use sigma ~ 0 + time

NAMESPACE

@@ -6,6 +6,7 @@ export(brm_simulate)
 importFrom(MASS,mvrnorm)
 importFrom(brms,brm)
 importFrom(brms,brmsformula)
+importFrom(brms,get_prior)
 importFrom(brms,prior)
 importFrom(brms,unstr)
 importFrom(rlang,warn)

R/brm_formula.R

@@ -89,7 +89,7 @@ brm_formula <- function(
   )
   right <- paste(terms, collapse = " + ")
   formula <- stats::as.formula(paste(response, "~", right))
-  formula_sigma <- stats::as.formula(paste("sigma ~", time))
+  formula_sigma <- stats::as.formula(paste("sigma ~ 0 +", time))
   brms::brmsformula(formula = formula, formula_sigma)
 }
 

R/brm_model.R

@@ -14,10 +14,7 @@
 #'   of the "intercept" class of parameters.
 #' @param sd_b Positive numeric of length 1, prior standard deviation
 #'   of the "b" class of parameters.
-#' @param sd_intercept_sigma Positive numeric of length 1,
-#'   prior standard deviation
-#'   of the "intercept" class of parameters with `dpar = "sigma"`.
-#' @param sd_b_sigma Positive numeric of length 1,
+#' @param sd_sigma Positive numeric of length 1,
 #'   prior standard deviation
 #'   of the "b" class of parameters with `dpar = "sigma"`.
 #' @param shape_cor Positive numeric of length 1. For unstructured
@@ -56,8 +53,7 @@ brm_model <- function(
   formula = brm_formula(),
   sd_intercept = 100,
   sd_b = 100,
-  sd_intercept_sigma = 100,
-  sd_b_sigma = 100,
+  sd_sigma = 100,
   shape_cor = 1,
   ...
 ) {
@@ -68,17 +64,17 @@ brm_model <- function(
   )
   assert_pos(sd_intercept)
   assert_pos(sd_b)
-  assert_pos(sd_intercept_sigma)
-  assert_pos(sd_b_sigma)
+  assert_pos(sd_sigma)
   prior_0 <- sprintf("normal(0, %s)", sd_intercept)
   prior_b <- sprintf("normal(0, %s)", sd_b)
-  prior_0_sigma <- sprintf("normal(0, %s)", sd_intercept_sigma)
-  prior_b_sigma <- sprintf("normal(0, %s)", sd_b_sigma)
+  prior_sigma <- sprintf("normal(0, %s)", sd_sigma)
   prior_cor <- sprintf("lkj_corr_cholesky(%s)", shape_cor)
-  prior <- brms::set_prior(prior = prior_0, class = "Intercept") +
-    brms::set_prior(prior = prior_b, class = "b") +
-    brms::set_prior(prior_0_sigma, class = "Intercept", dpar = "sigma") +
-    brms::set_prior(prior_b_sigma, class = "b", dpar = "sigma") +
+  prior <- brms::set_prior(prior = prior_b, class = "b") +
+    brms::set_prior(prior_sigma, class = "b", dpar = "sigma") +
     brms::set_prior(prior_cor, class = "Lcortime")
+  prior_classes <- brms::get_prior(formula = formula, data = data)$class
+  if ("Intercept" %in% prior_classes) {
+    prior <- prior + brms::set_prior(prior = prior_0, class = "Intercept")
+  }
   brms::brm(data = data, formula = formula, prior = prior, ...)
 }

R/brm_package.R

@@ -19,7 +19,7 @@
 #'     Ther Innov Regul Sci 42, 303–319 (2008).
 #'     doi:10.1177/009286150804200402
 #' @family help
-#' @importFrom brms brm brmsformula prior unstr
+#' @importFrom brms brm brmsformula get_prior prior unstr
 #' @importFrom MASS mvrnorm
 #' @importFrom rlang warn
 #' @importFrom stats as.formula model.matrix rnorm runif

tests/testthat/test-brm_formula.R

@@ -18,7 +18,7 @@ test_that("brm_formula() with default names and all terms", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -45,7 +45,7 @@ test_that("brm_formula() with all user-supplied columns and all terms", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ t"
+      "sigma ~ 0 + t"
     )
   )
 })
@@ -69,7 +69,7 @@ test_that("brm_formula() without intercept", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -93,7 +93,7 @@ test_that("brm_formula() without group effect", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -117,7 +117,7 @@ test_that("brm_formula() without time effect", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -141,7 +141,7 @@ test_that("brm_formula() without baseline effect", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -165,7 +165,7 @@ test_that("brm_formula() without baseline interaction", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })
@@ -189,7 +189,7 @@ test_that("brm_formula() without group interaction", {
   expect_equal(
     deparse(out[[2L]][[1L]], width.cutoff = 500L),
     paste(
-      "sigma ~ AVISIT"
+      "sigma ~ 0 + AVISIT"
     )
   )
 })