@synsci/cli-darwin-x64 1.1.97 → 1.1.99

package/bin/skills/clinical-reports/references/data_presentation.md

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-# Data Presentation in Clinical Reports
-
-## Tables for Clinical Data
-
-### Table Design Principles
-
-**General guidelines:**
-- Clear, concise title describing table contents
-- Column headers with units
-- Row labels aligned left, data aligned appropriately (numbers right, text left)
-- Footnotes for abbreviations, statistical notation, special cases
-- Consistent decimal places (typically 1-2 for percentages, 1-3 for continuous variables)
-- Consistent formatting throughout document
-
-**Title placement:**
-- Above table
-- Numbered sequentially (Table 1, Table 2, etc.)
-- Descriptive enough to stand alone
-
-**Footnote symbols (in order):**
-- *, †, ‡, §, ||, ¶, #
-- Or use superscript letters (a, b, c...)
-- Or use superscript numbers if not confused with references
-
-### Demographic and Baseline Characteristics Table
-
-**Purpose:** Describe study population at baseline
-
-**Standard format:**
-
-```
-Table 1. Baseline Demographics and Clinical Characteristics
-
-Characteristic                  Treatment Group    Control Group    Total
-                               (N=150)            (N=145)          (N=295)
-─────────────────────────────────────────────────────────────────────────
-Age, years
-  Mean (SD)                    64.2 (8.5)         63.8 (9.1)       64.0 (8.8)
-  Median (IQR)                 65 (58-71)         64 (57-70)       64 (58-71)
-  Range                        45-82              43-85            43-85
-
-Sex, n (%)
-  Male                         95 (63.3)          88 (60.7)        183 (62.0)
-  Female                       55 (36.7)          57 (39.3)        112 (38.0)
-
-Race, n (%)
-  White                        110 (73.3)         105 (72.4)       215 (72.9)
-  Black/African American       25 (16.7)          28 (19.3)        53 (18.0)
-  Asian                        10 (6.7)           8 (5.5)          18 (6.1)
-  Other                        5 (3.3)            4 (2.8)          9 (3.0)
-
-BMI, kg/m²
-  Mean (SD)                    28.5 (4.2)         28.1 (4.5)       28.3 (4.4)
-
-Baseline HbA1c, %
-  Mean (SD)                    8.9 (1.2)          9.0 (1.3)        9.0 (1.2)
-
-Disease duration, years
-  Median (IQR)                 6 (3-10)           5 (3-9)          6 (3-10)
-
-Prior medications, n (%)
-  Metformin                    135 (90.0)         130 (89.7)       265 (89.8)
-  Sulfonylurea                 45 (30.0)          42 (29.0)        87 (29.5)
-  Insulin                      20 (13.3)          18 (12.4)        38 (12.9)
-─────────────────────────────────────────────────────────────────────────
-SD = standard deviation; IQR = interquartile range; BMI = body mass index;
-HbA1c = hemoglobin A1c
-```
-
-**Key elements:**
-- Sample size for each group (N=)
-- Continuous variables: mean (SD), median (IQR), range
-- Categorical variables: n (%)
-- No p-values for baseline comparisons (debated but generally not recommended)
-
-### Efficacy Results Table
-
-**Purpose:** Present primary and secondary endpoint results
-
-**Example:**
-
-```
-Table 2. Primary and Secondary Efficacy Endpoints at Week 24
-
-Endpoint                           Treatment      Control        Difference    P-value
-                                   (N=150)        (N=145)        (95% CI)
-──────────────────────────────────────────────────────────────────────────────────
-Primary Endpoint
-Change in HbA1c from baseline, %
-  Mean (SE)                        -1.8 (0.1)     -0.6 (0.1)     -1.2          <0.001
-  95% CI                           (-2.0, -1.6)   (-0.8, -0.4)   (-1.5, -0.9)
-
-Secondary Endpoints
-Change in FPG, mg/dL
-  Mean (SE)                        -42.5 (3.2)    -15.2 (3.4)    -27.3         <0.001
-  95% CI                           (-48.8, -36.2) (-21.9, -8.5)  (-36.4, -18.2)
-
-% achieving HbA1c <7%
-  n (%)                            78 (52.0)      25 (17.2)      -              <0.001
-  95% CI                           (43.9, 60.1)   (11.4, 24.5)   
-
-Change in body weight, kg
-  Mean (SE)                        -3.2 (0.4)     -0.5 (0.4)     -2.7          <0.001
-  95% CI                           (-4.0, -2.4)   (-1.3, 0.3)    (-3.8, -1.6)
-──────────────────────────────────────────────────────────────────────────────
