Added unit tests for Priors

Genentech · Jan 31, 2024 · eba1bbd · eba1bbd
1 parent f52defc
commit eba1bbd
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Showing 18 changed files with 351 additions and 12 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -50,6 +50,7 @@ S3method(dim,Quantities)
 S3method(extractVariableNames,DataSubject)
 S3method(extractVariableNames,DataSurvival)
 S3method(generateQuantities,JointModelSamples)
+S3method(getParameters,default)
 S3method(initialValues,JointModel)
 S3method(initialValues,Parameter)
 S3method(initialValues,ParameterList)
@@ -107,10 +108,15 @@ export(merge)
 export(prior_beta)
 export(prior_cauchy)
 export(prior_gamma)
+export(prior_invgamma)
+export(prior_logistic)
+export(prior_loglogistic)
 export(prior_lognormal)
 export(prior_none)
 export(prior_normal)
 export(prior_std_normal)
+export(prior_student_t)
+export(prior_uniform)
 export(sampleStanModel)
 export(show)
 export(sim_lm_gsf)

diff --git a/R/StanModule.R b/R/StanModule.R
@@ -144,11 +144,13 @@ setMethod(
         stan_fragments <- lapply(
             names(stan_blocks),
             \(par) {
-                new_string <- c(slot(x, par), slot(y, par))
-                if (all(new_string == "")) {
-                    return("")
+                if (all(slot(y, par) == "")) {
+                    return(slot(x, par))
                 }
-                return(new_string)
+                if (all(slot(x, par) == "")) {
+                    return(slot(y, par))
+                }
+                return(c(slot(x, par), slot(y, par)))
             }
         )
         names(stan_fragments) <- names(stan_blocks)

diff --git a/R/defaults.R b/R/defaults.R
@@ -37,7 +37,7 @@ setMethod(
 )
 
 # getParameters ----
-
+#' @export
 getParameters.default <- function(object) {
     if (missing(object) || is.null(object)) {
         return(NULL)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -50,10 +50,15 @@ reference:
       - prior_beta
       - prior_cauchy
       - prior_gamma
+      - prior_invgamma
+      - prior_logistic
+      - prior_loglogistic
       - prior_lognormal
       - prior_none
       - prior_normal
+      - prior_uniform
       - prior_std_normal
+      - prior_student_t
 
   - title: Longitudinal Model Specification
     contents:

diff --git a/man/prior_beta.Rd b/man/prior_beta.Rd
diff --git a/man/prior_cauchy.Rd b/man/prior_cauchy.Rd
diff --git a/man/prior_gamma.Rd b/man/prior_gamma.Rd
diff --git a/man/prior_invgamma.Rd b/man/prior_invgamma.Rd
diff --git a/man/prior_logistic.Rd b/man/prior_logistic.Rd
diff --git a/man/prior_loglogistic.Rd b/man/prior_loglogistic.Rd
diff --git a/man/prior_lognormal.Rd b/man/prior_lognormal.Rd
diff --git a/man/prior_none.Rd b/man/prior_none.Rd
diff --git a/man/prior_normal.Rd b/man/prior_normal.Rd
diff --git a/man/prior_std_normal.Rd b/man/prior_std_normal.Rd
diff --git a/man/prior_student_t.Rd b/man/prior_student_t.Rd
diff --git a/man/prior_uniform.Rd b/man/prior_uniform.Rd