Last updated on 2022-09-11 12:56:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 667.97 | 230.54 | 898.51 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 515.40 | 174.57 | 689.97 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 1210.54 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 1233.54 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.1 | 857.00 | 375.00 | 1232.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.1 | 543.59 | 222.06 | 765.65 | OK | |
| r-release-linux-x86_64 | 1.0.1 | 537.02 | 227.51 | 764.53 | OK | |
| r-release-macos-arm64 | 1.0.1 | 280.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.1 | 332.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.1 | 653.00 | 374.00 | 1027.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.1 | 267.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.1 | 316.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 1497.00 | 423.00 | 1920.00 | NOTE |
Version: 1.0.1
Check: installed package size
Result: NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
data 4.2Mb
doc 1.7Mb
libs 2.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [91s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # Had the same issue as in this thread: https://github.com/hadley/testthat/issues/86
> # or maybe https://github.com/r-lib/devtools/issues/1526
> Sys.unsetenv("R_TESTS")
>
> options(deparse.max.lines = 5, testthat.summary.max_reports = 1000L)
> testthat::test_check("dynamichazard", reporter = "summary")
Loading required package: dynamichazard
Loading required package: survival
Tracing function "expect_known_value" in package "testthat"
Tracing function "expect_known_output" in package "testthat"
Loading required package: DBI
GMA:
Running tests for GMA: 12......345.......
LAPACK_BLAS:
Testing LAPACK wrapper functions: ..............................................
PF:
Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSSS..S..SS..SSSSSSSSSSSS
SMA:
Testing SMA: ........6.......S78........9...
UKF:
Testing UKF: .abc...d......e..........
bigglm_wrapper:
Testing bigglm_wrapper: ......SS
boot_est:
Testing boot: ...S.f................................................................................................................................................................................................................................................................................................................................................................................................................
cloglog:
testing cloglog link function: ghijS
cpp_sample_funcs:
Testing cpp sampling functions: S..S.............................................................S....
cpp_utils:
Running test_cpp_utils.R:: .S............
ddhazard_n_EKF:
Testing ddhazard w/ generic things and w/ the the EKF: k...........l........S.........m......
design_mat_and_risk_obj:
Testing design_mat_and_risk_obj: ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
fixed_effects_in_E_step:
Testing fixed_effects_in_E_step: nopWqr.stu
fixed_effects_in_M_step:
Testing test_fixed_effects_in_M_step: .v.....wxyS..
get_start_values:
Testing 'get_start_values': ....................
hatvalues:
Running tests for hatvalues: zWABWC
help_page_examples:
Testing examples in man files: ..DEFGHSIS....SSSSJKLM.NO.S
loglike:
Testing loglike: ............P...QR..WWSTWUV
options:
Testing options: .
parallelglm:
Testing parallelglm vs. glm: ................................................S
plot:
Testing plot functions: ..................W....................
predict:
Testing predict: ...............................................................................SS
print:
Testing print function: ...SSW.X..
residuals:
Testing residuals functions: ..................................................................................................................................................................................................SS
shiny_app:
Testing shiny app: S..
static_glm:
Testing static_glm: .............................
summary:
Testing summary function: YZFF.FF.FF.FFFFFF
test_utils:
Testing test_utils: ............S......................................
weights:
Testing weights in fit: ................
══ Skipped ═════════════════════════════════════════════════════════════════════
1. PF_smooth gives same results (test_PF.R:71:3) - Reason: On CRAN
2. Import and export PF cloud from Rcpp gives the same (test_PF.R:251:3) - Reason: On CRAN
3. PF_EM gives previous results on head neck data set (test_PF.R:344:3) - Reason: On CRAN
4. PF_EM gives previous results on head neck data set with fixed effects and the logit model (test_PF.R:411:3) - Reason: On CRAN
5. compute_PF_summary_stats gives previous results (test_PF.R:436:3) - Reason: On CRAN
6. 'get_cloud_means' and 'get_cloud_quantiles' gives previous results (test_PF.R:510:3) - Reason: On CRAN
7. 'get_ancestors' yields the correct result (test_PF.R:560:3) - Reason: On CRAN
8. ´est_params_dens´ gives the same as a R version (test_PF.R:582:3) - Reason: On CRAN
9. fixed effect estimation gives the same as an R implementation (test_PF.R:630:3) - Reason: On CRAN
10. A few iterations with `type = "VAR"' yields the same as before (test_PF.R:711:3) - Reason: On CRAN
11. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (test_PF.R:783:3) - Reason: On CRAN
12. Using `n_smooth_final` works as expected and yields previous results (test_PF.R:896:3) - Reason: On CRAN
13. sampling with a t-distribution gives previous results (test_PF.R:964:3) - Reason: On CRAN
14. 'PF_forward_filter' gives the same as 'PF_EM' when it should (test_PF.R:1002:3) - Reason: On CRAN
15. 'state_fw' gives correct results (test_PF.R:1131:3) - Reason: !dir.exists("pf-internals") is TRUE
16. 'state_bw' gives correct results (test_PF.R:1167:3) - Reason: !dir.exists("pf-internals") is TRUE
17. 'artificial_prior' gives correct results (test_PF.R:1202:3) - Reason: !dir.exists("pf-internals") is TRUE
