Metadata

What was declared

Everything the report was built from that is neither measured nor written: the study model, the document models, every display's and value's specification with its history, every text block's approval, the environments the iterations were built in, and the requirements the tests evidence. Each is read from the file that declares it.

3arms5 analysis sets
4document modelstemplate objects
30display specifications15 value declarations
10/33text blocks approved1 environment

Study

library/study.yaml declares what the study is; everything that names an arm, an analysis set or the cut-off reads it.

Id
CDISCPILOT01
Title
Safety and Efficacy of the Xanomeline Transdermal Therapeutic System (TTS) in Patients with Mild to Moderate Alzheimer's Disease
Phase
Phase 2
Cut-off
2014-07-01
Source
CDISCPILOT01 ADaM package (phuse-org/phuse-scripts, data/adam/cdiscpilot01) phuse
alternate: pharmaverseadam
Data
every dataset the package carries
Reference report
cdisc-pilot-csr · quality/data/reference-report-agreement.json
File
library/study.yaml

Arms, in print order

IdLabel
placeboPlacebo
lowXanomeline Low Dose
highXanomeline High Dose

Columns that carry an arm label

TRT01P
planned
TRT01A
actual
TRTP
planned
TRTA
actual

Analysis sets

The subjects each set holds per arm are data, measured from the package and re-measured by test-study-model.R on every run; the assembler's treatment-consistency gate holds every placed display to them.

SetLabelFlagPlaceboXanomeline Low DoseXanomeline High DoseTotal
allAll Randomised Subjects—868484254
safetySafety Analysis SetSAFFL868484254
ittIntent-to-Treat PopulationITTFL868484254
efficacyEfficacy Analysis SetEFFFL798174234
completersCompleters at Week 24COMP24FL602830118

Document models

A template object says what a kind of document IS (sections.yaml) and what this study puts in each section (assembly.yaml). Display numbers are derived from assembly order at build time, never written. The Templates view walks every section of a model; this table is the index of the models.

IdModelSectionsSlots / post-textDocuments assembled from it
display-packagePost-Text Display Package v1.0.0
ICH E3 (1995), Step 4 — Section 14, restricted to its display sections
110 / 5Post-Text Display Packageopen
e3-abbreviatedAbbreviated Clinical Study Report (ICH E3) v1.0.0
ICH E3 (1995), Step 4 — Introduction, restricted per the rule in this file
7515 / 4Abbreviated Clinical Study Report (ICH E3)open
e3-synopsisICH E3 Annex I Study Synopsis v1.0.0
ICH E3 (1995), Step 4 — Section 2 and Annex I
2518 / 1Study Synopsisopen
ich-e3ICH E3 Clinical Study Report v1.0.0
ICH E3 (1995), Step 4; E3 Q&A (R1)
12016 / 5Clinical Study Reportopen

Specifications

A display is declared twice — what to compute (analysis.yaml) and how to show it (display.yaml) — and every rebuild keeps a snapshot of both beside the ARD, so the history below is the specification's, iteration by iteration, with the hashes each manifest recorded.

t-demographics Demographic and Baseline Characteristics DMT01

Type
table
E3 position
§14.1
Files
analysis library/tfl/t-demographics/analysis.yaml
display library/tfl/t-demographics/display.yaml
custom library/tfl/t-demographics/custom.R
Current
v007 · spec bc60600 · display c2a1f17 · ARD 87af027
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:06Z@jwildfireInitial generation of DMT01 from the statistical analysis plan shell.0f1e9b947d64c367ad8d0
v0022026-07-27T03:23:35Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).0f1e9b947d64c3e03ca47
v0032026-09-02T15:19:11Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.0f1e9b942749daf2f974a
v0042026-09-02T15:39:23Z@obotclawTable 14-2.01 of the reference report (D0032, #61): intent-to-treat population, a Total and a p-value column (one-way ANOVA / Pearson chi-square per block), the report rows — age and its groups, sex, Race (Origin) recoded from race and ethnicity, MMSE, duration of disease and its groups, years of education, baseline weight, height, BMI and its groups. The FDA-standard DMT01 shape is superseded; CDISC-coded race and ethnicity stay in the ARD for the narrative bindings.1db216cb2e005bc9e63ef
v0052026-09-02T15:44:12Z@obotclawThe sub-1% percentage presentation made a display option (format: sub_one_pct) rather than an engine rule: the reference end-of-study table prints 1 ( 0%) where its demographics table prints 1 ( <1%). Every cell unchanged.1db216cce6678b3516f69
v0062026-09-02T16:10:27Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).1db216cce6678b7e45dc8
v0072026-09-02T16:11:27Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).bc60600c2a1f1787af027

t-disposition Subject Disposition DST01

Type
table
E3 position
§14.1
Files
analysis library/tfl/t-disposition/analysis.yaml
display library/tfl/t-disposition/display.yaml
Current
v003 · spec 8c432e5 · display c00f247 · ARD 5a073a0
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:07Z@jwildfireInitial generation of DST01 from the statistical analysis plan shell.8c432e518ca5ac1f4596b
v0022026-07-27T03:23:35Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).8c432e518ca5ac26f5652
v0032026-09-02T15:19:12Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.8c432e5c00f2475a073a0

