95 100644 --- a/tests/testthat/_snaps/LongitudinalClaretBruno.md +++ b/tests/testthat/_snaps/LongitudinalClaretBruno.md @@ -10,11 +10,11 @@ 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_omega_b ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_g ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_c ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_p ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_sigma ~ lognormal(mu = -2.30259, sigma = 0.5) T[0, ] lm_clbr_eta_b ~ std_normal() lm_clbr_eta_g ~ std_normal() lm_clbr_eta_c ~ std_normal() @@ -34,11 +34,11 @@ 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_omega_b ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_g ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_c ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_omega_p ~ lognormal(mu = -1.60944, sigma = 0.5) T[0, ] + lm_clbr_sigma ~ normal(mu = 0, sigma = 1) T[0, ] lm_clbr_eta_b ~ std_normal() lm_clbr_eta_g ~ std_normal() lm_clbr_eta_c ~ std_normal() diff --git a/tests/testthat/_snaps/LongitudinalGSF.md b/tests/testthat/_snaps/LongitudinalGSF.md index a02065f9e..ed7c8b70e 100644 --- a/tests/testthat/_snaps/LongitudinalGSF.md +++ b/tests/testthat/_snaps/LongitudinalGSF.md @@ -10,11 +10,11 @@ lm_gsf_mu_ks ~ normal(mu = -0.69315, sigma = 1) lm_gsf_mu_kg ~ normal(mu = -1.20397, sigma = 1) lm_gsf_mu_phi ~ normal(mu = 0, sigma = 1) - lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_sigma ~ lognormal(mu = -2.30259, sigma = 1) + lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_sigma ~ lognormal(mu = -2.30259, sigma = 1) T[0, ] lm_gsf_eta_tilde_bsld ~ std_normal() lm_gsf_eta_tilde_ks ~ std_normal() lm_gsf_eta_tilde_kg ~ std_normal() @@ -33,11 +33,11 @@ lm_gsf_mu_ks ~ normal(mu = -0.69315, sigma = 1) lm_gsf_mu_kg ~ gamma(alpha = 2, beta = 1) lm_gsf_mu_phi ~ normal(mu = 0, sigma = 1) - lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) - lm_gsf_sigma ~ normal(mu = 0, sigma = 1) + lm_gsf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_omega_phi ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_gsf_sigma ~ normal(mu = 0, sigma = 1) T[0, ] lm_gsf_eta_tilde_bsld ~ std_normal() lm_gsf_eta_tilde_ks ~ std_normal() lm_gsf_eta_tilde_kg ~ std_normal() diff --git a/tests/testthat/_snaps/LongitudinalRandomSlope.md b/tests/testthat/_snaps/LongitudinalRandomSlope.md index 997081e96..8694850fc 100644 --- a/tests/testthat/_snaps/LongitudinalRandomSlope.md +++ b/tests/testthat/_snaps/LongitudinalRandomSlope.md @@ -8,8 +8,8 @@ Random Slope Longitudinal Model with parameters: lm_rs_intercept ~ normal(mu = 30, sigma = 10) lm_rs_slope_mu ~ normal(mu = 1, sigma = 3) - lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) - lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) + lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] + lm_rs_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] lm_rs_ind_rnd_slope ~ @@ -24,8 +24,8 @@ Random Slope Longitudinal Model with parameters: lm_rs_intercept ~ normal(mu = 0, sigma = 1) lm_rs_slope_mu ~ normal(mu = 1, sigma = 3) - lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) - lm_rs_sigma ~ gamma(alpha = 2, beta = 1) + lm_rs_slope_sigma ~ lognormal(mu = 0, sigma = 1.5) T[0, ] + lm_rs_sigma ~ gamma(alpha = 2, beta = 1) T[0, ] lm_rs_ind_rnd_slope ~ diff --git a/tests/testthat/_snaps/LongitudinalSteinFojo.md b/tests/testthat/_snaps/LongitudinalSteinFojo.md index 1acd86a39..4ccd6682f 100644 --- a/tests/testthat/_snaps/LongitudinalSteinFojo.md +++ b/tests/testthat/_snaps/LongitudinalSteinFojo.md @@ -9,10 +9,10 @@ lm_sf_mu_bsld ~ normal(mu = 4.09434, sigma = 1) lm_sf_mu_ks ~ normal(mu = -0.69315, sigma = 1) lm_sf_mu_kg ~ normal(mu = -1.20397, sigma = 1) - lm_sf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_sigma ~ lognormal(mu = -2.30259, sigma = 1) + lm_sf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_sigma ~ lognormal(mu = -2.30259, sigma = 1) T[0, ] lm_sf_eta_tilde_bsld ~ std_normal() lm_sf_eta_tilde_ks ~ std_normal() lm_sf_eta_tilde_kg ~ std_normal() @@ -29,10 +29,10 @@ lm_sf_mu_bsld ~ normal(mu = 4.09434, sigma = 1) lm_sf_mu_ks ~ normal(mu = -0.69315, sigma = 1) lm_sf_mu_kg ~ gamma(alpha = 2, beta = 1) - lm_sf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) - lm_sf_sigma ~ normal(mu = 0, sigma = 1) + lm_sf_omega_bsld ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_omega_ks ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_omega_kg ~ lognormal(mu = -1.60944, sigma = 1) T[0, ] + lm_sf_sigma ~ normal(mu = 0, sigma = 1) T[0, ] lm_sf_eta_tilde_bsld ~ std_normal() lm_sf_eta_tilde_ks ~ std_normal() lm_sf_eta_tilde_kg ~ std_normal() diff --git a/tests/testthat/_snaps/SurvivalGamma.md b/tests/testthat/_snaps/SurvivalGamma.md index 2cb719671..ca86ce0ba 100644 --- a/tests/testthat/_snaps/SurvivalGamma.md +++ b/tests/testthat/_snaps/SurvivalGamma.md @@ -6,8 +6,8 @@ Output Gamma Survival Model with parameters: - sm_gamma_k ~ gamma(alpha = 2, beta = 0.5) - sm_gamma_theta ~ gamma(alpha = 2, beta = 0.5) + sm_gamma_k ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_gamma_theta ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) @@ -19,8 +19,8 @@ Output Gamma Survival Model with parameters: - sm_gamma_k ~ gamma(alpha = 3, beta = 4) - sm_gamma_theta ~ cauchy(mu = 0, sigma = 1) + sm_gamma_k ~ gamma(alpha = 3, beta = 4) T[0, ] + sm_gamma_theta ~ cauchy(mu = 0, sigma = 1) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) diff --git a/tests/testthat/_snaps/SurvivalWeibullPH.md b/tests/testthat/_snaps/SurvivalWeibullPH.md index 326b229e0..97e832c3e 100644 --- a/tests/testthat/_snaps/SurvivalWeibullPH.md +++ b/tests/testthat/_snaps/SurvivalWeibullPH.md @@ -6,8 +6,8 @@ Output Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5) T[0, ] beta_os_cov ~ normal(mu = 0, sigma = 2) @@ -19,8 +19,8 @@ Output Weibull-PH Survival Model with parameters: - sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) - sm_weibull_ph_gamma ~ cauchy(mu = 0, sigma = 1) + sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5) T[0, ] + sm_weibull_ph_gamma ~ cauchy(mu = 0, sigma = 1) T[0, ] beta_os_cov ~ gamma(alpha = 3, beta = 4) diff --git a/tests/testthat/test-Prior.R b/tests/testthat/test-Prior.R index aae5ab052..984d03ea2 100644 --- a/tests/testthat/test-Prior.R +++ b/tests/testthat/test-Prior.R @@ -277,3 +277,6 @@ test_that("Parameters in priors must be length 1 #422", { "Parameter `alpha`" ) }) + + + diff --git a/tests/testthat/test-stan_functions.R b/tests/testthat/test-stan_functions.R index 786fd2ef3..64b648987 100644 --- a/tests/testthat/test-stan_functions.R +++ b/tests/testthat/test-stan_functions.R @@ -22,6 +22,7 @@ run_stan_function <- function(stan_data, fun_files, dir, basename) { ) ) ) + # Completely silence call to STAN as we aren't fitting a real model devnull <- capture.output({ suppressMessages({ @@ -38,6 +39,7 @@ run_stan_function <- function(stan_data, fun_files, dir, basename) { }) }) return(fit) + mod$stan_file() }