cmdstanr and posterior updates

.github/workflows/R-CMD-check-build.yaml

@@ -45,10 +45,10 @@ jobs:
           cache-version: 1
           extra-packages: |
             stan-dev/cmdstanr
+            stan-dev/posterior
             rcmdcheck
             checkmate
             jsonlite
-            posterior
             processx
             R6
             BH

.github/workflows/R-CMD-check.yaml

@@ -50,10 +50,10 @@ jobs:
           cache-version: 1
           extra-packages: |
             stan-dev/cmdstanr
+            stan-dev/posterior
             rcmdcheck
             checkmate
             jsonlite
-            posterior
             processx
             R6
             BH

DESCRIPTION

@@ -13,10 +13,9 @@ RoxygenNote: 7.2.3
 Depends:
     R (>= 3.1.2)
 Imports:
-    abind,
     checkmate,
     matrixStats (>= 0.52),
-    posterior,
+    posterior (>= 1.5.0),
     stats
 Suggests: 
     bayesplot,
@@ -26,6 +25,7 @@ Suggests:
     rstan,
     testthat
 Enhances:
+    brms,
     cmdstanr
 VignetteBuilder: knitr
 Config/testthat/parallel: true

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(constrain_draws,stanfit)
 S3method(moment_match,CmdStanFit)
+S3method(moment_match,brmsfit)
 S3method(moment_match,draws_array)
 S3method(moment_match,draws_df)
 S3method(moment_match,draws_list)