t-populations Summary of Populations DST02

Type
table
E3 position
§14.1
Files
analysis library/tfl/t-populations/analysis.yaml
display library/tfl/t-populations/display.yaml
Current
v003 · spec c8dbaff · display 9ac815d · ARD a78a73c
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:18:05Z@jwildfireInitial generation of DST02 from the CDISCPILOT01 statistical analysis plan (Attachment 13.1.1 Template 1).f65fbf8a67aeb9a096a1d
v0022026-08-27T03:44:48Z@obotclawCorrect the population line. The reference report runs Table 14-1.01 over All Subjects; this display claimed Intent-to-Treat, and t-end-of-study claimed the reverse — the two were transcribed the wrong way round. In this study both select the same 254 subjects, so no figure moves; the table now states the population its reference states. The footnotes now name the two things this display defines that the reference does not: the derivation of Complete Study, and the meaning of N.c8dbaff9ac815d61a333a
v0032026-09-02T15:23:26Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.c8dbaff9ac815da78a73c

t-end-of-study Summary of End of Study Data DST03

Type
table
E3 position
§14.1
Files
analysis library/tfl/t-end-of-study/analysis.yaml
display library/tfl/t-end-of-study/display.yaml
custom library/tfl/t-end-of-study/custom.R
Current
v003 · spec d39450d · display 6a7d3f3 · ARD 4969678
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:18:15Z@jwildfireInitial generation of DST03 from the CDISCPILOT01 statistical analysis plan (Attachment 13.1.1 Template 2).b2230118ec9802979dd87
v0022026-08-27T03:44:50Z@obotclawCorrect the population line. The reference report runs Table 14-1.02 over Intent-to-Treat; this display claimed All Subjects. In this study both select the same 254 subjects, so no figure moves. The footnote for N now says where its wording departs from the reference.d39450d6a7d3f32a40e4c
v0032026-09-02T15:23:25Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.d39450d6a7d3f34969678

f-derm-time-to-event Time to Dermatologic Event by Treatment Group AEF01

Type
figure
E3 position
§14.2
Files
analysis library/tfl/f-derm-time-to-event/analysis.yaml
display library/tfl/f-derm-time-to-event/display.yaml
custom library/tfl/f-derm-time-to-event/custom.R
Current
v002 · spec dd67fc1 · display a900fd7 · ARD dae95ac
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T05:00:35Z@jwildfireInitial generation of Figure 14-1: Kaplan-Meier estimates of time to first dermatologic event, from the study own analysis results metadata (define.xml ResultDisplay Figure_14-1, PROC LIFETEST) and SAP section 11.2.dd67fc1a900fd72b62328
v0022026-09-02T15:23:21Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.dd67fc1a900fd7dae95ac

t-cibic-week24 Primary Endpoint Analysis: CIBIC+ — Summary at Week 24 — LOCF EFF02

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-cibic-week24/analysis.yaml
display library/tfl/t-cibic-week24/display.yaml
custom library/tfl/t-cibic-week24/custom.R
Current
v004 · spec 190d176 · display c326ce8 · ARD a8f78f3
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:19:21Z@jwildfireInitial generation from CDISCPILOT01 Table 14-3.02.190d1767d1c968b467544
v0022026-08-27T02:37:29Z@jwildfireInitial generation.190d1767d1c968ac80459
v0032026-08-27T03:53:36Z@jwildfireCorrect the digit plan so the pipeline reads it. The entry `N: 0` was resolved by YAML 1.1 as the boolean key FALSE, so the display declared a precision for N that no renderer ever saw; the key is now quoted. No statistic moves - the engine default for a count is the same zero decimals the specification asked for - and this regeneration is the proof of that.190d176c326ce8e45ea11
v0042026-09-02T15:23:21Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.190d176c326ce8a8f78f3

t-cibic-week8 CIBIC+ — Summary at Week 8 — LOCF EFF03

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-cibic-week8/analysis.yaml
display library/tfl/t-cibic-week8/display.yaml
custom library/tfl/t-cibic-week8/custom.R
Current
v002 · spec d243537 · display 9e6e7dd · ARD 3073ee5
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:53:34Z@jwildfireInitial generation of EFF03 from CDISCPILOT01 Table 14-3.04 and the analysis results metadata for Table_14-3.02, which states the model.d2435379e6e7dd7e4e612
v0022026-09-02T15:23:22Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.d2435379e6e7dd3073ee5

