Issue 442: Generalise to all brms distributions (#459)

* update gitignore to ignore local build paths for testing

* breaking rename

* start work on primarycensored port in and generalised predict and epred

* check new implementatons against ebola vignette

* refine posterior prediction and make vignettes faster

* rename and move around

* refactor tests

* check tests

* refine tess

* add note about direct usage failing but tidybayes working

Former-commit-id: 95b48ca
Former-commit-id: cf73454e616950a2f6debdc2d039d443fe5537ab
Former-commit-id: efd8befdd0b9b9e8f3f7abaefe9f81590bc3ad35 [formerly f61ea80]
Former-commit-id: aff38d5ec25ac9be287314158163bfafd6d8fa3a

.gitignore

@@ -25,3 +25,7 @@ data/models/*reparam
 docs
 /doc/
 /Meta/
+vignettes/**_cache/
+*.pdf
+.vscode/
+vignettes/figures/

DESCRIPTION

@@ -34,7 +34,8 @@ Imports:
     rstan (>= 2.26.0),
     dplyr,
     tibble,
-    lubridate
+    lubridate,
+    primarycensored
 Suggests:
     bookdown,
     testthat (>= 3.0.0),

NAMESPACE

@@ -38,6 +38,8 @@ export(epidist_family_prior)
 export(epidist_family_reparam)
 export(epidist_formula)
 export(epidist_formula_model)
+export(epidist_gen_posterior_epred)
+export(epidist_gen_posterior_predict)
 export(epidist_model_prior)
 export(epidist_prior)
 export(epidist_stancode)

R/gen.R

@@ -0,0 +1,73 @@
+#' Create a function to draw from the posterior predictive distribution for a
+#' latent model
+#'
+#' This function creates a function that draws from the posterior predictive
+#' distribution for a latent model using [primarycensored::rpcens()] to handle
+#' censoring and truncation. The returned function takes a `prep` argument from
+#' `brms` and returns posterior predictions. This is used internally by
+#' [brms::posterior_predict()] to generate predictions for latent models.
+#'
+#' @inheritParams epidist_family
+#'
+#' @return A function that takes a `prep` argument from brms and returns a
+#' matrix of posterior predictions, with one row per posterior draw and one
+#' column per observation. The `prep` object must have the following variables:
+#' * `vreal1`: relative observation time
+#' * `vreal2`: primary event window
+#' * `vreal3`: secondary event window
+#'
+#' @seealso [brms::posterior_predict()] for details on how this is used within
+#' `brms`, [primarycensored::rpcens()] for details on the censoring approach
+#' @autoglobal
+#' @family gen
+#' @export
+epidist_gen_posterior_predict <- function(family) {
+  dist_fn <- .get_brms_fn("posterior_predict", family)
+
+  rdist <- function(n, i, prep, ...) {
+    prep$ndraws <- n
+    do.call(dist_fn, list(i = i, prep = prep))
+  }
+
+  .predict <- function(i, prep, ...) {
+    relative_obs_time <- prep$data$vreal1[i]
+    pwindow <- prep$data$vreal2[i]
+    swindow <- prep$data$vreal3[i]
+
+    as.matrix(primarycensored::rpcens(
+      n = prep$ndraws,
+      rdist = rdist,
+      rprimary = stats::runif,
+      pwindow = prep$data$vreal2[i],
+      swindow = prep$data$vreal3[i],
+      D = prep$data$vreal1[i],
+      i = i,
+      prep = prep
+    ))
+  }
+  return(.predict)
+}
+
+#' Create a function to draw from the expected value of the posterior predictive
+#' distribution for a latent model
+#'
+#' This function creates a function that calculates the expected value of the
+#' posterior predictive distribution for a latent model. The returned function
+#' takes a `prep` argument (from brms) and returns posterior expected values.
+#' This is used internally by [brms::posterior_epred()] to calculate expected
+#' values for latent models.
+#'
+#' @inheritParams epidist_family
+#'
+#' @return A function that takes a prep argument from brms and returns a matrix
+#' of posterior expected values, with one row per posterior draw and one column
+#' per observation.
+#'
+#' @seealso [brms::posterior_epred()] for details on how this is used within
+#' `brms`.
+#' @autoglobal
+#' @family gen
+#' @export
+epidist_gen_posterior_epred <- function(family) {
+  .get_brms_fn("posterior_epred", family)
+}