18. 'observational_cdist' gives correct results (test_PF.R:1236:3) - Reason: !dir.exists("pf-internals") is TRUE
19. combining forward and backwards works (test_PF.R:1281:3) - Reason: !dir.exists("pf-internals") is TRUE
20. combining prior and backwards works (test_PF.R:1328:3) - Reason: !dir.exists("pf-internals") is TRUE
21. mode approximations give expected result (test_PF.R:1366:3) - Reason: !dir.exists("pf-internals") is TRUE
22. 'PF_get_score_n_hess' gives the same as an R implementation (test_PF.R:1486:3) - Reason: On CRAN
23. warns with randow walk model when covariates are in both fixed and random (test_PF.R:1624:3) - Reason: On CRAN
24. works when there are time periods outside where we have data and with a single fixed and random effect (test_PF.R:1645:3) - Reason: On CRAN
25. 'fix_seed = FALSE' yields different results at each call (test_PF.R:1670:3) - Reason: On CRAN
26. Chaning the learning changes the result for the posterior approx method (test_SMA.R:120:3) - Reason: On CRAN
27. bigglm and my c++ version yields similar results with offsets (test_bigglm_wrapper.R:298:5) - Reason: bigglm failed (likely biglm error in 0.9-1 release)
28. bigglm and my c++ version yields similar with weights (test_bigglm_wrapper.R:328:5) - Reason: bigglm failed (likely biglm error in 0.9-1 release)
29. boot yields previously computed values with pbc (test_boot_est.R:19:3) - Reason: On CRAN
30. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (test_cloglog.R:56:3) - Reason: On CRAN
31. sample_indices give the same as R with same seed (test_cpp_sample_funcs.R:4:3) - Reason: On CRAN
32. mvrnorm gives expected sample mean and variance (test_cpp_sample_funcs.R:51:3) - Reason: On CRAN
33. 'mvtrnorm' yields close to uniform sample (test_cpp_sample_funcs.R:112:3) - Reason: On CRAN
34. trunc_lp_in_exponential_dist does not truncate when not needed (test_cpp_utils.R:12:3) - Reason: On CRAN
35. Different non-integer time_scales gives the same result with ddhazard (test_ddhazard_n_EKF.R:165:3) - Reason: On CRAN
36. posterior_approx gives previous found values with fixed effects in M-step (test_fixed_effects_in_M_step.R:187:3) - Reason: On CRAN
37. residuals.ddhazard help page examples gives the same results (test_help_page_examples.R:43:3) - Reason: On CRAN
38. ddhazard_boot help page examples gives the same results (test_help_page_examples.R:67:3) - Reason: On CRAN
39. PF_EM help page example runs and gives previous computed results (test_help_page_examples.R:129:3) - Reason: On CRAN
40. Second example on PF help page gives the same result (test_help_page_examples.R:171:3) - Reason: On CRAN
41. example in 'PF_EM' with gives previous results w/ a few iterations (test_help_page_examples.R:227:3) - Reason: On CRAN
42. `PF_forward_filter` the results stated in the comments and does not alter the .Random.seed as stated on the help page (test_help_page_examples.R:358:3) - Reason: On CRAN
43. 'PF_get_score_n_hess' gives previous results (test_help_page_examples.R:516:3) - Reason: On CRAN
44. glm and parallelglm gives the same (test_parallelglm.R:80:3) - Reason: On CRAN
45. Terms from predict with exponential outcome are correct (test_predict.R:413:3) - Reason: On CRAN
46. Different non-integer time_scales gives the same result with predict results (test_predict.R:474:3) - Reason: On CRAN
47. print.ddhazard_boot gives the expected output (test_print.R:39:3) - Reason: On CRAN
48. Print function for PF objects gives previous results (test_print.R:89:3) - Reason: On CRAN
49. Gets previous results with Rossi (test_residuals.R:209:3) - Reason: On CRAN
50. Get prevoius residuals with whas500 (test_residuals.R:236:3) - Reason: On CRAN
51. Shiny app starts when no arguments are passed (test_shiny_app.R:3:1) - Reason: empty test
52. Testing util functions to sim series for tests (test_test_utils.R:28:3) - Reason: On CRAN
══ Warnings ════════════════════════════════════════════════════════════════════
1. Works with UKF and logit model (test_fixed_effects_in_E_step.R:60:2) - EM algorithm did not converge within the n_max number of iterations
2. hatvalues works with dynamic effects only and gives previous results (test_hatvalues.R:34:3) - EM algorithm did not converge within the n_max number of iterations
3. hatvalues works with dynamic and fixed effects and gives previous results (test_hatvalues.R:65:3) - EM algorithm did not converge within the n_max number of iterations
4. logLik for simulated data versus old results (test_loglike.R:170:3) - EM algorithm did not converge within the n_max number of iterations
5. logLik for simulated data versus old results (test_loglike.R:181:3) - Failed at least once to invert Q in the log likelihood evaluation with symmetrical inversion method
6. logLik for simulated data versus old results (test_loglike.R:210:3) - EM algorithm did not converge within the n_max number of iterations
7. Alters mfcol and sets it back (test_plot.R:74:3) - EM algorithm did not converge within the n_max number of iterations
══ Failed ══════════════════════════════════════════════════════════════════════
── 1. Failure (test_GMA.R:16:3): Gives same results w/ 1. order logit model ────
`result` not equal to read_to_test("GMA_head_neck_cancer_o1").
Component "state_vecs": Mean relative difference: 0.0285492
Component "state_vars": Mean relative difference: 0.06002911
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_GMA.R:16:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 2. Failure (test_GMA.R:35:3): GMA gives the same w/ all exponential model inp
`f1` not equal to read_to_test("GMA_pbc_o1_exp").
Component "state_vecs": Mean relative difference: 0.02391656
Component "state_vars": Mean relative difference: 0.02316135
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_GMA.R:35:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 3. Failure (test_GMA.R:57:3): GMA works w/ second order random walk ─────────
`f1` not equal to read_to_test("GMA_pbc_o2_logit").