t-cibic-week16 CIBIC+ — Summary at Week 16 — LOCF EFF04

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-cibic-week16/analysis.yaml
display library/tfl/t-cibic-week16/display.yaml
custom library/tfl/t-cibic-week16/custom.R
Current
v002 · spec 00a39ba · display ddcd203 · ARD 4f25a6b
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:53:35Z@jwildfireInitial generation of EFF04 from CDISCPILOT01 Table 14-3.06 and the analysis results metadata for Table_14-3.02, which states the model.00a39baddcd203f3551f2
v0022026-09-02T15:23:21Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.00a39baddcd2034f25a6b

t-cibic-categorical CIBIC+ — Categorical Analysis — LOCF EFF05

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-cibic-categorical/analysis.yaml
display library/tfl/t-cibic-categorical/display.yaml
custom library/tfl/t-cibic-categorical/custom.R
Current
v002 · spec f6675d7 · display 3e86f7c · ARD 4847131
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:53:35Z@jwildfireInitial generation of EFF05 from CDISCPILOT01 Table 14-3.13.f6675d73e86f7cbf869c3
v0022026-09-02T15:23:21Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.f6675d73e86f7c4847131

t-eff-adas-wk24 Primary Endpoint Analysis: ADAS-Cog (11) - Change from Baseline to Week 24 - LOCF EFT01

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk24/analysis.yaml
display library/tfl/t-eff-adas-wk24/display.yaml
custom library/tfl/t-eff-adas-wk24/custom.R
Current
v002 · spec b129304 · display e51fda2 · ARD 6e4dd40
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:21:19Zobot workerInitial generation of the ADAS-Cog Week 24 primary efficacy display (#43).b129304e51fda27769370
v0022026-09-02T15:23:23Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.b129304e51fda26e4dd40

t-eff-adas-wk8 ADAS-Cog (11) - Change from Baseline to Week 8 - LOCF EFT02

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk8/analysis.yaml
display library/tfl/t-eff-adas-wk8/display.yaml
custom library/tfl/t-eff-adas-wk8/custom.R
Current
v002 · spec 6508cc4 · display 675584e · ARD ec13102
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:21:30Zobot workerInitial generation of the ADAS-Cog efficacy displays (#43).6508cc4675584ec9148b1
v0022026-09-02T15:23:24Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.6508cc4675584eec13102

t-eff-adas-wk16 ADAS-Cog (11) - Change from Baseline to Week 16 - LOCF EFT03

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk16/analysis.yaml
display library/tfl/t-eff-adas-wk16/display.yaml
custom library/tfl/t-eff-adas-wk16/custom.R
Current
v002 · spec 304b616 · display 6bbf55b · ARD dd7d1cd
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T02:21:31Zobot workerInitial generation of the ADAS-Cog efficacy displays (#43).304b6166bbf55b6d94a1f
v0022026-09-02T15:23:23Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.304b6166bbf55bdd7d1cd

t-eff-adas-wk24-completers ADAS-Cog (11) - Change from Baseline to Week 24 - Completers at Week 24, Observed Cases, Windowed EFT04

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk24-completers/analysis.yaml
display library/tfl/t-eff-adas-wk24-completers/display.yaml
custom library/tfl/t-eff-adas-wk24-completers/custom.R
Current
v002 · spec 09b7453 · display 4cf74d8 · ARD 9c9aef7
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:41:22Zobot worker W0137Complete the preserved specification: first generation of numbers and rendered output.09b74534cf74d8fd50f5c
v0022026-09-02T15:23:24Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.09b74534cf74d89c9aef7

t-eff-adas-wk24-male ADAS-Cog (11) - Change from Baseline to Week 24 in Male Subjects - LOCF EFT05

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk24-male/analysis.yaml
display library/tfl/t-eff-adas-wk24-male/display.yaml
custom library/tfl/t-eff-adas-wk24-male/custom.R
Current
v002 · spec f08b78f · display cc16d83 · ARD bf57631
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:41:23Zobot worker W0137Complete the preserved specification: first generation of numbers and rendered output.f08b78fcc16d83f4ecc3b
v0022026-09-02T15:23:24Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.f08b78fcc16d83bf57631

t-eff-adas-wk24-female ADAS-Cog (11) - Change from Baseline to Week 24 in Female Subjects - LOCF EFT06

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-wk24-female/analysis.yaml
display library/tfl/t-eff-adas-wk24-female/display.yaml
custom library/tfl/t-eff-adas-wk24-female/custom.R
Current
v002 · spec 9b0ea9b · display 97fcb12 · ARD 92e3885
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:41:23Zobot worker W0137Complete the preserved specification: first generation of numbers and rendered output.9b0ea9b97fcb12a6fddf0
v0022026-09-02T15:23:24Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.9b0ea9b97fcb1292e3885

t-eff-adas-overtime ADAS-Cog (11) - Mean and Mean Change from Baseline over Time EFT07

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-overtime/analysis.yaml
display library/tfl/t-eff-adas-overtime/display.yaml
custom library/tfl/t-eff-adas-overtime/custom.R
Current
v002 · spec 37f6ffa · display cc82b9a · ARD ae89465
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:52:26Zobot worker W0137First generation of the over-time summary (reference report Table 14-3.10).37f6ffacc82b9a41c5098
v0022026-09-02T15:23:23Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.37f6ffacc82b9aae89465

t-eff-adas-mmrm ADAS-Cog (11) - Repeated Measures Analysis of Change from Baseline to Week 24 EFT08

