Skill Tracer
Skills › Scientific Agent Skills › clinical-reports › data_presentation.md

data_presentation.md

94 lines · skills/clinical-reports/references/data_presentation.md at 5f2bc03

Open on GitHub
1# Aggregate Data Presentation
2
3Present verified outputs without changing their meaning. Do not calculate a clinical conclusion, select an analysis, or repair source discrepancies.
4

Aggregate Data Presentation

Present verified outputs without changing their meaning. Do not calculate a clinical conclusion, select an analysis, or repair source discrepancies.

Raw lines 1 to 4
5## Mandatory table metadata
6
7Every table should identify:
8
9- artifact and analysis purpose;
10- data cut and source-output version;
11- analysis population/set;
12- treatment/group labels;
13- denominator for every group and row when it varies;
14- whether a value is a subject count, event count, observation count, or estimate;
15- units, time point/window, and summary statistic;
16- missing, unknown, not assessed, suppressed, or not applicable values;
17- coding dictionary/version/language where applicable;
18- statistical method and multiplicity status only when copied from a verified output;
19- provenance manifest and reviewer status.

Mandatory table metadata

Every table should identify:

  • artifact and analysis purpose;
  • data cut and source-output version;
  • analysis population/set;
  • treatment/group labels;
  • denominator for every group and row when it varies;
  • whether a value is a subject count, event count, observation count, or estimate;
  • units, time point/window, and summary statistic;
  • missing, unknown, not assessed, suppressed, or not applicable values;
  • coding dictionary/version/language where applicable;
  • statistical method and multiplicity status only when copied from a verified output;
  • provenance manifest and reviewer status.
Raw lines 5 to 20
21## Counts and denominators
23- Show `n/N (%)`, not a percentage alone, unless the governing output specifies another form.
24- For a proportion of distinct participants, require `0 <= n <= N` and `N > 0`. This bound does not apply to recurrent event counts; preserve the verified count or exposure-time rate and label its denominator separately.
25- Recalculate only for consistency checking; do not silently replace the reported percentage.
26- State the rounding rule and tolerance.
27- Do not add subgroup percentages when the subgroup denominator is unknown.
28- Do not infer that denominators are randomized, treated, evaluable, or safety populations.
29- Keep event counts distinct from subjects affected; event counts can exceed the number of subjects.
30- Do not sum non-mutually-exclusive categories.

Counts and denominators

  • Show n/N (%), not a percentage alone, unless the governing output specifies another form.
  • For a proportion of distinct participants, require 0 <= n <= N and N > 0. This bound does not apply to recurrent event counts; preserve the verified count or exposure-time rate and label its denominator separately.
  • Recalculate only for consistency checking; do not silently replace the reported percentage.
  • State the rounding rule and tolerance.
  • Do not add subgroup percentages when the subgroup denominator is unknown.
  • Do not infer that denominators are randomized, treated, evaluable, or safety populations.
  • Keep event counts distinct from subjects affected; event counts can exceed the number of subjects.
  • Do not sum non-mutually-exclusive categories.
Raw lines 21 to 31
32## Dates and time
34- Use `YYYY-MM-DD` calendar dates for the date checker; it rejects compact and week-date forms so precision and representation are not silently changed.
35- Preserve source timezone and precision.
36- Distinguish event date, collection date, database cut, report date, and verification date.
37- Flag start-after-end and conflicting dates.
38- Do not impute a missing day, month, timezone, or chronology.
39- For de-identified case reports, use an authorized relative timeline; do not distort intervals.