Component "state_vecs": Mean relative difference: 0.1223048
Component "state_vars": Mean relative difference: 0.03491603
Component "Q": Mean relative difference: 0.2259844
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_GMA.R:57:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 4. Failure (test_GMA.R:73:3): GMA works w/ fixed effects in E-step ──────────
`fit` not equal to read_to_test("GMA_pbc_fixed_E_step").
Component "state_vecs": Mean relative difference: 0.01152096
Component "state_vars": Mean relative difference: 0.006768784
Component "fixed_effects": Mean relative difference: 0.01350639
Component "Q": Mean relative difference: 0.1047468
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_GMA.R:73:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 5. Failure (test_GMA.R:91:3): GMA works w/ fixed effects in M-step ──────────
`fit` not equal to read_to_test("GMA_pbc_fixed_M_step").
Component "state_vecs": Mean relative difference: 0.09895941
Component "state_vars": Mean relative difference: 0.0452854
Component "fixed_effects": Mean relative difference: 0.6456444
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_GMA.R:91:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 6. Failure (test_SMA.R:59:3): Logit model for posterior_approx gives previous
`f1` has changed from known value recorded in './previous_results/posterior_approx_logit_pbc.RDS'.
Component "state_vecs": Mean relative difference: 0.01252619
Component "state_vecs": Mean relative difference: 0.01252619
── 7. Failure (test_SMA.R:164:3): Second order model gives previous found result
`f1` not equal to read_to_test("posterior_approx_logit_2_order").
Component "state_vecs": Mean relative difference: 0.03012467
Component "state_vecs": Mean relative difference: 0.03012467
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_SMA.R:164:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 8. Failure (test_SMA.R:179:3): Posterior gives previous found results with la
`f1` not equal to read_to_test("posterior_approx_logit_pbc_large_by").
Component "state_vecs": Mean relative difference: 0.05767921
Component "state_vecs": Mean relative difference: 0.05767921
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_SMA.R:179:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 9. Failure (test_SMA.R:232:3): Exponential model for posterior_approx gives p
`f1` not equal to read_to_test("posterior_approx_exp_pbc").
Component "state_vecs": Mean relative difference: 0.005300331
Component "state_vecs": Mean relative difference: 0.005300331
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_SMA.R:232:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 10. Failure (test_UKF.R:34:3): UKF on head_neck works with logit model ──────
`result` not equal to read_to_test("UKF1").
Component "state_vecs": Mean relative difference: 0.03331284
Component "state_vars": Mean relative difference: 0.05975059
Backtrace:
1. dynamichazard:::expect_equal(result, read_to_test("UKF1"))
at test_UKF.R:34:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 11. Failure (test_UKF.R:64:3): UKF does not fail and both methods give the sa
res_new$state_vecs not equal to res_old$state_vecs.
121/121 mismatches (average diff: 2.35e-06)
[1] -4.43 - -4.43 == -2.74e-06
[2] -4.33 - -4.33 == -2.14e-06
[3] -3.66 - -3.66 == -1.78e-06
[4] -3.63 - -3.63 == -1.49e-06
[5] -3.81 - -3.81 == -1.46e-06
[6] -4.04 - -4.04 == -1.87e-06
[7] -4.03 - -4.03 == -1.89e-06
[8] -4.03 - -4.03 == -1.90e-06
[9] -4.03 - -4.03 == -1.55e-06
...
Backtrace:
1. dynamichazard:::expect_equal(res_new$state_vecs, res_old$state_vecs)
at test_UKF.R:64:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 12. Failure (test_UKF.R:65:3): UKF does not fail and both methods give the sa
res_new$state_vars not equal to res_old$state_vars.
1132/1331 mismatches (average diff: 2.13e-07)
[2] 0.01652 - 0.01652 == 1.63e-08
[3] -0.02729 - -0.02729 == -3.84e-08
[4] 0.00786 - 0.00786 == -2.30e-08
[6] -0.02283 - -0.02283 == 2.49e-08
[7] 0.04152 - 0.04152 == 3.01e-08
[10] 0.00914 - 0.00914 == 2.04e-08
[11] -0.01573 - -0.01573 == 1.53e-08
[12] 0.01652 - 0.01652 == 1.63e-08
[13] 0.16859 - 0.16859 == -3.09e-07
...
Backtrace:
1. dynamichazard:::expect_equal(res_new$state_vars, res_old$state_vars)
at test_UKF.R:65:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 13. Failure (test_UKF.R:124:3): Testing UKF against prev computed values ────
`res` not equal to read_to_test("UKF2").
Component "state_vars": Mean relative difference: 0.3299086
Component "Q": Mean relative difference: 0.741008
Backtrace:
1. dynamichazard:::expect_equal(res, read_to_test("UKF2"))
at test_UKF.R:124:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 14. Failure (test_UKF.R:187:3): UKF works on simulated data works with expone
`result_exp` has changed from known value recorded in './previous_results/UKF4.RDS'.
Component "state_vars": Mean relative difference: 0.2390712
Component "state_vecs": Mean relative difference: 0.1748968
Component "Q": Mean relative difference: 0.3488511
── 15. Failure (test_boot_est.R:97:3): Boot works with posterior_approx and give
`tmp` not equal to read_to_test("boot_posterior_approx").
Component "t0": Mean relative difference: 0.01723293
Component "t": Mean relative difference: 0.0237839
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_boot_est.R:97:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 16. Failure (test_cloglog.R:20:3): cloglog function gives previous result wit
fit[names(fit) %in% do_check] has changed from known value recorded in './previous_results/cloglog-sim-ekf-1-it.RDS'.