-SE = standard error; CI = confidence interval; HbA1c = hemoglobin A1c; 
-FPG = fasting plasma glucose
-```
-
-**Statistical presentation:**
-- Point estimates with measures of precision (SE or CI)
-- p-values (consider adjustment for multiplicity)
-- Effect size (difference or ratio) with 95% CI
-- Significance level noted (e.g., p<0.05, p<0.01, p<0.001)
-
-### Adverse Events Table
-
-**Purpose:** Summarize safety data
-
-**Example:**
-
-```
-Table 3. Summary of Adverse Events
-
-Event Category                        Treatment     Control       P-value
-                                      (N=150)       (N=145)
-                                      n (%)         n (%)
-──────────────────────────────────────────────────────────────────────────
-Any adverse event                     120 (80.0)    95 (65.5)     0.004
-
-Treatment-related adverse events       85 (56.7)    42 (29.0)     <0.001
-
-Serious adverse events                 12 (8.0)     8 (5.5)       0.412
-
-Adverse events leading to              8 (5.3)      4 (2.8)       0.257
-discontinuation
-
-Deaths                                 0 (0.0)      1 (0.7)       0.492
-
-Common adverse events (≥5% in any group)
-  Nausea                              45 (30.0)     12 (8.3)      <0.001
-  Diarrhea                            38 (25.3)     10 (6.9)      <0.001
-  Headache                            22 (14.7)     18 (12.4)     0.568
-  Hypoglycemia                        18 (12.0)     5 (3.4)       0.007
-  Dizziness                           12 (8.0)      8 (5.5)       0.412
-──────────────────────────────────────────────────────────────────────────
-Adverse events coded using MedDRA version 24.0
-```
-
-**Key elements:**
-- Overall AE summary
-- Serious AEs highlighted
-- Deaths reported
-- Common AEs (typically ≥5% or ≥10% threshold)
-- MedDRA coding indicated
-
-### Laboratory Abnormalities Table
-
-**Shift tables showing changes from baseline:**
-
-```
-Table 4. Laboratory Values Meeting Predefined Criteria for Abnormality
-
-Laboratory Parameter                 Treatment      Control
-                                     (N=150)        (N=145)
-                                     n (%)          n (%)
-──────────────────────────────────────────────────────────────────────────
-ALT >3× ULN                          8 (5.3)        3 (2.1)
-AST >3× ULN                          5 (3.3)        2 (1.4)
-Total bilirubin >2× ULN              2 (1.3)        1 (0.7)
-Creatinine >1.5× baseline            12 (8.0)       5 (3.4)
-Hemoglobin <10 g/dL                  3 (2.0)        2 (1.4)
-Platelets <100 × 10³/μL              1 (0.7)        0 (0.0)
-──────────────────────────────────────────────────────────────────────────
-ULN = upper limit of normal; ALT = alanine aminotransferase; 
-AST = aspartate aminotransferase
-```
-
-### Patient Disposition Table (CONSORT Format)
-
-```
-Table 5. Patient Disposition
-
-Disposition                              Treatment     Control       Total
-                                         (N=150)       (N=145)       (N=295)
-────────────────────────────────────────────────────────────────────────────
-Screened                                 -             -             425
-
-Randomized                               150           145           295
-
-Completed study                          135 (90.0)    130 (89.7)    265 (89.8)
-
-Discontinued, n (%)                      15 (10.0)     15 (10.3)     30 (10.2)
-  Adverse event                          8 (5.3)       4 (2.8)       12 (4.1)
-  Lack of efficacy                       2 (1.3)       5 (3.4)       7 (2.4)
-  Lost to follow-up                      3 (2.0)       4 (2.8)       7 (2.4)
-  Withdrawal of consent                  2 (1.3)       2 (1.4)       4 (1.4)
-
-Included in efficacy analysis
-  ITT population                         150 (100)     145 (100)     295 (100)
-  Per-protocol population                142 (94.7)    138 (95.2)    280 (94.9)
-
-Included in safety analysis              150 (100)     145 (100)     295 (100)
-────────────────────────────────────────────────────────────────────────────
-ITT = intent-to-treat
-```
-
-## Figures for Clinical Data
-
-### Figure Design Principles
-
-**General guidelines:**
-- Clear, concise caption/legend below figure
-- Numbered sequentially (Figure 1, Figure 2, etc.)
