CRAN release: update description and news version to 0.8.3, [skip vbump] #970

shajoezhu · 2023-06-15T14:43:58Z

This PR tracks CRAN submission and release

github-actions · 2023-06-15T14:51:38Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      62       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   115-119
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   233-235
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_vars_in_cols.R                     113      23  79.65%   164, 188-193, 206, 219-225, 268-274, 305
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        139       5  96.40%   126-127, 137, 241, 259
R/control_incidence_rate.R                    10       0  100.00%
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          47       1  97.87%   63
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       6  92.86%   156-158, 161, 176-177
R/count_occurrences.R                         61       1  98.36%   92
R/count_patients_events_in_cols.R             67       1  98.51%   62
R/count_patients_with_event.R                 33       0  100.00%
R/count_patients_with_flags.R                 39       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    169       9  94.67%   19-20, 213-217, 261, 276, 284, 290-291
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            169      40  76.33%   232-263, 323-325, 332, 353-390
R/desctools_binom_diff.R                     663      66  90.05%   55, 90-91, 131-132, 135, 214, 240-249, 288, 290, 310, 314, 318, 322, 378, 381, 384, 387, 448, 456, 468-469, 475-478, 486, 489, 498, 501, 549-550, 552-553, 555-556, 558-559, 629, 641-654, 659, 706, 719, 723
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   60
R/estimate_proportion.R                      198      11  94.44%   75-82, 86, 91, 460, 565
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       3  97.39%   107, 145, 155
R/g_forest.R                                 437      23  94.74%   197, 248-249, 316, 333-334, 339-340, 353, 369, 416, 447, 523, 532, 613-617, 627, 702, 705, 829
R/g_lineplot.R                               199      29  85.43%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 449
R/g_step.R                                    68       1  98.53%   109
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    40       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        65       1  98.46%   91
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/incidence_rate.R                            93       7  92.47%   55-62
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        630      61  90.32%   260-295, 304-308, 508, 680-682, 690-692, 717, 724-725, 897, 1086, 1403-1414
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            88       0  100.00%
R/prop_diff.R                                260      16  93.85%   72-75, 107, 267-274, 413, 473, 578
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   273, 315-317
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   73-74, 129
R/summarize_ancova.R                          95       1  98.95%   180
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_coxreg.R                         156       2  98.72%   198, 410
R/summarize_glm_count.R                      164       4  97.56%   159, 164, 208, 261
R/summarize_num_patients.R                    74       9  87.84%   103-105, 150-151, 217-222
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   56
R/summarize_variables.R                      220       2  99.09%   266, 492
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   59-67
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       116       7  93.97%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              87       1  98.85%   84
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 346-347
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9124     424  95.35%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 1f9bf89

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-06-15T14:52:14Z

Unit Tests Summary

      1 files   78 suites 59s ⏱️
  735 tests 735 ✔️     0 💤 0 ❌
1 560 runs 979 ✔️ 581 💤 0 ❌

Results for commit 1e77a69.

♻️ This comment has been updated with latest results.

Signed-off-by: Joe Zhu <joe.zhu@roche.com>

shajoezhu · 2023-06-16T00:49:40Z

CRAN feedback:

If there are references describing the methods in your package, please
add these in the description field of your DESCRIPTION file in the form
authors (year) doi:...
authors (year) arXiv:...
authors (year, ISBN:...)
or if those are not available: https:...
with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for
auto-linking. (If you want to add a title as well please put it in
quotes: "Title")
We do not need "| file LICENSE" and the file as these are part of R.
This is only needed in case of attribution requirements or other
possible restrictions. Hence please omit it.
"Using foo:::f instead of foo::f allows access to unexported objects.
This is generally not recommended, as the semantics of unexported
objects may be changed by the package author in routine maintenance."
Used ::: in documentation:
man/cox_regression.Rd:
tern:::a_coxreg(df = dta_bladder, labelstr = "Label 1",
variables = u1_variables, .spl_context = list(value = "COVAR1"), .stats
= "n", .formats = "xx")
man/cox_regression.Rd:
tern:::a_coxreg(df = dta_bladder, labelstr = "", variables =
u1_variables, .spl_context = list(value = "COVAR2"), .stats = "pval",
.formats = "xx.xxxx")
man/summarize_patients_exposure_in_cols.Rd:
tern:::a_count_patients_sum_exposure(df = df, var = "SEX",
.N_col = nrow(df), .stats = "n_patients")
Please omit one colon.
You have examples for unexported functions. Please either omit these
examples or export these functions.
\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by
the user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user. Does not seem necessary.
Please replace \dontrun with \donttest.
Please unwrap the examples if they are executable in < 5 sec, or replace
dontrun{} with \donttest{}.