Component "state_vecs": Mean relative difference: 0.02811361
Component "fixed_effects": Mean relative difference: 0.005497433
Component "Q": Mean relative difference: 0.07592254
── 17. Failure (test_cloglog.R:31:3): cloglog function gives previous result wit
fit[names(fit) %in% do_check] has changed from known value recorded in './previous_results/cloglog-sim-ekf-more-it.RDS'.
Component "state_vecs": Mean relative difference: 0.02493511
Component "fixed_effects": Mean relative difference: 0.00417566
Component "Q": Mean relative difference: 0.07573582
── 18. Failure (test_cloglog.R:41:3): cloglog function gives previous result wit
fit[names(fit) %in% do_check] has changed from known value recorded in './previous_results/cloglog-sim-gma.RDS'.
Component "state_vecs": Mean relative difference: 0.02544887
Component "fixed_effects": Mean relative difference: 0.00408945
Component "Q": Mean relative difference: 0.09205915
── 19. Failure (test_cloglog.R:50:3): cloglog function gives previous result wit
`preds` has changed from known value recorded in './previous_results/cloglog-preds.RDS'.
Component "fits": Mean relative difference: 0.01026991
── 20. Failure (test_ddhazard_n_EKF.R:17:3): get previous results with head_neck
`result` not equal to read_to_test("ddhazard_head_neck").
Component "state_vecs": Mean relative difference: 0.03523593
Component "state_vars": Mean relative difference: 0.1743707
Component "lag_one_cov": Mean relative difference: 0.1392337
Backtrace:
1. dynamichazard:::expect_equal(result, read_to_test("ddhazard_head_neck"))
at test_ddhazard_n_EKF.R:17:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 21. Failure (test_ddhazard_n_EKF.R:117:3): Result of exponential model on hea
`result_exp` has changed from known value recorded in './previous_results/head_neck_exp.RDS'.
Component "state_vecs": Mean relative difference: 0.03190441
Component "state_vars": Mean relative difference: 0.1563975
Component "Q": Mean relative difference: 0.4377389
── 22. Failure (test_ddhazard_n_EKF.R:262:3): Result of exponential model gives
`result_exp` has changed from known value recorded in './previous_results/sim_exp.RDS'.
Component "state_vars": Mean relative difference: 1.0885
Component "state_vecs": Mean relative difference: 0.2911368
Component "Q": Mean relative difference: 1.291585
── 23. Failure (test_fixed_effects_in_E_step.R:17:11): Works with EKF and logit
`fit` not equal to read_to_test("E_step_fixed_head_neck").
Component "state_vecs": Mean relative difference: 0.002112043
Component "state_vars": Mean relative difference: 0.01084764
Component "Q": Mean relative difference: 0.01825154
Component "fixed_effects": Mean relative difference: 0.005204874
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_fixed_effects_in_E_step.R:17:10
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 24. Failure (test_fixed_effects_in_E_step.R:34:3): Gives previous results wit
`dd_fit` not equal to read_to_test("E_step_fixed_pbc").
Component "state_vars": Mean relative difference: 0.02486807
Component "state_vecs": Mean relative difference: 0.02772646
Component "Q": Mean relative difference: 0.03618232
Component "fixed_effects": Mean relative difference: 0.007311928
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_fixed_effects_in_E_step.R:34:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 25. Failure (test_fixed_effects_in_E_step.R:49:3): Works with EKF and contino
`fit` has changed from known value recorded in './previous_results/E_step_fixed_exp_head_neck.RDS'.
Component "state_vecs": Mean relative difference: 0.03565882
Component "state_vars": Mean relative difference: 0.1577926
Component "Q": Mean relative difference: 0.3350547
Component "fixed_effects": Mean relative difference: 0.05312166
── 26. Failure (test_fixed_effects_in_E_step.R:76:3): Works with UKF and logit m
`fit` not equal to read_to_test("E_step_sim_UKF").
Component "state_vars": Mean relative difference: 0.321167
Component "state_vecs": Mean relative difference: 0.4786628
Component "Q": Mean relative difference: 0.6686382
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_fixed_effects_in_E_step.R:76:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 27. Failure (test_fixed_effects_in_E_step.R:94:3): Works with second order ra
`fit` not equal to read_to_test("E_step_sim_EKF_order_two").
Component "state_vecs": Mean relative difference: 0.4639852
Component "Q": Mean relative difference: 0.5187474
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_fixed_effects_in_E_step.R:94:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 28. Failure (test_fixed_effects_in_E_step.R:133:3): Works with UKF and contin
`fit` has changed from known value recorded in './previous_results/E_step_sim_exp_UKF.RDS'.
Component "state_vars": Mean relative difference: 0.03747593
Component "state_vecs": Mean relative difference: 0.1012082
Component "Q": Mean relative difference: 0.07840899
── 29. Failure (test_fixed_effects_in_E_step.R:152:3): Works with second order r
`fit` has changed from known value recorded in './previous_results/E_step_sim_exp_UKF_order_two.RDS'.
Component "state_vars": Mean relative difference: 0.1455572
Component "state_vecs": Mean relative difference: 0.3259164
Component "Q": Mean relative difference: 0.2811269
── 30. Failure (test_fixed_effects_in_E_step.R:168:3): posterior_approx gives pr
`f1` has changed from known value recorded in './previous_results/posterior_approx_logit_fixed_E.RDS'.
Component "state_vecs": Mean relative difference: 0.01337207
Component "state_vecs": Mean relative difference: 0.01337207
── 31. Failure (test_fixed_effects_in_M_step.R:48:3): Get previous results with
`dd_fit` not equal to read_to_test("fixed_terms_pbc").
