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epinowcast · Jul 22, 2024 · 705cdc5 · 705cdc5
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Showing 13 changed files with 127 additions and 10 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(add_natural_scale_mean_sd,default)
+S3method(add_natural_scale_mean_sd,latent_gamma)
+S3method(add_natural_scale_mean_sd,latent_lognormal)
 S3method(as_latent_individual,data.frame)
 S3method(epidist,default)
 S3method(epidist_family,default)

diff --git a/R/globals.R b/R/globals.R
@@ -5,9 +5,6 @@ utils::globalVariables(c(
   "max_treedepth", # <epidist_diagnostics>
   "per_at_max_treedepth", # <epidist_diagnostics>
   "samples", # <epidist_diagnostics>
-  "meanlog", # <add_natural_scale_mean_sd>
-  "sdlog", # <add_natural_scale_mean_sd>
-  "sd", # <add_natural_scale_mean_sd>
   "sdlog", # <extract_lognormal_draws>
   "sdlog_log", # <extract_lognormal_draws>
   "meanlog", # <extract_lognormal_draws>
@@ -72,6 +69,13 @@ utils::globalVariables(c(
   "ptime_daily", # <plot_mean_posterior_pred>
   "n", # <plot_mean_posterior_pred>
   "obs_horizon", # <plot_mean_posterior_pred>
+  "mu", # <add_natural_scale_mean_sd.latent_lognormal>
+  "sigma", # <add_natural_scale_mean_sd.latent_lognormal>
+  "sd", # <add_natural_scale_mean_sd.latent_lognormal>
+  "sigma", # <add_natural_scale_mean_sd.latent_gamma>
+  "sd", # <add_natural_scale_mean_sd.latent_gamma>
+  "mu", # <add_natural_scale_mean_sd.latent_gamma>
+  "shape", # <add_natural_scale_mean_sd.latent_gamma>
   "time", # <linelist_to_counts>
   "primary", # <linelist_to_cases>
   "secondary", # <linelist_to_cases>

diff --git a/R/postprocess.R b/R/postprocess.R
@@ -13,6 +13,7 @@ add_natural_scale_mean_sd <- function(data, ...) {
 #' @inheritParams add_natural_scale_mean_sd
 #' @param ... Additional arguments for method.
 #' @family postprocess
+#' @method add_natural_scale_mean_sd default
 #' @export
 add_natural_scale_mean_sd.default <- function(data, ...) {
   cli::cli_inform(
@@ -31,6 +32,7 @@ add_natural_scale_mean_sd.default <- function(data, ...) {
 #' @inheritParams add_natural_scale_mean_sd
 #' @param ... Additional arguments for method.
 #' @family postprocess
+#' @method add_natural_scale_mean_sd latent_lognormal
 #' @autoglobal
 #' @export
 add_natural_scale_mean_sd.latent_lognormal <- function(data, ...) {
@@ -47,6 +49,7 @@ add_natural_scale_mean_sd.latent_lognormal <- function(data, ...) {
 #' @inheritParams add_natural_scale_mean_sd
 #' @param ... Additional arguments for method.
 #' @family postprocess
+#' @method add_natural_scale_mean_sd latent_gamma
 #' @autoglobal
 #' @export
 add_natural_scale_mean_sd.latent_gamma <- function(data, ...) {

diff --git a/man/add_natural_scale_mean_sd.Rd b/man/add_natural_scale_mean_sd.Rd
diff --git a/man/add_natural_scale_mean_sd.default.Rd b/man/add_natural_scale_mean_sd.default.Rd
diff --git a/man/add_natural_scale_mean_sd.latent_gamma.Rd b/man/add_natural_scale_mean_sd.latent_gamma.Rd
diff --git a/man/add_natural_scale_mean_sd.latent_lognormal.Rd b/man/add_natural_scale_mean_sd.latent_lognormal.Rd
diff --git a/man/draws_to_long.Rd b/man/draws_to_long.Rd
diff --git a/man/extract_lognormal_draws.Rd b/man/extract_lognormal_draws.Rd
diff --git a/man/make_relative_to_truth.Rd b/man/make_relative_to_truth.Rd
diff --git a/man/summarise_draws.Rd b/man/summarise_draws.Rd
diff --git a/man/summarise_variable.Rd b/man/summarise_variable.Rd
diff --git a/tests/testthat/test-unit-postprocess.R b/tests/testthat/test-unit-postprocess.R
@@ -16,10 +16,12 @@ brms::posterior_predict(fit)
 linpred_mu <- brms::posterior_linpred(fit, transform = TRUE, dpar = "mu")
 linpred_sigma <- brms::posterior_linpred(fit, transform = TRUE, dpar = "sigma")
 
-linpred_mu_melt <- reshape2::melt(linpred_mu, varnames = c("aaa", "bbb"), value.name = "mu")
-linpred_sigma_melt <- reshape2::melt(linpred_sigma, varnames = c("aaa", "bbb"), value.name = "sigma")
+linpred_mu_melt <- reshape2::melt(linpred_mu, varnames = c("draw", "index"), value.name = "mu")
+linpred_sigma_melt <- reshape2::melt(linpred_sigma, varnames = c("draw", "index"), value.name = "sigma")
 
 linpred_melt <- dplyr::left_join(linpred_mu_melt, linpred_sigma_melt)
+class(linpred_melt) <- c(class(linpred_melt), "latent_lognormal")
+add_natural_scale_mean_sd(data.table::as.data.table(linpred_melt))
 
 pp <- brms::prepare_predictions(fit)
 pp$dpars$mu$fe$b