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-adas-mmrm/analysis.yaml
display library/tfl/t-eff-adas-mmrm/display.yaml
custom library/tfl/t-eff-adas-mmrm/custom.R
Current
v004 · spec 3070e2a · display 2b6b835 · ARD 8953a87
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:57:31Zobot worker W0137First generation of the MMRM supportive analysis (reference report Table 14-3.11).3070e2a85693015300381
v0022026-08-27T03:58:05Zobot worker W0137State in the display footnotes exactly which five cells differ from the reference report, and why: Kenward-Roger degrees of freedom and PRJKH standard errors are not implemented.3070e2aedf50019df5a53
v0032026-09-02T15:23:22Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.3070e2aedf50013f78c39
v0042026-09-02T16:32:01Z@obotclawFootnote records the Kenward-Roger spike (D0032 Issue H, #66): tried with mmrm, reproduces the REML criterion, moves one of the five cells and not the other four; model-based fit kept. Every statistic unchanged.3070e2a2b6b8358953a87

t-eff-npix-mean Mean NPI-X Total Score from Week 4 through Week 24 - Windowed EFT09

Type
table
E3 position
§14.2
Files
analysis library/tfl/t-eff-npix-mean/analysis.yaml
display library/tfl/t-eff-npix-mean/display.yaml
custom library/tfl/t-eff-npix-mean/custom.R
Current
v003 · spec 80f5f0c · display c321095 · ARD 670210c
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T03:49:43Zobot worker W0137First generation of the secondary efficacy endpoint (reference report Table 14-3.12).80f5f0c2a125283672359
v0022026-08-27T03:50:45Zobot worker W0137Record in the display's own footnotes that this endpoint is derived from the per-visit NPTOT records rather than the study's NPTOTMN parameter, and what the two differ by.80f5f0cc32109586751a3
v0032026-09-02T15:23:25Z@obotclawOne study (D0032 R2, #59): regenerated so the ARD carries its population record for the treatment-consistency gate. Spec and lane unchanged; every statistic identical.80f5f0cc321095670210c

t-ae-overview Overview of Treatment-Emergent Adverse Events AET01

Type
table
E3 position
§14.3.1
Files
analysis library/tfl/t-ae-overview/analysis.yaml
display library/tfl/t-ae-overview/display.yaml
custom library/tfl/t-ae-overview/custom.R
Current
v003 · spec 6b0ba69 · display ea18faf · ARD c428956
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:08Z@jwildfireInitial generation of AET01 from the statistical analysis plan shell.6b0ba6904520448c7cee6
v0022026-07-27T03:23:34Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).6b0ba69045204496f9dbf
v0032026-09-02T15:19:13Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.6b0ba69ea18fafc428956

t-ae-common Treatment-Emergent Adverse Events by System Organ Class and Preferred Term AET02

Type
table
E3 position
§14.3.1
Files
analysis library/tfl/t-ae-common/analysis.yaml
display library/tfl/t-ae-common/display.yaml
Current
v004 · spec a45e3a1 · display 3027c71 · ARD adf6d63
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:08Z@jwildfireInitial generation of AET02 from the statistical analysis plan shell: treatment-emergent adverse events by system organ class and preferred term, with a 5% threshold on the in-text variant.750a0b3dc5fa1ce62a942
v0022026-07-25T06:39:10Z@medical-writerChange request CR-001 (medical writer, Section 12.2.1 review): add an All Subjects (Total) column to AET02 so the in-text summary can quote a pooled overall rate alongside the by-arm rates. Applied as a spec edit - analysis.yaml `total: false` -> `true`, display.yaml `columns.order` gains Total - and regenerated; no output was hand-edited.a45e3a1c749510ed1716a
v0032026-07-27T03:23:32Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).a45e3a1c7495105f250be
v0042026-09-02T15:19:14Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.a45e3a13027c71adf6d63

t-exposure Extent of Exposure to Study Drug EXT01

Type
table
E3 position
§14.3.1
Files
analysis library/tfl/t-exposure/analysis.yaml
display library/tfl/t-exposure/display.yaml
Current
v004 · spec 065027f · display d4dbe63 · ARD de9e7ac
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:07Z@jwildfireInitial generation of EXT01 from the statistical analysis plan shell.dcb569b5cf918af6624be
v0022026-07-27T03:23:36Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).dcb569b5cf918af14f5e3
v0032026-09-02T15:19:12Z@obotclawOne study (D0032 R2, #60): rebuilt from ADSL AVGDD and CUMDOSE for the safety population and the Week 24 completers, as Table 14-4.01 of the reference report summarises them. No exposure dataset is read.a9667a1e8dbf5cc110b87
v0042026-09-02T15:23:19Z@obotclawOne study (D0032 R2, #60): rebuilt from ADSL AVGDD and CUMDOSE for the safety population and the Week 24 completers, as Table 14-4.01 of the reference report summarises them; duration of treatment (TRTDUR) and the exposure categories kept for the Section 12.1 narrative under their existing binding names. No exposure dataset is read.065027fd4dbe63de9e7ac