R/brmsfit_functions.R

@@ -0,0 +1,176 @@
+#' Generic importance weighted moment matching algorithm for `brmsfit` objects.
+#' See additional arguments from `moment_match.matrix`
+#'
+#' @param x A fitted `brmsfit` object.
+#' @param log_prob_target_fun Log density of the target.  The function
+#'   takes argument `draws`, which are the unconstrained draws.
+#'   Can also take the argument `fit` which is the stan model fit.
+#' @param log_ratio_fun Log of the density ratio (target/proposal).
+#'   The function takes argument `draws`, which are the unconstrained
+#'   draws. Can also take the argument `fit` which is the stan model fit.
+#' @param target_observation_weights A vector of weights for observations for
+#' defining the target distribution. A value 0 means dropping the observation,
+#' a value 1 means including the observation similarly as in the current data,
+#' and a value 2 means including the observation twice.
+#' @param expectation_fun Optional argument, NULL by default. A
+#'   function whose expectation is being computed. The function takes
+#'   arguments `draws`.
+#' @param log_expectation_fun Logical indicating whether the
+#'   expectation_fun returns its values as logarithms or not. Defaults
+#'   to FALSE. If set to TRUE, the expectation function must be
+#'   nonnegative (before taking the logarithm).  Ignored if
+#'   `expectation_fun` is NULL.
+#' @param constrain Logical specifying whether to return draws on the
+#'   constrained space? Default is TRUE.
+#' @param ... Further arguments passed to `moment_match.matrix`.
+#'
+#' @return Returns a list with 3 elements: transformed draws, updated
+#'   importance weights, and the pareto k diagnostic value. If expectation_fun
+#'   is given, also returns the expectation.
+#'
+#' @export
+moment_match.brmsfit <- function(x,
+                                 log_prob_target_fun = NULL,
+                                 log_ratio_fun = NULL,
+                                 target_observation_weights = NULL,
+                                 expectation_fun = NULL,
+                                 log_expectation_fun = FALSE,
+                                 constrain = TRUE,
+                                 ...) {
+  if (!is.null(target_observation_weights) && (!is.null(log_prob_target_fun) || !is.null(log_ratio_fun))) {
+    stop("You must give only one of target_observation_weights, log_prob_target_fun, or log_ratio_fun.")
+  }
+
+  # ensure draws are in matrix form
+  draws <- posterior::as_draws_matrix(x)
+  # draws <- as.matrix(draws)
+
+  if (!is.null(target_observation_weights)) {
+    out <- tryCatch(log_lik(x),
+                    error = function(cond) {
+                      message(cond)
+                      message("\nYour brmsfit does not include a parameter called log_lik.")
+                      message("This should not happen. Perhaps you are using an unsupported observation model?")
+                      return(NA)
+                    }
+    )
+
+    function(draws, fit, extra_data, ...) {
+      fit <- brms:::.update_pars(x = fit, upars = draws)
+      ll <- log_lik(fit, newdata = extra_data)
+      rowSums(ll)
+    }
+
+    log_ratio_fun <- function(draws, fit, ...) {
+      fit <- brms:::.update_pars(x = fit, upars = draws)
+      ll <- log_lik(fit)
+      colSums(t(drop(ll)) * (target_observation_weights - 1))
+    }
+  }
+
+
+  # transform the draws to unconstrained space
+  udraws <- unconstrain_draws.brmsfit(x, draws = draws, ...)
+
+  out <- moment_match.matrix(
+    # as.matrix(udraws),
+    udraws,
+    log_prob_prop_fun = log_prob_draws.brmsfit,
+    log_prob_target_fun = log_prob_target_fun,
+    log_ratio_fun = log_ratio_fun,
+    expectation_fun = expectation_fun,
+    log_expectation_fun = log_expectation_fun,
+    fit = x,
+    ...
+  )
+
+  # TODO: this does not work for some reason
+  # x <- brms:::.update_pars(x = x, upars = out$draws)
+  # x <- update_pars_brmsfit(x = x, draws = out$draws)
+
+  if (constrain) {
+    out$draws <- constrain_draws.stanfit(x$fit, out$draws, ...)
+  }
+
+  list(adapted_importance_sampling = out,
+       brmsfit_object = x)
+}
+
+
+log_prob_draws.brmsfit <- function(fit, draws, ...) {
+  # x <- update_misc_env(x, only_windows = TRUE)
+  log_prob_draws.stanfit(fit$fit, draws = draws, ...)
+}
+
+unconstrain_draws.brmsfit <- function(x, draws, ...) {
+  unconstrain_draws.stanfit(x$fit, draws = draws, ...)
+}
+
+constrain_draws.brmsfit <- function(x, udraws, ...) {
+  out <- rstan::constrain_pars(udraws, object = x$fit)
+  out[x$exclude] <- NULL
+  out
+}
+
+# # transform parameters to the constraint space
+update_pars_brmsfit <- function(x, draws, ...) {
+  # list with one element per posterior draw
+  pars <- apply(draws, 1, constrain_draws.brmsfit, x = x)
+  # select required parameters only
+  pars <- lapply(pars, "[", x$fit@sim$pars_oi_old)
+  # transform draws
+  ndraws <- length(pars)
+  pars <- unlist(pars)
+  npars <- length(pars) / ndraws
+  dim(pars) <- c(npars, ndraws)
+  # add dummy 'lp__' draws
+  pars <- rbind(pars, rep(0, ndraws))
+  # bring draws into the right structure
+  new_draws <- named_list(x$fit@sim$fnames_oi_old, list(numeric(ndraws)))
+  if (length(new_draws) != nrow(pars)) {
+    stop2("Updating parameters in `update_pars_brmsfit' failed.")
+  }
+  for (i in seq_len(npars)) {
+    new_draws[[i]] <- pars[i, ]
+  }
+  # create new sim object to overwrite x$fit@sim
+  x$fit@sim <- list(
+    samples = list(new_draws),
+    iter = ndraws,
+    thin = 1,
+    warmup = 0,
+    chains = 1,
+    n_save = ndraws,
+    warmup2 = 0,
+    permutation = list(seq_len(ndraws)),
+    pars_oi = x$fit@sim$pars_oi_old,
+    dims_oi = x$fit@sim$dims_oi_old,
+    fnames_oi = x$fit@sim$fnames_oi_old,
+    n_flatnames = length(x$fit@sim$fnames_oi_old)
+  )
+  x$fit@stan_args <- list(
+    list(chain_id = 1, iter = ndraws, thin = 1, warmup = 0)
+  )
+  brms::rename_pars(x)
+}
+
+# update .MISC environment of the stanfit object
+# allows to call log_prob and other C++ using methods
+# on objects not created in the current R session
+# or objects created via another backend
+# update_misc_env <- function(x, recompile = FALSE, only_windows = FALSE) {
+#   stopifnot(is.brmsfit(x))
+#   recompile <- as_one_logical(recompile)
+#   only_windows <- as_one_logical(only_windows)
+#   if (recompile || !has_rstan_model(x)) {
+#     x <- add_rstan_model(x, overwrite = TRUE)
+#   } else if (os_is_windows() || !only_windows) {
+#     # TODO: detect when updating .MISC is not required
+#     # TODO: find a more efficient way to update .MISC
+#     old_backend <- x$backend
+#     x$backend <- "rstan"
+#     [email protected] <- suppressMessages(brm(fit = x, chains = 0))[email protected]
+#     x$backend <- old_backend
+#   }
+#   x
+# }

R/constrain_draws.R

@@ -8,6 +8,7 @@ constrain_draws <- function(x, ...) {
   UseMethod("constrain_draws")
 }
 
+##' @export
 constrain_draws.CmdStanFit <- function(x, udraws, ...) {
   # list with one element per posterior draw
   draws <- apply(udraws, 1, x$constrain_variables)