Dates and time

  • Use YYYY-MM-DD calendar dates for the date checker; it rejects compact and week-date forms so precision and representation are not silently changed.
  • Preserve source timezone and precision.
  • Distinguish event date, collection date, database cut, report date, and verification date.
  • Flag start-after-end and conflicting dates.
  • Do not impute a missing day, month, timezone, or chronology.
  • For de-identified case reports, use an authorized relative timeline; do not distort intervals.
Raw lines 32 to 40
41## Units and precision
43- Preserve source units.
44- Require a unit for every dimensional quantity.
45- Use one verified unit per comparable series or expose the mismatch.
46- Do not convert or normalize without an authorized traceable conversion rule.
47- Preserve clinically meaningful precision; do not create extra significant digits.
48- Identify SD, SE, CI, IQR, range, and denominator explicitly.

Units and precision

  • Preserve source units.
  • Require a unit for every dimensional quantity.
  • Use one verified unit per comparable series or expose the mismatch.
  • Do not convert or normalize without an authorized traceable conversion rule.
  • Preserve clinically meaningful precision; do not create extra significant digits.
  • Identify SD, SE, CI, IQR, range, and denominator explicitly.
Raw lines 41 to 49
50## Missing and suppressed values
52Keep these states distinct:
54- `missing`;
55- `not_collected`;
56- `not_assessed`;
57- `unknown`;
58- `not_applicable`;
59- `suppressed_for_privacy`;
60- `zero`.
62Never convert a blank to zero. State small-cell suppression rules and ensure totals or complementary cells do not reveal suppressed values.

Missing and suppressed values

Keep these states distinct:

  • missing;
  • not_collected;
  • not_assessed;
  • unknown;
  • not_applicable;
  • suppressed_for_privacy;
  • zero.

Never convert a blank to zero. State small-cell suppression rules and ensure totals or complementary cells do not reveal suppressed values.

Raw lines 50 to 63
64## Adverse-event tables
66For term-level aggregate tables:
68- use each required CSV header exactly once, with no surrounding whitespace; duplicate headers can overwrite values during dictionary parsing and are rejected;
70- state MedDRA version and language;
71- state analysis set and denominator;
72- state counting rule from the verified SAP/output;
73- show subjects affected and event count separately;
74- do not add p-values or causal labels;
75- do not interpret between-group differences;
76- preserve threshold rules exactly;
77- have safety and statistical reviewers verify deduplication, hierarchy, and population.

Adverse-event tables

For term-level aggregate tables:

  • use each required CSV header exactly once, with no surrounding whitespace; duplicate headers can overwrite values during dictionary parsing and are rejected;
  • state MedDRA version and language;
  • state analysis set and denominator;
  • state counting rule from the verified SAP/output;
  • show subjects affected and event count separately;
  • do not add p-values or causal labels;
  • do not interpret between-group differences;
  • preserve threshold rules exactly;
  • have safety and statistical reviewers verify deduplication, hierarchy, and population.
Raw lines 64 to 78
79## Figures
81No figure is mandatory. Create one only when requested, supported by verified aggregate data, allowed by the target guidance, and reviewable without external image generation.
83A CONSORT flow diagram is part of CONSORT 2025 reporting, but every count and reason must come from verified trial outputs. A missing count remains missing; do not create a decorative or inferred diagram.

Figures

No figure is mandatory. Create one only when requested, supported by verified aggregate data, allowed by the target guidance, and reviewable without external image generation.

A CONSORT flow diagram is part of CONSORT 2025 reporting, but every count and reason must come from verified trial outputs. A missing count remains missing; do not create a decorative or inferred diagram.

Raw lines 79 to 84
85## Deterministic consistency check
87`consistency_checker.py` can inspect:
89- ISO date and range ordering;
90- unit-label consistency;
91- `n/N (%)` arithmetic;
92- component-total arithmetic.
94It reports mismatches and review needs. It does not change the input, choose the correct source, or validate clinical/statistical meaning.

Deterministic consistency check

consistency_checker.py can inspect:

  • ISO date and range ordering;
  • unit-label consistency;
  • n/N (%) arithmetic;
  • component-total arithmetic.

It reports mismatches and review needs. It does not change the input, choose the correct source, or validate clinical/statistical meaning.

Raw lines 85 to 94