l-ae-serious Listing of Serious Adverse Events AEL01

Type
listing
E3 position
§14.3.2
Files
analysis library/tfl/l-ae-serious/analysis.yaml
display library/tfl/l-ae-serious/display.yaml
Current
v003 · spec a046fb1 · display 11a00d0 · ARD cde8256
IterationCreatedActorChange requestSpecDisplayARD
v0012026-07-25T06:39:08Z@jwildfireInitial generation of AEL01 from the statistical analysis plan shell.a046fb1b865356f3a6c72
v0022026-07-27T03:23:31Z@obotclawAdd submission-format RTF artifacts to every variant (obot.roadmap #129 A).a046fb1b8653560395149
v0032026-09-02T15:19:13Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.a046fb111a00d0cde8256

t-conmeds Summary of Concomitant Medications CMT01

Type
table
E3 position
§14.3.5
Files
analysis library/tfl/t-conmeds/analysis.yaml
display library/tfl/t-conmeds/display.yaml
Current
v003 · spec 5b8045e · display a79342e · ARD 95799f7
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T04:06:04Z@jwildfireInitial generation of CMT01, targeting Table 14-7.04 of the reference clinical study report for this study.5b8045e6f1a46f87b879c
v0022026-09-02T15:19:45Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.5b8045ea79342ef548b4f
v0032026-09-02T16:21:44Z@obotclawConcomitant medications derived from the study own SDTM CM domain (D0032, #65): every statistic identical to the relabelled PHUSE copy it replaces, which stays vendored for the check that proves it.5b8045ea79342e95799f7

t-vitals Summary of Vital Signs at Baseline and End of Treatment VST01

Type
table
E3 position
§14.3.5
Files
analysis library/tfl/t-vitals/analysis.yaml
display library/tfl/t-vitals/display.yaml
Current
v002 · spec 2aeb258 · display eb31735 · ARD 80334ea
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T04:06:01Z@jwildfireInitial generation of VST01, targeting Table 14-7.01 of the reference clinical study report for this study.2aeb258faa409a88e8ee0
v0022026-09-02T15:19:43Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.2aeb258eb3173580334ea

t-vitals-change Summary of Vital Signs Change from Baseline at End of Treatment VST02

Type
table
E3 position
§14.3.5
Files
analysis library/tfl/t-vitals-change/analysis.yaml
display library/tfl/t-vitals-change/display.yaml
Current
v002 · spec 0d204e9 · display 840b226 · ARD 4a0f857
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T04:06:03Z@jwildfireInitial generation of VST02, targeting Table 14-7.02 of the reference clinical study report for this study.0d204e9590c09c2561647
v0022026-09-02T15:19:44Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.0d204e9840b2264a0f857

t-weight Summary of Weight and Weight Change from Baseline at End of Treatment VST03

Type
table
E3 position
§14.3.5
Files
analysis library/tfl/t-weight/analysis.yaml
display library/tfl/t-weight/display.yaml
Current
v004 · spec 14be68b · display e1621d7 · ARD 39d684c
IterationCreatedActorChange requestSpecDisplayARD
v0012026-08-27T04:10:09Z@w-vitalsInitial generation of VST03, targeting Table 14-7.03 of the reference clinical study report: weight and weight change from baseline at Week 24 and end of treatment.14be68bc1a16fdce01673
v0022026-09-02T15:19:45Z@obotclawOne study (D0032 R2, #60): read the CDISC pilot own ADaM package, which assigns every subject the arm the rest of the report uses. Spec unchanged; lane changed.14be68bd8f04f81611911
v0032026-09-02T16:10:30Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).14be68bd8f04f81b3da96
v0042026-09-02T16:11:30Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).14be68be1621d739d684c

t-ae-incidence Incidence of Treatment Emergent Adverse Events by Treatment Group AET03

