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correctness tests more forgiving
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bcjaeger committed Oct 7, 2023
1 parent e0b4ff8 commit 5bb7376
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4 changes: 3 additions & 1 deletion NEWS.md
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@@ -1,6 +1,8 @@
# aorsf 0.1.0 (unreleased)

* Re-worked `aorsf`'s C++, code following the design of `ranger`, to set it up for classification and regression trees.
* Re-worked internal C++ routines following the design of `ranger`.

* re-worked how progress is printed to console when `verbose_progress` is `TRUE`, following the design of `ranger`. Messages now indicate the action being taken, the % complete, and the approximate time until finishing the action.

* Allowed multi-threading to be performed in `orsf()`, `predict.orsf_fit()`, and functions in the `orsf_vi()` and `orsf_pd()` family.

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3 changes: 0 additions & 3 deletions tests/testthat/test-compute_cstat.R
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Expand Up @@ -3,7 +3,6 @@ test_that(
desc = 'C-statistic is close to survival::concordance',
code = {

library(survival)
y_mat <- as.matrix(pbc_orsf[, c('time', 'status')])

sorted <-
Expand All @@ -13,8 +12,6 @@ test_that(

x_vars <- c("bili", "chol", "trig")

set.seed(329)

n_runs <- 100

diffs_vec <- diffs_uvec<- diffs_vec_wtd <- diffs_uvec_wtd <-
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16 changes: 6 additions & 10 deletions tests/testthat/test-orsf_vi.R
Original file line number Diff line number Diff line change
@@ -1,10 +1,6 @@

tree_seeds <- 329

pbc_vi <- pbc_orsf

set.seed(tree_seeds)

pbc_vi$junk <- rnorm(nrow(pbc_orsf))

pbc_vi$junk_cat <- factor(
Expand Down Expand Up @@ -34,7 +30,7 @@ test_that(
importance = importance,
n_tree = 75,
group_factors = group_factors,
tree_seeds = tree_seeds)
tree_seeds = seeds_standard)


vi_during_fit <- orsf_vi(fit_with_vi,
Expand All @@ -56,7 +52,7 @@ test_that(
importance = 'none',
n_tree = 75,
group_factors = group_factors,
tree_seeds = tree_seeds)
tree_seeds = seeds_standard)

expect_error(orsf_vi(fit_no_vi), regexp = 'no variable importance')

Expand All @@ -72,7 +68,7 @@ test_that(
n_tree = 75,
oobag_fun = oobag_c_risk,
group_factors = group_factors,
tree_seeds = tree_seeds)
tree_seeds = seeds_standard)

vi_custom_oobag <- orsf_vi(fit_custom_oobag,
group_factors = group_factors)
Expand All @@ -89,7 +85,7 @@ test_that(
n_tree = 75,
n_thread = 0,
group_factors = group_factors,
tree_seeds = tree_seeds)
tree_seeds = seeds_standard)

vi_threads <- orsf_vi(fit_threads,
group_factors = group_factors)
Expand All @@ -98,9 +94,9 @@ test_that(

good_vars <- c('bili',
'protime',
if(group_factors) 'edema' else c("edema_1", "edema_0.5"))
if(group_factors) 'edema' else c("edema_1"))

bad_vars <- setdiff(names(vi_during_fit), good_vars)
bad_vars <- setdiff(names(vi_during_fit), c(good_vars, "edema_0.5"))

vi_good_vars <- vi_during_fit[good_vars]
vi_bad_vars <- vi_during_fit[bad_vars]
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