fix estimate_truncation example

epiforecasts · Jan 12, 2024 · 05f3d71 · 05f3d71
1 parent 3fe524f
commit 05f3d71
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R
@@ -114,7 +114,7 @@
 #'      )
 #'    )
 #'  )
-#'   cmf <- cmf / cmf[dist$max + 1]
+#'   cmf <- cmf / cmf[max(dist) + 1]
 #'   cmf <- rev(cmf)[-1]
 #'   trunc_cases <- data.table::copy(cases)[1:(.N - index)]
 #'   trunc_cases[
@@ -217,13 +217,13 @@ estimate_truncation <- function(obs, max_truncation, trunc_max = 10,
   if (construct_trunc) {
     params_mean <- c(0, 1)
     params_sd <- c(1, 1)
-    parameters <- lapply(seq_along(params_mean), function (id) {
+    parameters <- lapply(seq_along(params_mean), function(id) {
       Normal(params_mean, params_sd)
     })
     names(parameters) <- natural_params(trunc_dist)
     parameters$max <- trunc_max
     truncation <- new_dist_spec(
-      parameters = parameters,
+      params = parameters,
       distribution = trunc_dist
     )
   }
@@ -278,18 +278,18 @@ estimate_truncation <- function(obs, max_truncation, trunc_max = 10,
 
   out <- list()
   # Summarise fit truncation distribution for downstream usage
-  params_mean <- round(
+  params_mean <- unname(round(
     rstan::summary(fit, pars = "delay_params")$summary[, 1], 3
-  )
-  params_sd <- round(
+  ))
+  params_sd <- unname(round(
     rstan::summary(fit, pars = "delay_params")$summary[, 3], 3
-  )
+  ))
   parameters <- lapply(seq_along(params_mean), function (id) {
     Normal(params_mean[id], params_sd[id])
   })
   names(parameters) <- natural_params(truncation[[1]]$distribution)
   out$dist <- truncation
-  out$dist$parameters <- parameters
+  out$dist[[1]]$parameters <- parameters
 
   # summarise reconstructed observations
   recon_obs <- extract_stan_param(fit, "recon_obs",

diff --git a/man/estimate_truncation.Rd b/man/estimate_truncation.Rd