Type
table
E3 position
§14.3.1
Files
analysis library/tfl/t-ae-incidence/analysis.yaml
display library/tfl/t-ae-incidence/display.yaml
custom library/tfl/t-ae-incidence/custom.R
Custom code
custom code shared with t-sae-incidence
Current
v007 · spec a94b85b · display 0511d99 · ARD 091de51
IterationCreatedActorChange requestSpecDisplayARD
v0012026-09-02T15:52:27Z@obotclawTable 14-5.01 of the reference report (D0032, #62): subjects, percentages and event counts per system organ class and preferred term, with Fisher exact tests of placebo against each active arm; organ classes alphabetical, terms by high-dose count then name.a94b85b3834d198e97f64
v0022026-09-02T15:53:49Z@obotclawEvent counts printed as integers; serious-events terms ordered as the reference serious-events program orders them (descending subjects across groups, then name).a94b85b607f4ae9940015
v0032026-09-02T15:56:53Z@obotclawA p-value under 0.0005 prints as 0.000, as the reference report prints it.a94b85b607f4ae3652173
v0042026-09-02T16:01:54Z@obotclawA trailing zero at the third decimal of a p-value is dropped, as the report prints it; the four p-values the reference rounded a thousandth higher are stated in the footnotes.a94b85beec75fe129545c
v0052026-09-02T16:02:56Z@obotclawA p-value of 0.000 keeps its zeros; only a single trailing zero at the third decimal is dropped, as the report prints.a94b85beec75fec8613b3
v0062026-09-02T16:10:29Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).a94b85beec75fe4ded035
v0072026-09-02T16:11:28Z@obotclawIn-text variant redrawn as the reference report prints it (Tables 11-1, 12-1, 12-4; D0032, #63).a94b85b0511d99091de51

t-sae-incidence Incidence of Treatment Emergent Serious Adverse Events by Treatment Group AET04

Type
table
E3 position
§14.3.2
Files
analysis library/tfl/t-sae-incidence/analysis.yaml
display library/tfl/t-sae-incidence/display.yaml
Custom code
borrows t-ae-incidence's custom code
Current
v006 · spec 065d87f · display 2e8296c · ARD 94a983c
IterationCreatedActorChange requestSpecDisplayARD
v0012026-09-02T15:52:30Z@obotclawTable 14-5.02 of the reference report (D0032, #62): subjects, percentages and event counts per system organ class and preferred term, with Fisher exact tests of placebo against each active arm; organ classes alphabetical, terms by high-dose count then name.065d87f474d8248a8cacc
v0022026-09-02T15:53:51Z@obotclawEvent counts printed as integers; serious-events terms ordered as the reference serious-events program orders them (descending subjects across groups, then name).065d87f194d3e4f16e533
v0032026-09-02T15:55:20Z@obotclawTerms ordered by subjects summed across the arms, then name, which is the order the reference serious-events program prints.065d87f2e8296c2d64159
v0042026-09-02T15:56:55Z@obotclawA p-value under 0.0005 prints as 0.000, as the reference report prints it.065d87f2e8296cebb3ef5
v0052026-09-02T16:01:56Z@obotclawA trailing zero at the third decimal of a p-value is dropped, as the report prints it; the four p-values the reference rounded a thousandth higher are stated in the footnotes.065d87f2e8296cab0d387
v0062026-09-02T16:02:57Z@obotclawA p-value of 0.000 keeps its zeros; only a single trailing zero at the third decimal is dropped, as the report prints.065d87f2e8296c94a983c

t-subjects-by-site Summary of Number of Subjects By Site DST04

Type
table
E3 position
§14.1
Files
analysis library/tfl/t-subjects-by-site/analysis.yaml
display library/tfl/t-subjects-by-site/display.yaml
Current
v002 · spec 9b145f6 · display 3087fc5 · ARD 6887f57
IterationCreatedActorChange requestSpecDisplayARD
v0012026-09-02T16:10:26Z@obotclawTable 14-1.03 of the reference report (D0032, #63): intent-to-treat, efficacy and Week 24 completer counts per site and arm, small sites pooled under 900, twelve columns of arm by population.9b145f63087fc577ce981
v0022026-09-02T16:15:18Z@obotclawSite carried as a factor over every site, so a site with no subjects in a population prints 0 rather than nothing.9b145f63087fc56887f57

f-disposition Subject Disposition DSF01

Type
figure
E3 position
§10.1
Files
analysis library/tfl/f-disposition/analysis.yaml
display library/tfl/f-disposition/display.yaml
custom library/tfl/f-disposition/custom.R
Current
v001 · spec abf4fa1 · display 334133a · ARD 700d5e7
IterationCreatedActorChange requestSpecDisplayARD
v0012026-09-02T16:24:32Z@obotclawFigure 10-1 of the reference report (D0032, #63): subjects screened, screen failures, randomised, completed Week 24 and completed the study, as a flow from the study SDTM DM and ADSL.abf4fa1334133a700d5e7

Value declarations

library/values/values.yaml: a number the report reuses, named once. The store the pipeline resolves from it is the Values view.