Component "state_vars": Mean relative difference: 0.02486807
Component "state_vecs": Mean relative difference: 0.02772646
Component "Q": Mean relative difference: 0.03618232
Component "fixed_effects": Mean relative difference: 0.007311928
Backtrace:
1. dynamichazard:::expect_equal(dd_fit, read_to_test("fixed_terms_pbc"))
at test_fixed_effects_in_M_step.R:48:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 32. Failure (test_fixed_effects_in_M_step.R:143:3): Gets previous results wit
`res1` has changed from known value recorded in './previous_results/fixed_terms1.RDS'.
Component "state_vars": Mean relative difference: 0.1138452
Component "state_vecs": Mean relative difference: 0.1238712
Component "fixed_effects": Mean relative difference: 0.007962499
── 33. Failure (test_fixed_effects_in_M_step.R:165:3): UKF with fixed effects wo
`fit` not equal to read_to_test("fixed_terms_UKF").
Component "state_vars": Mean relative difference: 0.03048427
Component "state_vecs": Mean relative difference: 0.1381641
Component "fixed_effects": Mean relative difference: 0.004059524
Backtrace:
1. dynamichazard:::expect_equal(fit, read_to_test("fixed_terms_UKF"))
at test_fixed_effects_in_M_step.R:165:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 34. Failure (test_fixed_effects_in_M_step.R:182:3): UKF with fixed effects wo
`fit` has changed from known value recorded in './previous_results/fixed_terms_UKF_exp.RDS'.
Component "state_vars": Mean relative difference: 0.03125271
Component "state_vecs": Mean relative difference: 0.01906509
Component "fixed_effects": Mean relative difference: 0.0008455944
── 35. Failure (test_hatvalues.R:31:3): hatvalues works with dynamic effects onl
`hats` not equal to read_to_test("hats_dym_Rossi").
Component 1: Mean relative difference: 0.5557248
Component 2: Mean relative difference: 0.2498971
Component 3: Mean relative difference: 0.2511235
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_hatvalues.R:31:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 36. Failure (test_hatvalues.R:45:3): hatvalues works with dynamic effects onl
`hats` not equal to read_to_test("hats_dym_whas500").
Component 1: Mean relative difference: 0.5890506
Component 2: Mean relative difference: 0.8200427
Component 3: 'is.NA' value mismatch: 0 in current 305 in target
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_hatvalues.R:45:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 37. Failure (test_hatvalues.R:62:3): hatvalues works with dynamic and fixed e
`hats` not equal to read_to_test("hats_dym_n_fixed_Rossi").
Component 1: Mean relative difference: 0.5234734
Component 2: Mean relative difference: 0.1441677
Component 3: Mean relative difference: 0.1026647
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_hatvalues.R:62:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 38. Failure (test_hatvalues.R:78:3): hatvalues works with dynamic and fixed e
`hats` not equal to read_to_test("hats_dym_n_fixed_whas500").
Component 1: Mean relative difference: 1.01135
Component 2: Mean relative difference: 0.9860124
Component 3: Mean relative difference: 0.9953203
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_hatvalues.R:78:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 39. Failure (test_help_page_examples.R:18:3): ddhazard help page examples giv
`pred` has changed from known value recorded in './previous_results/ddhazard_help_page_predict_response.RDS'.
Component "fits": Mean relative difference: 0.02164082
── 40. Failure (test_help_page_examples.R:21:3): ddhazard help page examples giv
`pred` has changed from known value recorded in './previous_results/ddhazard_help_page_predict_term.RDS'.
Component "terms": Component 1: Mean relative difference: 0.004300199
── 41. Failure (test_help_page_examples.R:26:3): ddhazard help page examples giv
`ll` has changed from known value recorded in './previous_results/ddhazard_help_page_loglike.RDS'.
Mean relative difference: 0.2239128
── 42. Failure (test_help_page_examples.R:30:3): ddhazard help page examples giv
`fit` has changed from known value recorded in './previous_results/ddhazard_help_page_order_one.RDS'.
Component "state_vecs": Mean relative difference: 0.007105684
Component "state_vars": Mean relative difference: 0.01206265
── 43. Failure (test_help_page_examples.R:39:3): ddhazard help page examples giv
`fit` has changed from known value recorded in './previous_results/ddhazard_help_page_order_two.RDS'.
Component "state_vecs": Mean relative difference: 0.01926281
Component "state_vars": Mean relative difference: 0.03541948
── 44. Failure (test_help_page_examples.R:63:3): hatvalues.ddhazard help page ex
hvs[1:2] has changed from known value recorded in './previous_results/hatvalues_help_page.RDS'.
Component 1: Mean relative difference: 0.1840772
Component 2: Mean relative difference: 0.005969771
── 45. Failure (test_help_page_examples.R:454:3): ddsurvcurve manual page exampl
`ddcurve` has changed from known value recorded in './previous_results/ddsurvcurve-fix-cont.RDS'.
Component "psurv": Mean relative difference: 0.004494265
Component "dhazard": Mean relative difference: 0.03174887
── 46. Failure (test_help_page_examples.R:455:3): ddsurvcurve manual page exampl
z$S(c((0:3) * 1000)) not equal to c(1, 0.967806836427118, 0.937426234451691, 0.904842879418892).
3/4 mismatches (average diff: 0.00419)
[2] 0.963 - 0.968 == -0.00433
[3] 0.933 - 0.937 == -0.00419
[4] 0.901 - 0.905 == -0.00405
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_help_page_examples.R:455:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 47. Failure (test_help_page_examples.R:460:3): ddsurvcurve manual page exampl
z$S(c((0:3) * 1000)) not equal to c(1, 0.866618493229879, 0.75375407181175, 0.64567672043475).