R/moment_match.R

@@ -287,11 +287,14 @@
            target density is equal to your proposal density.")
     }
 
-    pareto_smoothed_w <- posterior::pareto_smooth(exp(lw - matrixStats::logSumExp(lw)),
-      tail = "right", extra_diags = TRUE, r_eff = 1
+    pareto_smoothed_w <- posterior::pareto_smooth(
+      lw - matrixStats::logSumExp(lw), are_log_weights = TRUE,
+      tail = "right", extra_diags = TRUE, r_eff = 1,
+      return_k = TRUE,
+      verbose = FALSE
     )
     k <- pareto_smoothed_w$diagnostics$khat
-    lw <- log(as.vector(pareto_smoothed_w$x))
+    lw <- as.vector(pareto_smoothed_w$x)
 
     if (any(is.infinite(k))) {
       stop("Something went wrong, and encountered infinite Pareto k values..")
@@ -339,8 +342,10 @@
     lwf <- compute_lwf(draws, lw, expectation_fun, log_expectation_fun, draws_transformation_fun, ...)
 
     pareto_smoothed_wf <- apply(lwf, 2, function(x) {
-      posterior::pareto_smooth(exp(x),
-        tail = "right", extra_diags = TRUE, r_eff = 1
+      posterior::pareto_smooth(
+        x, are_log_weights = TRUE,
+        tail = "right", extra_diags = TRUE, r_eff = 1,
+        return_k = TRUE, verbose = FALSE
       )
     })
     pareto_smoothed_wf <- do.call(mapply, c(cbind, pareto_smoothed_wf))
@@ -369,7 +374,7 @@
               that return a matrix. As a workaround, you can wrap your function
               call using apply.")
       }
-      lwf <- log(as.vector(pareto_smoothed_wf$x))
+      lwf <- as.vector(pareto_smoothed_wf$x)
 
       if (is.null(log_prob_target_fun) && is.null(log_ratio_fun)) {
         update_properties <- list(
@@ -598,26 +603,22 @@
   # and add tests for that
 
   # transform the model parameters to unconstrained space
-  udraws <- x$unconstrain_draws()
-  udraws <- aperm(
-    abind::abind(
-      lapply(udraws, function(x) abind::abind(x, along = 2)),
-      along = 3
-    ),
-    perm = c(2, 3, 1)
-  )
+    udraws <- x$unconstrain_draws(format = "draws_matrix")
 
-  udraws <- matrix(
-    udraws,
-    nrow = dim(udraws)[1] * dim(udraws)[2],
-    ncol = dim(udraws)[3]
-  )
+  if (constrain_draws) {
+    draws_transformation_fun <- function(draws, ...) {
+      return(constrain_draws(x, draws, ...))
+    }
+  } else {
+    draws_transformation_fun <- NULL
+  }
 
-  out <- moment_match.matrix(
+  out <- moment_match(
     x = udraws,
     log_prob_prop_fun = log_prob_draws.CmdStanFit,
     log_prob_target_fun = log_prob_target_fun,
     log_ratio_fun = log_ratio_fun,
+    draws_transformation_fun = draws_transformation_fun,
     fit = x,
     ...
   )
@@ -697,11 +698,11 @@
 
 
   # transform the draws to unconstrained space
-  udraws <- unconstrain_draws.stanfit(x, draws = draws, ...)
+  udraws <- unconstrain_draws(x, draws = draws, ...)
 
   if (constrain_draws) {
     draws_transformation_fun <- function(draws, ...) {
-      return(constrain_draws.stanfit(x, draws, ...))
+      return(constrain_draws(x, draws, ...))
     }
   } else {
     draws_transformation_fun <- NULL

R/update_quantities.R

@@ -42,12 +42,15 @@ update_quantities <- function(draws, orig_log_prob_prop,
     )
   }
 
-  pareto_smoothed_w_new <- posterior::pareto_smooth(exp(lw_new - matrixStats::logSumExp(lw_new)),
-                                                    tail = "right", r_eff = 1,
-                                                    return_k = TRUE
+  pareto_smoothed_w_new <- posterior::pareto_smooth(
+    lw_new - matrixStats::logSumExp(lw_new),
+    are_log_weights = TRUE,
+    tail = "right", r_eff = 1, return_k = TRUE,
+    verbose = FALSE
   )
   k <- pareto_smoothed_w_new$diagnostics$khat
-  lw <- log(as.vector(pareto_smoothed_w_new$x))
+  lw <- as.vector(pareto_smoothed_w_new$x)
+
   # normalize log weights
   lw <- lw - matrixStats::logSumExp(lw)