IdLabelKindDeclarationFormat
randomised-nSubjects randomisedARDt-disposition:randomised:n;group=Totaldigits 0
treated-nSubjects treated (safety analysis set)ARDt-disposition:treated:n;group=Totaldigits 0
completed-nSubjects who completed the studyARDt-disposition:completed:n;group=Totaldigits 0
discontinued-nSubjects who discontinuedARDt-disposition:discontinued:n;group=Totaldigits 0
completed-pctPercentage of randomised subjects who completedARDt-disposition:completed:p;group=Totalscale 100, digits 1
age-median-totalMedian age (years), all subjectsARDt-demographics:age:median;group=Totaldigits 1
female-n-totalFemale subjectsARDt-demographics:sex:n;group=Total;variable_level=Fdigits 0
ae-any-n-totalSubjects with at least one adverse eventARDt-ae-overview:any_ae:n;group=Totaldigits 0
ae-any-n-placeboSubjects with at least one adverse event (Placebo)ARDt-ae-overview:any_ae:n;group=Placebodigits 0
ae-any-n-lowSubjects with at least one adverse event (Xanomeline Low Dose)ARDt-ae-overview:any_ae:n;group=Xanomeline Low Dosedigits 0
ae-any-n-highSubjects with at least one adverse event (Xanomeline High Dose)ARDt-ae-overview:any_ae:n;group=Xanomeline High Dosedigits 0
ae-any-pct-highPercentage of high-dose subjects with at least one adverse eventARDt-ae-overview:any_ae:p;group=Xanomeline High Dosescale 100, digits 1
safety-n-highSubjects in the safety analysis set (Xanomeline High Dose)ARDt-ae-overview:any_ae:N;group=Xanomeline High Dosedigits 0
ae-any-n-xanomelineSubjects with at least one adverse event, both xanomeline armsderivedsum(ae-any-n-low, ae-any-n-high)digits 0
ae-excess-high-vs-placeboAdditional subjects with an adverse event, high dose versus placeboderiveddifference(ae-any-n-high, ae-any-n-placebo)digits 0

Approvals

Every text block's frontmatter carries its tier, its version and its approval — who, and when. A generated block stays out of the report until that approval exists; the assembler's gate enforces it.

33text blocksboilerplate, parameterized, generated
10approvedby name and date in the frontmatter
23drafta lifecycle state, not a failure
5generated blocks held outuntil a person approves them
BlockTitleTierStateByAtDrafted by
TXT-SYN-0101Name of Sponsor, Finished Product and Active Ingredient §1.1boilerplatedraft———
TXT-SYN-0102Title of Study §1.2boilerplatedraft———
TXT-SYN-0103Investigators and Study Centres §1.3boilerplatedraft———
TXT-SYN-0104Publication (Reference) §1.4boilerplatedraft———
TXT-SYN-0105Studied Period §1.5boilerplatedraft———
TXT-SYN-0106Phase of Development §1.6boilerplatedraft———
TXT-SYN-1000Statistical Methods §10boilerplatedraft———
TXT-E3-1001Disposition of Patients §10.1parameterizedapproved@jwildfire2026-07-25—
TXT-E3-1002Disposition of Patients: Summary of Named Values §10.1generateddraft——claude-opus-5
TXT-E3-1101Data Sets Analysed §11.1parameterizedapproved@jwildfire2026-09-02—
TXT-E3-1102Demographic and Other Baseline Characteristics §11.2parameterizedapproved@jwildfire2026-07-25—
TXT-SYN-1102Safety Results §11.2parameterizeddraft———
TXT-SYN-1103Conclusion §11.3boilerplatedraft———
TXT-SYN-1200Date of the Report §12boilerplatedraft———
TXT-E3-1201Extent of Exposure §12.1parameterizedapproved@jwildfire2026-07-25—
TXT-E3-1221Brief Summary of Adverse Events §12.2.1parameterizedapproved@jwildfire2026-07-25—
TXT-E3-1222Display of Adverse Events §12.2.2generateddraft——claude-opus-5
TXT-E3-1224Listing of Adverse Events by Patient §12.2.4boilerplateapproved@jwildfire2026-07-25—
TXT-E3-1231Listing of Deaths, Other Serious Adverse Events and Other Significant Adverse Events §12.3.1generateddraft——claude-opus-5
TXT-E3-1206Safety Conclusions §12.6generateddraft——claude-opus-5
TXT-E3-1300Discussion and Overall Conclusions §13generateddraft——claude-opus-5
TXT-SYN-0200Objectives §2boilerplatedraft———
TXT-SYN-0300Methodology §3boilerplatedraft———
TXT-SYN-0400Number of Patients (Planned and Analysed) §4parameterizeddraft———
TXT-SYN-0500Diagnosis and Main Criteria for Inclusion §5boilerplatedraft———
TXT-E3-0502Ethical Conduct of the Study §5.2boilerplateapproved@jwildfire2026-07-25—
TXT-E3-0503Patient Information and Consent §5.3boilerplateapproved@jwildfire2026-07-25—
TXT-SYN-0600Test Product, Dose and Mode of Administration, Batch Number §6boilerplatedraft———
TXT-SYN-0700Duration of Treatment §7parameterizeddraft———
TXT-SYN-0800Reference Therapy, Dose and Mode of Administration, Batch Number §8boilerplatedraft———
TXT-E3-0901Overall Study Design and Plan: Description §9.1parameterizedapproved@jwildfire2026-07-25—
TXT-SYN-0902Criteria for Evaluation: Safety §9.2boilerplatedraft———
TXT-E3-0908Changes in the Conduct of the Study or Planned Analyses §9.8boilerplateapproved@jwildfire2026-07-25—

Environments

Every iteration's manifest records the R version, the operating system and the package versions it was built with. This is every distinct record across the library, with the iterations built in each.