-- Axis labels with units
-- Legible font size (minimum 8-10 point)
-- High resolution (300 dpi for print, 150 dpi for web)
-- Color-blind friendly palette
-- Black and white compatible (use different symbols/patterns)
-
-**Figure caption:**
-- Describes what is shown
-- Explains symbols, error bars, statistical annotations
-- Defines abbreviations
-- Provides context for interpretation
-
-### CONSORT Flow Diagram
-
-**Purpose:** Show patient flow through randomized trial
-
-```
-                    Assessed for eligibility (n=425)
-                              │
-        ┌─────────────────────┴─────────────────────┐
-        │                                           │
-    Excluded (n=130)                                │
-    • Not meeting inclusion criteria (n=85)         │
-    • Declined to participate (n=32)                │
-    • Other reasons (n=13)                          │
-                                                    │
-                                           Randomized (n=295)
-                                                    │
-                    ┌───────────────────────────────┴───────────────────────────────┐
-                    │                                                               │
-        Allocated to Treatment (n=150)                             Allocated to Control (n=145)
-        • Received allocated intervention (n=148)                  • Received allocated intervention (n=143)
-        • Did not receive allocated intervention (n=2)             • Did not receive allocated intervention (n=2)
-          Reasons: withdrew consent before treatment                Reasons: withdrew consent before treatment
-                    │                                                               │
-        ┌───────────┴────────────┐                                  ┌──────────────┴─────────────┐
-        │                        │                                  │                            │
-    Lost to follow-up (n=3)  Discontinued (n=12)              Lost to follow-up (n=4)     Discontinued (n=11)
-                             • Adverse events (n=8)                                       • Adverse events (n=4)
-                             • Lack of efficacy (n=2)                                     • Lack of efficacy (n=5)
-                             • Withdrew consent (n=2)                                     • Withdrew consent (n=2)
-                    │                                                               │
-            Analyzed (n=150)                                               Analyzed (n=145)
-            • ITT analysis (n=150)                                         • ITT analysis (n=145)
-            • Per-protocol analysis (n=142)                                • Per-protocol analysis (n=138)
-            • Excluded from analysis (n=0)                                 • Excluded from analysis (n=0)
-```
-
-### Kaplan-Meier Survival Curve
-
-**Purpose:** Show time-to-event data
-
-**Elements:**
-- X-axis: Time (weeks, months, years)
-- Y-axis: Probability of event-free survival (0 to 1 or 0% to 100%)
-- Separate curves for each treatment group
-- Censored observations marked (often with vertical tick marks)
-- Number at risk table below graph
-- Median survival time indicated
-- Log-rank p-value
-- Hazard ratio with 95% CI
-
-**Caption example:**
-```
-Figure 1. Kaplan-Meier Curves for Overall Survival
-
-Kaplan-Meier estimates of overall survival in the treatment and control groups.
-Tick marks indicate censored observations. Number at risk shown below graph.
