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commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com>
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commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com>
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commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com>
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* removed worst_resp calculation! * isolate calc_best_response() * add .remove_post_pd() * improve/fix inner checks * isolate .encode_response * use slice_min instead of filter for better tie management * output: select and rename +clean +add ellipsis argument * grstat_data_warn default subjid * doc * waterfall: change interface from raw recist to best response * add .check_legacy() error message to signal the function has changed * add .get_shape_layer() more versatile than stars * add .get_fill_scale() get fill colors from parameter "resp_colors" * clean labs and theme * doc * autoimport * add tests * signal dev lifecycle * grstat_dev_warn: add verbosity control for tests * improve globalVariables management * fixes for check * grstat_dev_warn fix * Squashed commit of the following: commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * Update _pkgdown.yml * Squashed commit of the following: commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * deduplicate `.remove_post_pd()` * update globals * .check_best_resp: consider NE as NA * doc * update snapshots with new recist data * Squashed commit of the following: commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * remove use of `\(` shorthand * fix for check --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com>
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commit f220fb5 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 18 14:08:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9015 [skip ci] commit 972e13e Author: Lpierott <pierotti.livia@gmail.com> Date: Fri Jul 18 16:06:01 2025 +0200 Improve KaplanMeier vignette (#74) * Create kaplan_meier_v2.Rmd * remove v2 to the name of the rmd script commit 6f32680 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Tue Jul 15 10:08:48 2025 +0200 Delete .github/ISSUE_TEMPLATE directory [skip ci] commit bf2d483 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Sat Jul 12 14:09:51 2025 +0200 Waterfallplot: séparation calcul réponse / plot (#71) * removed worst_resp calculation! * isolate calc_best_response() * add .remove_post_pd() * improve/fix inner checks * isolate .encode_response * use slice_min instead of filter for better tie management * output: select and rename +clean +add ellipsis argument * grstat_data_warn default subjid * doc * waterfall: change interface from raw recist to best response * add .check_legacy() error message to signal the function has changed * add .get_shape_layer() more versatile than stars * add .get_fill_scale() get fill colors from parameter "resp_colors" * clean labs and theme * doc * autoimport * add tests * signal dev lifecycle * grstat_dev_warn: add verbosity control for tests * improve globalVariables management * fixes for check * grstat_dev_warn fix * Squashed commit of the following: commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * Update _pkgdown.yml * Squashed commit of the following: commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * deduplicate `.remove_post_pd()` * update globals * .check_best_resp: consider NE as NA * doc * update snapshots with new recist data * Squashed commit of the following: commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> * remove use of `\(` shorthand * fix for check --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit a304e92 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:58:20 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9014 [skip ci] commit 165566a Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:56:53 2025 +0200 new gr_officer_template() (#72) * new gr_officer_template() * doc * Update _pkgdown.yml * autoimport * fix for check * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 63d0d15 Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 16:07:16 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9013 [skip ci] commit f95b324 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 18:06:07 2025 +0200 Implémenter les checks RECIST (#63) * WIP * recist_check: .add_to_recist_issues() instead of warn use an environment to centralize the issues instead of warning for each. + heavy reformat (should have made 2 commits...) * recist_check reorder * check_recist: .apply_recist_mapping() * check_lesion_number() * fixed .apply_recist_mapping * check_constancy * check_baseline_lesions * hotfix: add rtn objects * check_constancy: Response should be constant per date * check_baseline_lesions: baseline response should be missing * check_derived_columns * check_lesion_number() becomes check_target_lesions() * check_missing * check_target_response * fix check_missing * check_constancy: add nontarget_yn * check_target_response (for real) * check_global_response * .summarise_recist (for rc_short) * move utils to utils.R * check_global_response: fix arguments * .apply_recist_mapping: add mandatory variables * recist_issue: allow newline in message * backup commit * remove old code OLD_check_bare_recist OLD_check_response FIX_check_crf_structure * check_nontarget_response Patients with no Non-Target Lesions should not have a NTL response. * check_global_response: check NTL progressions Progressions due only to Non-Target Lesions are seldom and should be checked * remove legacy code * print.check_recist * remove unused grstat_env * gr_recist_mapping: remove unused variables * print.check_recist : nicer * document * check_recist: add mapping as attribute * rephrase most issue messages * recist_report() !!! * autoimport * check_derived_columns: conditional checks * improve documentation * Update _pkgdown.yml * recist_report: add title parameter * Delete test-recist.R * add globalVariables * fix for check * check_derived_columns: deduplicate checks * check_global_response: fix nlt-only progressions * template recist: improve options remove rownames, remove research * add assert_extension() * recist_report: split into HTML and XLSX * move to recist_utils.R * renamed to .recist_to_num() (and improved) * Remove rows posterior to the first progression * rewrote error messages * check that CR are terminal * check: Target Lesion should be <2 lymph nodes * signal dev state improves #69 * clean browser() reliquates * Update .gitignore * check_global_response: fix NA/NE * improve globalVariables() management * improve doc * fix for check * Update .gitignore * remove nonsensical check nadir can evolve over time, obviously * prefix internal check function with rc_ * add some tests * Update _pkgdown.yml * update doc --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit 48afe41 Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 14:05:35 2025 +0200 changed check action [skip ci] commit 33dd5ee Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Fri Jul 11 10:36:13 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9012 [skip ci] commit 68d87be Author: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Date: Fri Jul 11 12:35:04 2025 +0200 Update check-standard.yaml commit 42db0f2 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Fri Jul 11 12:07:07 2025 +0200 add BOIN plot (#77) * add boin plot * autoimport * doc * add tests * Update _pkgdown.yml * fix for check * legend inside the gantt plot * clean unused variable * use boin$boundary_tab if full_boundary_tab is not available * improve documentation * update tests with newer example * fix for check * renamed data_patients columns + doc * test: check for unknown dose * typo * update tests * Update .gitignore * add experimental badge * update globals --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> commit ebbf206 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 15:52:32 2025 +0200 Update check-standard.yaml [skip ci] commit a65605f Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Date: Wed Jul 9 09:13:24 2025 +0000 Update dev version (Github Actions) Bump to v0.1.0.9011 [skip ci] commit 05b7e51 Author: Dan Chaltiel <dan.chaltiel@gmail.com> Date: Wed Jul 9 11:11:56 2025 +0200 Improve recist data (#75) * better arm repartition * improve date_inclusion calculation * improve documentation * example_rc: removed rctlsum_b & rctlmin * moved test-alexis.R to test-data.R * example_rc: add NTL yesno column `rcntlyn` NTL are NE mostly when non present * example_rc: fixed labels bind_rows removed them, added at last * improved documentation * example_rc: reformat * add .sample_yesno() * example_rc: improve workflow * example_rc: fix number of timepoints baseline was added * example_rc: removed unused variables * example_rc: minor reformat, renaming, and doc * example_rc: internalise things inside .simulate_one_patient() rctlsum_b + calculate rcdt from delai example_rc: simulate baseline inside .simulate_one_patient() also, decrease linearly (% of baseline) instead of exponentially (% of previous date) for simplicity * example_rc: revert baseline being not missing +response factor level management * example_rc: tweak default values * add tests on RECIST data (survival rates...) * add dev tests on RECIST (skipped, for viz only) * fix for check * add missing values * update doc * add NA/NE for real this time * update test for NE values --------- Co-authored-by: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com> Revert "suite modif dan" This reverts commit 15a2cff.
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Reprise du code couleur du MD Anderson pour la partie haute, mais couleurs ggplot par défaut pour le Gantt.