3/4 mismatches (average diff: 0.00837)
[2] 0.854 - 0.867 == -0.01283
[3] 0.746 - 0.754 == -0.00816
[4] 0.642 - 0.646 == -0.00413
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_help_page_examples.R:460:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 48. Failure (test_help_page_examples.R:476:3): ddsurvcurve manual page exampl
z$S(c((0:3) * 1000)) not equal to c(1, 0.831340175284127, 0.694231628800056, 0.423403100827788).
3/4 mismatches (average diff: 0.0199)
[2] 0.806 - 0.831 == -0.0255
[3] 0.673 - 0.694 == -0.0213
[4] 0.410 - 0.423 == -0.0130
Backtrace:
1. dynamichazard:::expect_equal(...)
at test_help_page_examples.R:476:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 49. Failure (test_help_page_examples.R:495:3): ddsurvcurve manual page exampl
`z` has changed from known value recorded in './previous_results/ddsurvcurve-fix-disc-1.RDS'.
Component "yold": Mean relative difference: 0.004465081
Component "psurv": Mean relative difference: 0.004465081
── 50. Failure (test_help_page_examples.R:501:3): ddsurvcurve manual page exampl
`z` has changed from known value recorded in './previous_results/ddsurvcurve-fix-disc-2.RDS'.
Component "yold": Mean relative difference: 0.001776025
Component "psurv": Mean relative difference: 0.001776025
── 51. Failure (test_loglike.R:61:3): logLik for head_neck_cancer data set match
`log_like` not equal to `old`.
Mean relative difference: 0.08749016
Backtrace:
1. dynamichazard:::expect_equal(log_like, old)
at test_loglike.R:61:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 52. Failure (test_loglike.R:114:3): logLik for head_neck_cancer data set with
`log_like` not equal to `old`.
Mean absolute difference: Inf
Backtrace:
1. dynamichazard:::expect_equal(log_like, old, tolerance = 1e-04)
at test_loglike.R:114:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 53. Failure (test_loglike.R:135:3): logLik for head_neck_cancer data set matc
`log_like` not equal to `old`.
Mean relative difference: 0.05468732
Backtrace:
1. dynamichazard:::expect_equal(log_like, old, tolerance = 0.005)
at test_loglike.R:135:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 54. Failure (test_loglike.R:186:3): logLik for simulated data versus old resu
`log_like` not equal to `old`.
Mean absolute difference: Inf
Backtrace:
1. dynamichazard:::expect_equal(log_like, old)
at test_loglike.R:186:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 55. Failure (test_loglike.R:206:3): logLik for simulated data versus old resu
`log_like` not equal to `old`.
Mean relative difference: 0.1717293
Backtrace:
1. dynamichazard:::expect_equal(log_like, old, tolerance = 0.001)
at test_loglike.R:206:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 56. Failure (test_loglike.R:229:3): logLik for simulated data versus old resu
`log_like` not equal to `old`.
'is.NA' value mismatch: 0 in current 1 in target
Backtrace:
1. dynamichazard:::expect_equal(log_like, old, tolerance = 1e-06)
at test_loglike.R:229:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 57. Failure (test_loglike.R:251:3): logLik for simulated data versus old resu
`log_like` not equal to `old`.
Mean relative difference: 0.114511
Backtrace:
1. dynamichazard:::expect_equal(log_like, old, tolerance = 1e-06)
at test_loglike.R:251:2
2. testthat::expect_equal(..., check.environment = FALSE)
at tests/testthat/helper.R:4:16
── 58. Failure (test_print.R:122:3): Print function for ddhazard_space_errors ob
Results have changed from known value recorded in './previous_results/std_space_error_print'.
old vs new
"Standardized state space errors from a model with 20 periods and 2 coefficients. The errors in the first 5 time periods are:"
" Coefficient"
- "Period (Intercept) group1"
+ "Period (Intercept) group1"
- " 1 -0.3063691 0.01592371"
+ " 1 0.2765201 0.42947615"
- " 2 0.0668897 0.15746972"
+ " 2 1.2715248 -2.44187831"
- " 3 0.6635947 0.65261772"
+ " 3 1.0591828 0.55902850"
- " 4 0.7938611 0.21916597"
+ " 4 0.9099885 0.06153994"
- " 5 1.2738940 1.10542988"
+ " 5 1.2627138 1.01258365"
── 59. Failure (test_print.R:126:3): Print function for ddhazard_space_errors ob
Results have changed from known value recorded in './previous_results/space_error_print'.
old vs new
"State space errors from a model with 20 periods and 2 coefficients. The errors in the first 5 time periods are:"
" Coefficient"
"Period (Intercept) group1"
- " 1 -0.09380651 0.005700393"
+ " 1 0.08495322 0.12634795"
- " 2 0.01752106 0.039134066"
+ " 2 0.36015472 -0.72932531"
- " 3 0.17683204 0.149767476"
+ " 3 0.29784565 0.11447487"
- " 4 0.21209763 0.027302980"
+ " 4 0.25169839 -0.02151633"
- " 5 0.33849448 0.244158825"
+ " 5 0.34231836 0.21442988"
── 60. Failure (test_summary.R:22:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_object.RDS'.