Melkiades

Lgtm! unblocking it if needed ;)

shajoezhu · 2023-06-16T15:35:03Z

Well, the point is that an examples suggests that a user could use it.
But unexported functions should not be used, hence non exporting but
ptoviding examples that show how to use this is somehow contradicting.

…ring/tern into cran_releae_0.8.3_branch

R/count_missed_doses.R

R/summarize_patients_exposure_in_cols.R

Melkiades · 2023-06-19T10:58:35Z

R/utils.R

-#' range_noinf(c(Inf, NA), na.rm = FALSE, finite = TRUE)
-#' range_noinf(c(1, Inf, NA), na.rm = FALSE, finite = TRUE)
-#' }
-#'
 #' @keywords internal
 range_noinf <- function(x, na.rm = FALSE, finite = FALSE) { # nolint


Maybe these utils should be exported. Looks like useful

I think this can be migrated into the "tern.s" package as a statistics, would you agree?

maybe this one yes. The other ones in utils.R should be exported probably

.Rbuildignore

Melkiades

I think we need more than one reviewer here as there is a major removal of information. @edelarua @ayogasekaram what do you think?

edelarua

Lgtm! I agree with Davide's comments but overall it looks fine.

shajoezhu · 2023-06-19T22:20:57Z

hi @Melkiades , the package has been successfuly submitted. Can you unblock this merge, and we will address these as new issues. Thanks

shajoezhu · 2023-06-20T07:40:04Z

awesome! Thanks guys!

update description and news version to 0.8.3, [skip vbum]

3284d66

Merge branch 'main' into cran_releae_0.8.3_branch

bf67b53

Signed-off-by: Joe Zhu <joe.zhu@roche.com>

shajoezhu added the sme label Jun 15, 2023

shajoezhu and others added 2 commits June 16, 2023 06:45

Merge branch 'main' into cran_releae_0.8.3_branch

b8bf440

Signed-off-by: Joe Zhu <joe.zhu@roche.com>

rbuildignore license

5a5fc83

shajoezhu added 3 commits June 16, 2023 13:06

remove :::

d7a8e51

export a_coxreg

b57e9ae

export a_count_patients_sum_exposure function

7a8f485

Melkiades approved these changes Jun 16, 2023

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update documentation

8fc7281

shajoezhu mentioned this pull request Jun 16, 2023

Removing examples for unxported functions, reinstate them in tern.s #972

Open

shajoezhu and others added 15 commits June 16, 2023 23:55

stash changes

e69e38b

Merge e69e38b into 395503f

40b9a45

[skip actions] Restyle files

8f857f1

fixng example

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[skip actions] Roxygen Man Pages Auto Update

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stash changes

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Merge branch 'cran_releae_0.8.3_branch' of github.com:insightsenginee…

abf3f51

…ring/tern into cran_releae_0.8.3_branch

stash changes

ebf461d

Merge ebf461d into 395503f

4e84d36

[skip actions] Restyle files

a5eb4c1

Empty-Commit

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Merge branch 'cran_releae_0.8.3_branch' of github.com:insightsenginee…

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…ring/tern into cran_releae_0.8.3_branch

Empty-Commit

9a60172

[skip actions] Roxygen Man Pages Auto Update

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updte doc

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shajoezhu added 10 commits June 17, 2023 08:24

Merge branch 'cran_releae_0.8.3_branch' of github.com:insightsenginee…

ee6912a

…ring/tern into cran_releae_0.8.3_branch

make groups_list_to_df internal

ac347c5

export forest_viewport

7951383

Empty-Commit

47dbd40

export groups_list_to_df

fcf2aca

export groups_list_to_df

621265e

fixing r build check complains

5909c30

fix spell

59b5f90

updat eexample

efbc46e

update exmaple

1e77a69

Melkiades reviewed Jun 19, 2023

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Melkiades changed the title ~~update description and news version to 0.8.3, [skip vbump]~~ CRAN release: update description and news version to 0.8.3, [skip vbump] Jun 19, 2023

edelarua approved these changes Jun 19, 2023

View reviewed changes

shajoezhu requested a review from Melkiades June 19, 2023 22:19

Melkiades approved these changes Jun 20, 2023

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shajoezhu merged commit c69a6f7 into main Jun 20, 2023

shajoezhu deleted the cran_releae_0.8.3_branch branch June 20, 2023 07:39

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CRAN release: update description and news version to 0.8.3, [skip vbump] #970

CRAN release: update description and news version to 0.8.3, [skip vbump] #970

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CRAN release: update description and news version to 0.8.3, [skip vbump] #970

CRAN release: update description and news version to 0.8.3, [skip vbump] #970

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