-Log-rank p<0.001. Median survival: Treatment 24.5 months (95% CI: 22.1-26.8),
-Control 18.2 months (95% CI: 16.5-20.1). Hazard ratio 0.68 (95% CI: 0.55-0.84).
-```
-
-### Forest Plot
-
-**Purpose:** Display subgroup analyses or meta-analysis results
-
-**Elements:**
-- Point estimates (squares or diamonds)
-- Size of symbol proportional to precision (inverse variance) or sample size
-- Horizontal lines showing 95% CI
-- Vertical line at null effect (HR=1.0, OR=1.0, or difference=0)
-- Subgroup labels on left
-- Effect size values on right
-- Overall estimate (if meta-analysis)
-- Heterogeneity statistics (I², p-value)
-
-**Caption example:**
-```
-Figure 2. Forest Plot of Treatment Effect by Subgroup
-
-Effect of treatment vs. control on primary endpoint across pre-specified subgroups.
-Squares represent point estimates; horizontal lines represent 95% confidence intervals.
-Square size is proportional to subgroup sample size. Overall effect shown as diamond.
-p-value for interaction testing heterogeneity of treatment effect across subgroups.
-```
-
-### Box Plot
-
-**Purpose:** Show distribution of continuous variable
-
-**Elements:**
-- Box: IQR (25th to 75th percentile)
-- Line in box: Median
-- Whiskers: Extend to most extreme data point within 1.5 × IQR
-- Outliers: Points beyond whiskers (often shown as circles)
-- X-axis: Groups or time points
-- Y-axis: Continuous variable with units
-
-### Scatter Plot with Regression
-
-**Purpose:** Show relationship between two continuous variables
-
-**Elements:**
-- X-axis: Independent variable
-- Y-axis: Dependent variable
-- Individual data points
-- Regression line (if appropriate)
-- Regression equation
-- R² value
-- P-value for slope
-- 95% confidence interval for regression line (optional, shown as shaded area)
-
-### Spaghetti Plot
-
-**Purpose:** Show individual trajectories over time
-
-**Elements:**
-- X-axis: Time
-- Y-axis: Outcome variable
-- Individual patient lines (often semi-transparent)
-- Mean trajectory (bold line)
-- Separate colors for treatment groups
-
-### Bar Chart
-
-**Purpose:** Compare proportions or means across groups
-
-**Elements:**
-- Clear separation between bars
-- Error bars (SEM or 95% CI)
-- Y-axis starts at 0 (do not truncate for bar charts)
-- Group labels on X-axis
-- Value labels on Y-axis with units
-- Statistical significance indicated (p-values or asterisks)
-
-**Avoid:**
-- 3D bar charts (distort perception)
-- Excessive decoration
-- Truncated Y-axis for bars
-
-### Line Graph
-
-**Purpose:** Show changes over time
-
-**Elements:**
-- X-axis: Time (with consistent intervals)
-- Y-axis: Outcome variable
-- Separate lines for each group (different colors/patterns)
-- Data points marked (circles, squares, triangles)
-- Error bars at each time point (SE or 95% CI)
-- Legend identifying groups
-- Grid lines (optional, light gray)
-
-### Histogram
-
-**Purpose:** Show distribution of continuous variable
-
-**Elements:**
-- X-axis: Variable (divided into bins)
-- Y-axis: Frequency or density
-- Appropriate bin width (not too few, not too many)
-- Overlay normal distribution curve (if testing normality)
-
-## Special Considerations for Clinical Data
-
-### Presenting Proportions
-
-**Numerator and denominator:**
-- Always provide both: 25/100 (25%)
-- Not just percentage (25%)
-
-**Percentages:**
-- No decimal places if n<100
-- 1 decimal place if n≥100
-- Never report >1 decimal place for percentages
-
-**Confidence intervals for proportions:**
-- Wilson score interval or exact binomial (better than Wald for small samples)
-- Always report with percentage
-
-### Presenting Continuous Data
-
-**Measures of central tendency:**
-- Mean for normally distributed data
-- Median for skewed data or ordinal data