Component "coefficients": Mean relative difference: 0.05097401
Component "Q": Mean relative difference: 0.04466497
Backtrace:
1. dynamichazard (local) test_func(fit, file = "summary_ddhazard", update = FALSE)
at test_summary.R:22:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 61. Failure (test_summary.R:22:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_print'.
old[7:25] vs new[7:25]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd group1 sd "
- " 0 -2.806424 0.4064023 0.1519309 0.4488750"
+ " 0 -3.509650 0.4745462 0.9489301 0.5019166"
- " 2 -2.882709 0.3038966 0.1967654 0.3681009"
+ " 2 -3.064542 0.3866873 0.3459527 0.4292792"
- " 4 -2.493780 0.3060795 0.3738359 0.3596999"
+ " 4 -2.514998 0.3428695 0.4389113 0.3870829"
- " 6 -2.220863 0.2842865 0.6247045 0.3420799"
+ " 6 -2.235363 0.2933744 0.6501559 0.3521324"
- " 9 -2.888184 0.3244203 0.5569002 0.3892709"
+ " 9 -2.896428 0.3261371 0.5700679 0.3915364"
- "11 -3.211450 0.3551100 0.4901311 0.4309866"
+ "11 -3.217745 0.3561520 0.4998852 0.4320199"
- "13 -3.398163 0.3907957 0.6133135 0.4794959"
+ "13 -3.403157 0.3915261 0.6207233 0.4800482"
and 9 more ...
Backtrace:
1. dynamichazard (local) test_func(fit, file = "summary_ddhazard", update = FALSE)
at test_summary.R:22:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 62. Failure (test_summary.R:25:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_all_coef_object.RDS'.
Component "coefficients": Mean relative difference: 0.04640414
Component "Q": Mean relative difference: 0.04466497
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:25:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 63. Failure (test_summary.R:25:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_all_coef_print'.
old[7:36] vs new[7:36]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd group1 sd "
- " 0 -2.806424 0.4064023 0.1519309 0.4488750"
+ " 0 -3.509650 0.4745462 0.9489301 0.5019166"
- " 1 -2.900230 0.2963087 0.1576313 0.3710721"
+ " 1 -3.424697 0.4010118 1.0752780 0.4451899"
- " 2 -2.882709 0.3038966 0.1967654 0.3681009"
+ " 2 -3.064542 0.3866873 0.3459527 0.4292792"
- " 3 -2.705877 0.3083772 0.3465329 0.3669497"
+ " 3 -2.766696 0.3662213 0.4604276 0.4104354"
- " 4 -2.493780 0.3060795 0.3738359 0.3596999"
+ " 4 -2.514998 0.3428695 0.4389113 0.3870829"
- " 5 -2.155285 0.3000692 0.6179947 0.3550072"
+ " 5 -2.172679 0.3196961 0.6533411 0.3716108"
- " 6 -2.220863 0.2842865 0.6247045 0.3420799"
+ " 6 -2.235363 0.2933744 0.6501559 0.3521324"
and 20 more ...
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:25:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 64. Failure (test_summary.R:30:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_one_coef_object.RDS'.
Component "coefficients": Mean relative difference: 0.03266901
Component "Q": Mean relative difference: 0.04466497
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:30:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 65. Failure (test_summary.R:30:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_one_coef_print'.
old[7:25] vs new[7:25]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd "
- " 0 -2.806424 0.4064023"
+ " 0 -3.509650 0.4745462"
- " 2 -2.882709 0.3038966"
+ " 2 -3.064542 0.3866873"
- " 4 -2.493780 0.3060795"
+ " 4 -2.514998 0.3428695"
- " 6 -2.220863 0.2842865"
+ " 6 -2.235363 0.2933744"
- " 9 -2.888184 0.3244203"
+ " 9 -2.896428 0.3261371"
- "11 -3.211450 0.3551100"
+ "11 -3.217745 0.3561520"
- "13 -3.398163 0.3907957"
+ "13 -3.403157 0.3915261"
and 9 more ...
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:30:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 66. Failure (test_summary.R:37:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_one_digit_object.RDS'.
Component "coefficients": Mean relative difference: 0.05
Component "Q": Mean relative difference: 0.04
Backtrace:
1. dynamichazard (local) test_func(fit, file = "summary_ddhazard_one_digit", update = FALSE)
at test_summary.R:37:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 67. Failure (test_summary.R:37:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_one_digit_print'.
old[7:16] vs new[7:16]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd group1 sd "
- " 0 -3 0.4 0.2 0.4"
+ " 0 -4 0.5 0.9 0.5"
- " 2 -3 0.3 0.2 0.4"
+ " 2 -3 0.4 0.3 0.4"
- " 4 -2 0.3 0.4 0.4"
+ " 4 -3 0.3 0.4 0.4"
- " 6 -2 0.3 0.6 0.3"
+ " 6 -2 0.3 0.7 0.4"
" 9 -3 0.3 0.6 0.4"
"11 -3 0.4 0.5 0.4"
"13 -3 0.4 0.6 0.5"
old[20:25] vs new[20:25]
""
"The estimated diagonal entries of the covariance matrix in the state equation are:"
"(Intercept) group1 "
- " 0.10 0.09 "
+ " 0.11 0.09 "
""
"96 individuals used in estimation with 65 observed events."
Backtrace:
1. dynamichazard (local) test_func(fit, file = "summary_ddhazard_one_digit", update = FALSE)
at test_summary.R:37:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 68. Failure (test_summary.R:43:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_fixed_object.RDS'.