Environment 1 · R 4.3.3 · Darwin 23.6.0

cards 0.6.1 · cardx 0.2.5 · digest 0.6.37 · dplyr 1.1.4 · gt 1.0.0 · gtsummary 2.3.0 · jsonlite 2.0.0 · pharmaverseadam 1.1.0 · yaml 2.3.10

90 iterations built here: t-demographics v001 2026-07-25, t-disposition v001 2026-07-25, t-exposure v001 2026-07-25, l-ae-serious v001 2026-07-25, t-ae-common v001 2026-07-25, t-ae-overview v001 2026-07-25, t-ae-common v002 2026-07-25, l-ae-serious v002 2026-07-27, t-ae-common v003 2026-07-27, t-ae-overview v002 2026-07-27, t-demographics v002 2026-07-27, t-disposition v002 2026-07-27, t-exposure v002 2026-07-27, t-populations v001 2026-08-27, t-end-of-study v001 2026-08-27, t-cibic-week24 v001 2026-08-27, t-eff-adas-wk24 v001 2026-08-27, t-eff-adas-wk8 v001 2026-08-27, t-eff-adas-wk16 v001 2026-08-27, t-cibic-week24 v002 2026-08-27, t-eff-adas-wk24-completers v001 2026-08-27, t-eff-adas-wk24-female v001 2026-08-27, t-eff-adas-wk24-male v001 2026-08-27, t-populations v002 2026-08-27, t-end-of-study v002 2026-08-27, t-eff-npix-mean v001 2026-08-27, t-eff-npix-mean v002 2026-08-27, t-eff-adas-overtime v001 2026-08-27, t-cibic-week8 v001 2026-08-27, t-cibic-categorical v001 2026-08-27, t-cibic-week16 v001 2026-08-27, t-cibic-week24 v003 2026-08-27, t-eff-adas-mmrm v001 2026-08-27, t-eff-adas-mmrm v002 2026-08-27, t-vitals v001 2026-08-27, t-vitals-change v001 2026-08-27, t-conmeds v001 2026-08-27, t-weight v001 2026-08-27, f-derm-time-to-event v001 2026-08-27, t-demographics v003 2026-09-02, t-disposition v003 2026-09-02, t-exposure v003 2026-09-02, l-ae-serious v003 2026-09-02, t-ae-overview v003 2026-09-02, t-ae-common v004 2026-09-02, t-vitals v002 2026-09-02, t-vitals-change v002 2026-09-02, t-conmeds v002 2026-09-02, t-weight v002 2026-09-02, t-exposure v004 2026-09-02, f-derm-time-to-event v002 2026-09-02, t-cibic-categorical v002 2026-09-02, t-cibic-week16 v002 2026-09-02, t-cibic-week24 v004 2026-09-02, t-cibic-week8 v002 2026-09-02, t-eff-adas-mmrm v003 2026-09-02, t-eff-adas-overtime v002 2026-09-02, t-eff-adas-wk16 v002 2026-09-02, t-eff-adas-wk24 v002 2026-09-02, t-eff-adas-wk24-completers v002 2026-09-02, t-eff-adas-wk24-female v002 2026-09-02, t-eff-adas-wk24-male v002 2026-09-02, t-eff-adas-wk8 v002 2026-09-02, t-eff-npix-mean v003 2026-09-02, t-end-of-study v003 2026-09-02, t-populations v003 2026-09-02, t-demographics v004 2026-09-02, t-demographics v005 2026-09-02, t-ae-incidence v001 2026-09-02, t-sae-incidence v001 2026-09-02, t-ae-incidence v002 2026-09-02, t-sae-incidence v002 2026-09-02, t-sae-incidence v003 2026-09-02, t-ae-incidence v003 2026-09-02, t-sae-incidence v004 2026-09-02, t-ae-incidence v004 2026-09-02, t-sae-incidence v005 2026-09-02, t-ae-incidence v005 2026-09-02, t-sae-incidence v006 2026-09-02, t-subjects-by-site v001 2026-09-02, t-demographics v006 2026-09-02, t-ae-incidence v006 2026-09-02, t-weight v003 2026-09-02, t-demographics v007 2026-09-02, t-ae-incidence v007 2026-09-02, t-weight v004 2026-09-02, t-subjects-by-site v002 2026-09-02, t-conmeds v003 2026-09-02, f-disposition v001 2026-09-02, t-eff-adas-mmrm v004 2026-09-02

Requirements

Requirements live in matrices under quality/requirements/; every test names the requirement it evidences, and the Quality pages trace each one to its tests.

MatrixFileRows
displaysdisplays.md64evidence
Quality Frameworkquality.md98evidence
Report Template Librarytemplates.md61evidence
Text Librarytext.md86evidence
TFL Enginetfl-engine.md88evidence
Traceabilitytraceability.md16evidence