-- Report both if distribution unclear
-
-**Measures of dispersion:**
-- **Standard deviation (SD)**: Describes variability in data
-- **Standard error (SE)**: Describes precision of mean estimate
-- **95% Confidence interval**: Preferred for inferential statistics
-- **Interquartile range (IQR)**: With median for skewed data
-- **Range**: Min to max
-
-**When to use each:**
-- Descriptive statistics → Mean (SD) or Median (IQR)
-- Inferential statistics → Mean (95% CI) or Mean (SE)
-- Never use ± without specifying SD, SE, or CI
-
-### Presenting P-values
-
-**Reporting guidelines:**
-- Report exact p-values to 2-3 decimal places (p=0.042)
-- For very small p-values, use p<0.001 (not p=0.000)
-- Do not report as "NS" or "p=NS"
-- For non-significant results, report exact p-value (p=0.18, not p>0.05)
-- Specify two-tailed unless pre-specified one-tailed
-- Correct for multiple comparisons when appropriate
-- Report significance threshold used (α=0.05 is standard)
-
-**Avoid:**
-- p<0.05 (report exact value)
-- p=0.00 (impossible)
-- Multiple decimal places (p=0.04235891)
-
-### Statistical Significance Indicators
-
-**Options:**
-1. Report p-values in table
-2. Use asterisks with legend:
-   - *p<0.05
-   - **p<0.01
-   - ***p<0.001
-3. Use confidence intervals (preferred)
-
-### Confidence Intervals
-
-**Reporting:**
-- 95% CI is standard
-- Format: (lower limit, upper limit)
-- Or: lower limit to upper limit
-- Or: lower limit-upper limit
-
-**Interpretation:**
-- If CI for difference excludes 0 → significant
-- If CI for ratio excludes 1 → significant
-- Width of CI indicates precision
-
-### Missing Data
-
-**Indicate clearly:**
-- Footnote explaining missing data
-- State clearly if analysis is complete case
-- Describe imputation method if used
-- Report amount of missing data per variable
-
-### Decimal Places and Rounding
-
-**General rules:**
-- Report to level of measurement precision
-- Consistent decimal places within table
-- Round p-values to 2-3 decimal places
-- Round percentages to 0-1 decimal place
-- Round means/medians to 1-2 decimal places
-- Include appropriate significant figures
-
-## Software for Creating Figures
-
-**Statistical software:**
-- R (ggplot2) - highly customizable
-- GraphPad Prism - user-friendly for biomedical
-- SAS, Stata, SPSS - comprehensive statistical packages
-- Python (matplotlib, seaborn) - flexible and powerful
-
-**General graphics software:**
-- Adobe Illustrator - professional publication-quality
-- Inkscape - free vector graphics editor
-- PowerPoint - basic graphs, easy to use
-- BioRender - biological schematics and figures
-
-## Color Schemes
-
-**Color-blind friendly palettes:**
-- Avoid red-green combinations
-- Use blue-orange, blue-yellow
-- Include shape/pattern differences
-- Test figures in grayscale
-
-**Recommended palettes:**
-- ColorBrewer (designed for data visualization)
-- Viridis (perceptually uniform)
-- IBM Color Blind Safe Palette
-
-## Image Quality Standards
-
-**Resolution:**
-- 300 dpi for print publication
-- 150 dpi for web/screen
-- Vector graphics (PDF, SVG) preferred for graphs
-
-**File formats:**
-- TIFF or EPS for print
-- PNG for web
-- PDF for vector graphics
-- JPEG acceptable for photographs (high quality)
-
-**Image editing:**
-- No manipulation that alters data
-- Only acceptable adjustments: brightness, contrast, color balance applied to entire image
-- Document all adjustments
-- Provide original images if requested
-
----
-
-This reference provides comprehensive guidance for presenting clinical data in tables and figures following best practices and publication standards. Use these guidelines to create clear, accurate, and professional data presentations.
-