fix rcmdcheck

Genentech · Feb 3, 2025 · 81bd1c1 · 81bd1c1
1 parent f7bade8
commit 81bd1c1
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Showing 10 changed files with 71 additions and 62 deletions.
diff --git 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 != "<None>") {
+        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
@@ -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 ~ <None>
            
         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 ~ <None>
            
         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 ~ <None>
            
         Link:     

diff --git 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
@@ -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
@@ -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 ~ <None>
       
 
@@ -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 ~ <None>
       
 
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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()
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -277,3 +277,6 @@ test_that("Parameters in priors must be length 1 #422", {
		"Parameter `alpha`"
		)
		})

Check warning on line 280 in tests/testthat/test-Prior.R View workflow job for this annotation GitHub Actions / SuperLinter 🦸‍♀️ / Lint R code 🧶 `file=tests/testthat/test-Prior.R,line=280,col=1,[trailing_blank_lines_linter] Trailing blank lines are superfluous.`

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