Avoid Matrix::diagonal and limit progress bar updates (#47)

* Use diag rather than Matrix::diagonal

* Limit progress bar updates

* Increase maximum complexity in lintr config

.lintr

@@ -1,6 +1,7 @@
 linters: linters_with_defaults(
     line_length_linter = line_length_linter(88L),
-    object_length_linter = object_length_linter(length=50L)
+    object_length_linter = object_length_linter(length=50L),
+    cyclocomp_linter = cyclocomp_linter(complexity_limit = 25L)
   )
 encoding: "UTF-8"
 exclusions: list(

R/chains.R

@@ -162,6 +162,9 @@ chain_loop <- function(
     trace_function,
     statistic_names) {
   progress_bar <- get_progress_bar(use_progress_bar, n_iteration, stage_name)
+  # Only show 10% increments in progress bar to avoid progress bar updates being
+  # a bottleneck when chain iteration rate is high
+  tick_amount <- max(n_iteration %/% 10, 1)
   for (adapter in adapters) {
     adapter$initialize(proposal, state)
   }
@@ -191,8 +194,13 @@ chain_loop <- function(
         c(state_and_statistics$statistics, adapter_states)
       )
     }
-    if (!is.null(progress_bar)) progress_bar$tick()
+    if (!is.null(progress_bar) && (chain_iteration %% tick_amount == 0)) {
+      progress_bar$tick(tick_amount)
+    }
   }
+  # Ensure progress bar shows completed in cases tick_amount not a factor of
+  # n_iteration
+  if (!is.null(progress_bar) && !progress_bar$finished) progress_bar$update(1)
   for (adapter in adapters) {
     if (!is.null(adapter$finalize)) adapter$finalize(proposal)
   }

R/proposal.R

@@ -7,7 +7,7 @@ get_shape_matrix <- function(scale, shape) {
     stop("Scale should be a non-negative scalar")
   }
   if (!is.null(shape) && is_non_scalar_vector(shape)) {
-    shape <- Matrix::Diagonal(x = shape)
+    shape <- diag(shape)
   }
   if (is.null(scale) && is.null(shape)) {
     stop("One of scale and shape parameters must be set")

tests/testthat/test-proposal.R

@@ -11,8 +11,8 @@ test_that("get_shape_matrix works", {
   expect_identical(get_shape_matrix(NULL, 1), 1)
   expect_identical(get_shape_matrix(0.5, 3), 1.5)
   expect_identical(get_shape_matrix(0.5, 3), 1.5)
-  expect_identical(get_shape_matrix(2, c(3, 0.5)), Matrix::Diagonal(x = c(6, 1)))
-  expect_identical(get_shape_matrix(NULL, c(3, 2)), Matrix::Diagonal(x = c(3, 2)))
+  expect_identical(get_shape_matrix(2, c(3, 0.5)), diag(x = c(6, 1)))
+  expect_identical(get_shape_matrix(NULL, c(3, 2)), diag(x = c(3, 2)))
   expect_identical(get_shape_matrix(0.5, diag(3, 2)), diag(1.5, 2))
   expect_identical(get_shape_matrix(NULL, diag(3)), diag(3))
   expect_error(get_shape_matrix(NULL, NULL), "must be set")