R/globals.R

@@ -1,16 +1,9 @@
 # Generated by roxyglobals: do not edit by hand
 
 utils::globalVariables(c(
-  ".data", # <epidist_diagnostics>
   "samples", # <epidist_diagnostics>
-  ".data", # <as_epidist_latent_model.epidist_linelist_data>
   "woverlap", # <epidist_stancode.epidist_latent_model>
-  ".data", # <as_epidist_naive_model.epidist_linelist_data>
-  ".data", # <add_mean_sd.lognormal_samples>
-  ".data", # <add_mean_sd.gamma_samples>
   "rlnorm", # <simulate_secondary>
-  ".data", # <simulate_secondary>
-  ".data", # <.replace_prior>
   "prior_new", # <.replace_prior>
   "source_new", # <.replace_prior>
   NULL

R/latent_model.R

@@ -89,12 +89,76 @@ epidist_family_model.epidist_latent_model <- function(
     ub = c(NA, as.numeric(lapply(family$other_bounds, "[[", "ub"))),
     type = family$type,
     vars = c("pwindow", "swindow", "vreal1"),
-    loop = FALSE
+    loop = FALSE,
+    log_lik = epidist_gen_log_lik_latent(family),
+    posterior_predict = epidist_gen_posterior_predict(family),
+    posterior_epred = epidist_gen_posterior_epred(family)
   )
   custom_family$reparm <- family$reparm
   return(custom_family)
 }
 
+#' Create a function to calculate the pointwise log likelihood of the latent
+#' model
+#'
+#' This function creates a log likelihood function that accounts for the latent
+#' variables in the model, including primary and secondary event windows and
+#' their overlap. The returned function calculates the log likelihood for a
+#' single observation by augmenting the data with the latent variables and
+#' using the underlying brms log likelihood function.
+#'
+#' @seealso [brms::log_lik()] for details on the brms log likelihood interface.
+#'
+#' @inheritParams epidist_family
+#'
+#' @return A function that calculates the log likelihood for a single
+#' observation. The prep object must have the following variables:
+#' * `vreal1`: relative observation time
+#' * `vreal2`: primary event window
+#' * `vreal3`: secondary event window
+#'
+#' @family latent_model
+#' @autoglobal
+epidist_gen_log_lik_latent <- function(family) {
+  # Get internal brms log_lik function
+  log_lik_brms <- .get_brms_fn("log_lik", family)
+
+  .log_lik <- function(i, prep) {
+    y <- prep$data$Y[i]
+    relative_obs_time <- prep$data$vreal1[i]
+    pwindow <- prep$data$vreal2[i]
+    swindow <- prep$data$vreal3[i]
+
+    # Generates values of the swindow_raw and pwindow_raw, but really these
+    # should be extracted from prep or the fitted raws somehow. See:
+    # https://github.com/epinowcast/epidist/issues/267
+    swindow_raw <- stats::runif(prep$ndraws)
+    pwindow_raw <- stats::runif(prep$ndraws)
+
+    swindow <- swindow_raw * swindow
+
+    # For no overlap calculate as usual, for overlap ensure pwindow < swindow
+    if (i %in% prep$data$noverlap) {
+      pwindow <- pwindow_raw * pwindow
+    } else {
+      pwindow <- pwindow_raw * swindow
+    }
+
+    d <- y - pwindow + swindow
+    obs_time <- relative_obs_time - pwindow
+    # Create brms truncation upper bound
+    prep$data$ub <- rep(obs_time, length(prep$data$Y))
+    # Update augmented data
+    prep$data$Y <- rep(d, length(prep$data$Y))
+
+    # Call internal brms log_lik function with augmented data
+    lpdf <- log_lik_brms(i, prep)
+    return(lpdf)
+  }
+
+  return(.log_lik)
+}
+
 #' Define the model-specific component of an `epidist` custom formula
 #'
 #' @inheritParams epidist_formula_model

R/utils.R

@@ -157,3 +157,22 @@
 
   return(df)
 }
+
+#' Get a brms function by prefix and family
+#'
+#' Helper function to get internal brms functions by constructing their name
+#' from a prefix and family. Used to get functions like `log_lik_*`,
+#' `posterior_predict_*` etc.
+#'
+#' @param prefix Character string prefix of the brms function to get (e.g.
+#' "log_lik")
+#'
+#' @inheritParams epidist_family
+#' @return The requested brms function
+#' @keywords internal
+.get_brms_fn <- function(prefix, family) {
+  get(
+    paste0(prefix, "_", tolower(family$family)),
+    asNamespace("brms")
+  )
+}