Component "coefficients": Mean relative difference: 0.00507805
Component "Q": Mean relative difference: 0.07106102
Component "fixed_effects": Mean relative difference: 0.01437951
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:43:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 69. Failure (test_summary.R:43:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_fixed_print'.
old[7:29] vs new[7:29]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd "
- " 0 -3.361807 0.4352707"
+ " 0 -3.364324 0.4598908"
- " 2 -3.144430 0.3373489"
+ " 2 -3.150289 0.3598381"
- " 4 -2.541832 0.3153470"
+ " 4 -2.534468 0.3234280"
- " 6 -2.199481 0.2769990"
+ " 6 -2.187812 0.2802740"
- " 9 -2.876340 0.3130687"
+ " 9 -2.883253 0.3186852"
- "11 -3.198257 0.3391213"
+ "11 -3.211435 0.3453979"
- "13 -3.355439 0.3704239"
+ "13 -3.369502 0.3779088"
and 13 more ...
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:43:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 70. Failure (test_summary.R:54:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_exp_object.RDS'.
Component "coefficients": Mean relative difference: 0.05227089
Component "Q": Mean relative difference: 0.08320196
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:54:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 71. Failure (test_summary.R:54:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_exp_print'.
old[7:25] vs new[7:25]
""
"Smoothed time-varying coefficients are:"
" (Intercept) sd group1 sd "
- " 0 -2.798676 0.4089161 0.2061481 0.4224645"
+ " 0 -3.559528 0.4913696 0.9183825 0.4897513"
- " 2 -2.930983 0.2973609 0.2158858 0.3434407"
+ " 2 -3.139851 0.3965366 0.3398119 0.4184502"
- " 4 -2.562075 0.3056163 0.3338213 0.3406258"
+ " 4 -2.569760 0.3474726 0.3825346 0.3724245"
- " 6 -2.279532 0.2760625 0.5405756 0.3199528"
+ " 6 -2.275635 0.2852083 0.5541571 0.3297327"
- " 9 -2.945673 0.3252552 0.5221775 0.3711318"
+ " 9 -2.953501 0.3308731 0.5317156 0.3741726"
- "11 -3.269451 0.3591172 0.4799476 0.4141353"
+ "11 -3.282310 0.3650256 0.4889166 0.4164740"
- "13 -3.456494 0.3984923 0.6012750 0.4625997"
+ "13 -3.470296 0.4054547 0.6107641 0.4648256"
and 9 more ...
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:54:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
── 72. Failure (test_summary.R:65:3): summary.ddhazard yields previous results a
`.summary` has changed from known value recorded in './previous_results/summary_ddhazard_UKF_object.RDS'.
Component "coefficients": Mean relative difference: 0.04963109
Component "Q": Mean relative difference: 0.09488771
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:65:2
2. testthat::expect_known_value(...)
at test_summary.R:7:4
── 73. Failure (test_summary.R:65:3): summary.ddhazard yields previous results a
Results have changed from known value recorded in './previous_results/summary_ddhazard_UKF_print'.
old[7:26] vs new[7:26]
"'exponential' model fitted with the 'UKF' method in 3 iterations of the EM algorithm."
""
"Smoothed time-varying coefficients are:"
- " (Intercept) sd group1 sd "
+ " (Intercept) sd group1 sd "
- " 0 -3.255478 0.4587125 -0.04778766 0.5031436"
+ " 0 -3.762509 0.5043091 0.8121867 0.5184270"
- " 2 -3.120941 0.3597162 0.12999999 0.4335355"
+ " 2 -3.251172 0.4179465 0.3156328 0.4516540"
- " 4 -2.680845 0.3264705 0.33298262 0.3856080"
+ " 4 -2.720673 0.3596579 0.4059368 0.3962788"
- " 6 -2.463108 0.2877733 0.52279810 0.3457136"
+ " 6 -2.482108 0.2995750 0.5567259 0.3521446"
- " 9 -3.084883 0.3281004 0.46542344 0.3901447"
+ " 9 -3.115360 0.3378981 0.4910585 0.3923296"
- "11 -3.397330 0.3605039 0.40243974 0.4335337"
+ "11 -3.434283 0.3708051 0.4270690 0.4350556"
and 10 more ...
Backtrace:
1. dynamichazard (local) test_func(...)
at test_summary.R:65:2
2. testthat::expect_known_output(...)
at test_summary.R:8:4
══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Comparing_methods_for_logistic_models.Rmd’ using rmarkdown
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
--- finished re-building ‘Comparing_methods_for_logistic_models.Rmd’
--- re-building ‘Diagnostics.Rmd’ using rmarkdown
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
Warning in ddhazard_fit_cpp(a_0 = a_0, Q_0 = Q_0, F_ = F., verbose = verbose, :
EM algorithm did not converge within the n_max number of iterations
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
Warning in ddhazard_fit_cpp(a_0 = a_0, Q_0 = Q_0, F_ = F., verbose = verbose, :
EM algorithm did not converge within the n_max number of iterations
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
Quitting from lines 564-565 (Diagnostics.Rmd)
Error: processing vignette 'Diagnostics.Rmd' failed with diagnostics:
all(abs(stat_res$residuals) < 1.96) is not TRUE
--- failed re-building ‘Diagnostics.Rmd’
--- re-building ‘ddhazard.Rnw’ using knitr
fatal: not a git repository (or any parent up to mount point /data)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Warning in system("git rev-parse --short HEAD", intern = TRUE) :
running command 'git rev-parse --short HEAD' had status 128
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
--- finished re-building ‘ddhazard.Rnw’
--- re-building ‘Bootstrap_illustration.pdf.asis’ using asis
--- finished re-building ‘Bootstrap_illustration.pdf.asis’
--- re-building ‘Particle_filtering.pdf.asis’ using asis
--- finished re-building ‘Particle_filtering.pdf.asis’
SUMMARY: processing the following file failed:
‘Diagnostics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc