Merge pull request #97 from jsocolar/reduce-size

Reduce size
jsocolar · Dec 5, 2023 · 1b3982b · 1b3982b
2 parents 04d77cd + 2327b89
commit 1b3982b
Show file tree

Hide file tree

Showing 13 changed files with 15 additions and 15 deletions.
diff --git a/data-raw/example_flocker_model.R b/data-raw/example_flocker_model.R
@@ -15,7 +15,7 @@ example_flocker_model_single <- flock(
   backend = "cmdstanr",
   cores = 4,
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 #### single-season rep-constant model ####
@@ -30,7 +30,7 @@ example_flocker_model_single_C <- flock(
   backend = "cmdstanr",
   cores = 4,
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 #### data augmented model ####
@@ -51,7 +51,7 @@ example_flocker_model_aug <- flock(
   backend = "cmdstanr",
   cores = 4,
   iter = 1000,
-  warmup = 990
+  warmup = 996
   )
 
 #### multiseason colex with explicit inits ####
@@ -74,7 +74,7 @@ example_flocker_model_multi_colex_ex <- flock(
   cores = 4,
   backend = "cmdstanr",
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 #### multiseason colex with equilibrium inits ####
@@ -96,7 +96,7 @@ example_flocker_model_multi_colex_eq <- flock(
   cores = 4,
   backend = "cmdstanr",
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 #### multiseason autologistic with explicit inits ####
@@ -119,7 +119,7 @@ example_flocker_model_multi_auto_ex <- flock(
   cores = 4,
   backend = "cmdstanr",
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 #### multiseason autologistic with equilibrium inits ####
@@ -141,7 +141,7 @@ example_flocker_model_multi_auto_eq <- flock(
   cores = 4,
   backend = "cmdstanr",
   iter = 1000,
-  warmup = 990
+  warmup = 996
 )
 
 usethis::use_data(example_flocker_model_single, overwrite = TRUE)

diff --git a/data/example_flocker_model_aug.rda b/data/example_flocker_model_aug.rda
diff --git a/data/example_flocker_model_multi_auto_eq.rda b/data/example_flocker_model_multi_auto_eq.rda
diff --git a/data/example_flocker_model_multi_auto_ex.rda b/data/example_flocker_model_multi_auto_ex.rda
diff --git a/data/example_flocker_model_multi_colex_eq.rda b/data/example_flocker_model_multi_colex_eq.rda
diff --git a/data/example_flocker_model_multi_colex_ex.rda b/data/example_flocker_model_multi_colex_ex.rda
diff --git a/data/example_flocker_model_single.rda b/data/example_flocker_model_single.rda
diff --git a/data/example_flocker_model_single_C.rda b/data/example_flocker_model_single_C.rda
diff --git a/man/figures/logo2.png b/man/figures/logo2.png
diff --git a/man/figures/logo3.png b/man/figures/logo3.png
diff --git a/tests/test_data/test_fit.rds b/tests/test_data/test_fit.rds
diff --git a/tests/testthat/test-log_lik_functions.R b/tests/testthat/test-log_lik_functions.R
@@ -1,9 +1,9 @@
 test_that("check log_lik functions work correctly", {
   # check dims
   ll_test <- log_lik_flocker(example_flocker_model_single)
-  expect_equal(dim(ll_test), c(40, 900))
-  ll_test <- log_lik_flocker(example_flocker_model_single, draw_ids = 1:20)
-  expect_equal(dim(ll_test), c(20, 900))
+  expect_equal(dim(ll_test), c(16, 900))
+  ll_test <- log_lik_flocker(example_flocker_model_single, draw_ids = 1:10)
+  expect_equal(dim(ll_test), c(10, 900))
 
   # check classes/values
   expect_equal(class(ll_test), c("matrix", "array"))

diff --git a/tests/testthat/test-loo_flocker.R b/tests/testthat/test-loo_flocker.R
@@ -1,6 +1,6 @@
 test_that("loo_flocker_onefit works correctly", {
   suppressWarnings(test_loo <- loo_flocker(example_flocker_model_single))
-  suppressWarnings(test_loo_thinned <- loo_flocker(example_flocker_model_single, 5))
+  suppressWarnings(test_loo_thinned <- loo_flocker(example_flocker_model_single, 2))
   suppressWarnings(test_loo_list <- loo_flocker(rep(list(example_flocker_model_single), 2)))
 
   # check error
@@ -10,7 +10,7 @@ test_that("loo_flocker_onefit works correctly", {
   expect_error(loo_flocker(list(example_flocker_model_single, 1)), "x is a list, but x\\[\\[2\\]\\] is not a flocker_fit object.")
 
   # check dims
-  expect_equal(attributes(test_loo)$dims, c(40, 900))
+  expect_equal(attributes(test_loo)$dims, c(16, 900))
   expect_equal(attributes(test_loo_thinned)$dims, c(8, 900))
 
   # check list output
@@ -26,10 +26,10 @@ test_that("loo_flocker_onefit works correctly", {
 
   suppressWarnings(test_loo <- loo_flocker_onefit(example_flocker_model_single, thin = NULL))
   suppressWarnings(test_loo_alt <- loo_flocker_onefit(example_flocker_model_single, thin=1))
-  suppressWarnings(test_loo_thinned <- loo_flocker_onefit(example_flocker_model_single, thin = 5))
+  suppressWarnings(test_loo_thinned <- loo_flocker_onefit(example_flocker_model_single, thin = 2))
 
   # check dimensions
-  expect_equal(attributes(test_loo)$dims, c(40, 900))
+  expect_equal(attributes(test_loo)$dims, c(16, 900))
   expect_equal(attributes(test_loo_thinned)$dims, c(8, 900))
 
   # check thin = NULL specification returns same output 
@@ -42,7 +42,7 @@ test_that("loo_flocker_onefit works correctly", {
 
   # check model naming
   suppressWarnings(test_compare <- loo_compare_flocker(list(example_flocker_model_single, example_flocker_model_single), 
-                                      model_names = c("m1", "m2"), thin = 5))
+                                      model_names = c("m1", "m2"), thin = 2))
   expect_identical(row.names(test_compare), c("m1", "m2"))
 
   # check test output identical