From a7b07621affdaf2e23f8055225de4365ac78bc30 Mon Sep 17 00:00:00 2001
From: bjaeger <bjaeger@wakehealth.edu>
Date: Thu, 5 Oct 2023 00:16:10 -0400
Subject: [PATCH] smoothing the new tests

---
 man/orsf.Rd                        | 18 ++++++------------
 tests/testthat/test-leaf_kaplan.R  |  6 ++++--
 tests/testthat/test-orsf_formula.R |  6 +++---
 tests/testthat/test-orsf_vi.R      |  2 ++
 4 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/man/orsf.Rd b/man/orsf.Rd
index 67b98670..fe59b988 100644
--- a/man/orsf.Rd
+++ b/man/orsf.Rd
@@ -383,8 +383,7 @@ function to find linear combinations of predictors.
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{fit_accel <- orsf(pbc_orsf, 
                   control = orsf_control_fast(),
-                  formula = Surv(time, status) ~ . - id,
-                  tree_seeds = 1:500)
+                  formula = Surv(time, status) ~ . - id)
 }\if{html}{\out{</div>}}
 }
 
@@ -396,8 +395,7 @@ combinations of predictors:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{fit_cph <- orsf(pbc_orsf, 
                 control = orsf_control_cph(),
-                formula = Surv(time, status) ~ . - id,
-                tree_seeds = 1:500)
+                formula = Surv(time, status) ~ . - id)
 }\if{html}{\out{</div>}}
 }
 
@@ -413,8 +411,7 @@ than the other options.
                 # select 3 predictors out of 5 to be used in
                 # each linear combination of predictors.
                 control = orsf_control_net(df_target = 3),
-                formula = Surv(time, status) ~ . - id,
-                tree_seeds = 1:500)
+                formula = Surv(time, status) ~ . - id)
 }\if{html}{\out{</div>}}
 }
 
@@ -475,17 +472,14 @@ the result into \code{orsf()}:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{fit_rando <- orsf(pbc_orsf,
                   Surv(time, status) ~ . - id,
-                  control = orsf_control_custom(beta_fun = f_rando),
-                  tree_seeds = 1:500)
+                  control = orsf_control_custom(beta_fun = f_rando))
 
 fit_pca <- orsf(pbc_orsf,
                 Surv(time, status) ~ . - id,
-                control = orsf_control_custom(beta_fun = f_pca),
-                tree_seeds = 1:500)
+                control = orsf_control_custom(beta_fun = f_pca))
 
 fit_rlt <- orsf(pbc_orsf, time + status ~ . - id, 
-                control = orsf_control_custom(beta_fun = f_aorsf),
-                tree_seeds = 1:500)
+                control = orsf_control_custom(beta_fun = f_aorsf))
 }\if{html}{\out{</div>}}
 
 So which fit seems to work best in this example? Let’s find out by
diff --git a/tests/testthat/test-leaf_kaplan.R b/tests/testthat/test-leaf_kaplan.R
index d9ccd61b..f9156c47 100644
--- a/tests/testthat/test-leaf_kaplan.R
+++ b/tests/testthat/test-leaf_kaplan.R
@@ -6,11 +6,13 @@
 #' @srrstats {G5.5} *Correctness tests are run with a fixed random seed*
 set.seed(329)
 
+flc <- flc[flc$status==1, ]
+
 weights <- sample(1:5, nrow(flc), replace = TRUE)
 
 # fit a normal tree with no bootstrap weights
 fit <- orsf(flc,
-            futime + death ~ .,
+            time + status ~ .,
             n_tree = 1,
             weights = weights,
             tree_seeds = 1,
@@ -27,7 +29,7 @@ fit <- orsf(flc,
 aorsf_surv <- fit$forest$leaf_pred_prob[[1]][[1]]
 aorsf_time <- fit$forest$leaf_pred_indx[[1]][[1]]
 
-kap <- survfit(Surv(futime, death) ~ 1, data = flc, weights = weights)
+kap <- survfit(Surv(time, status) ~ 1, data = flc, weights = weights)
 
 test_that(
  desc = 'aorsf kaplan has same time values as survfit',
diff --git a/tests/testthat/test-orsf_formula.R b/tests/testthat/test-orsf_formula.R
index ac48a3c7..cccb2ec8 100644
--- a/tests/testthat/test-orsf_formula.R
+++ b/tests/testthat/test-orsf_formula.R
@@ -68,7 +68,7 @@ test_that(
   # keeps unique names
   expect_equal(x_vars, get_names_x(fit_long))
   # is the same forest as standard
-  expect_equal_leaf_summary(fit_long, fit_standard)
+  expect_equal_leaf_summary(fit_long, fit_standard_pbc)
 
  }
 )
@@ -95,7 +95,7 @@ test_that(
   )
 
   # different formula but same as standard forest
-  expect_equal_leaf_summary(fit_surv, fit_standard)
+  expect_equal_leaf_summary(fit_surv, fit_standard_pbc)
  }
 )
 
@@ -111,7 +111,7 @@ test_that(
                               n_tree = 10,
                               tree_seeds = seeds_standard)
 
-  expect_equal_leaf_summary(fit_status_modified, fit_standard)
+  expect_equal_leaf_summary(fit_status_modified, fit_standard_pbc)
 
   expect_error(
    orsf(pbc_orsf, Surv(status, time) ~ . - id),
diff --git a/tests/testthat/test-orsf_vi.R b/tests/testthat/test-orsf_vi.R
index 56517df8..e66026b6 100644
--- a/tests/testthat/test-orsf_vi.R
+++ b/tests/testthat/test-orsf_vi.R
@@ -140,6 +140,8 @@ test_that(
  desc = 'informative errors for custom functions',
  code = {
 
+  fit_no_vi <- orsf(pbc_vi, formula, importance = 'none', n_tree = 1)
+
   expect_error(
    orsf_vi_anova(object = 'nope'),
    regexp = 'inherit'