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name clinical-assessment description Use this Skill to score and interpret clinical scales: PHQ-9, GAD-7, PCL-5, reliable change index (RCI), norm comparison, and longitudinal change visualization.
tags ["psychology","clinical-assessment","PHQ-9","PCL-5","reliable-change-index","questionnaire"] version 1.0.0 authors [{"name":"awesome-rosetta-skills contributors","github":"@xjtulyc"}] license MIT platforms ["claude-code","codex","gemini-cli","cursor"] dependencies {"python":["pandas>=1.5","numpy>=1.23","matplotlib>=3.6","scipy>=1.9"]} last_updated 2026-03-18 status stable
Clinical Assessment Scoring and Interpretation
TL;DR — Batch-score PHQ-9, GAD-7, PCL-5, BDI-II, and SWLS questionnaires.
Compute the Reliable Change Index (RCI) for clinically significant change,
handle missing items with prorated scoring, compare against published norms,
and generate longitudinal trajectory visualizations.
When to Use
Use this Skill when you need to:
Score clinical questionnaires from raw item responses in a data frame
Apply standard severity cutoffs (minimal, mild, moderate, severe)
Determine whether pre-post change is statistically reliable (RCI)
Classify individuals as recovered, improved, unchanged, or deteriorated
Compute prorated scores when 1–2 items are missing
Generate per-participant longitudinal plots showing clinical trajectories
Compare scores to published normative samples (z-score lookup)
Background
Scoring Rules Summary
Scale Items Range Cutoffs PHQ-9 9 items, 0–3 each 0–27 0–4 minimal, 5–9 mild, 10–14 moderate, 15–27 severe GAD-7 7 items, 0–3 each 0–21 0–4 minimal, 5–9 mild, 10–14 moderate, 15–21 severe PCL-5 20 items, 0–4 each 0–80 ≥ 33 provisional PTSD BDI-II 21 items, 0–3 each 0–63 0–13 minimal, 14–19 mild, 20–28 moderate, 29–63 severe SWLS 5 items, 1–7 each 5–35 5–9 extremely dissatisfied, ≥31 extremely satisfied
PCL-5 DSM-5 Cluster Subscores
Cluster Items (1-indexed) Symptom Group B (Intrusion) 1–5 Re-experiencing C (Avoidance) 6–7 Avoidance D (Neg cognition) 8–14 Negative alterations in cognition/mood E (Hyperarousal) 15–20 Alterations in arousal/reactivity
Reliable Change Index (RCI)
Jacobson & Truax (1991):
SE_diff = SD_pre × √(2) × √(1 − r_tt)
RCI = (post_score − pre_score) / SE_diff
Where r_tt is the test-retest reliability of the scale. Reliable change:
|RCI| ≥ 1.96 (two-tailed, α = .05).
Clinical significance requires BOTH reliable change AND movement from the
dysfunctional distribution (above cutoff) to the functional distribution
(below cutoff).
Environment Setup conda create -n clinical_env python=3.11 -y
conda activate clinical_env
pip install pandas>=1.5 numpy>=1.23 matplotlib>=3.6 scipy>=1.9
python -c "import pandas, numpy, matplotlib, scipy; print('All OK')"
Core Workflow
Step 1 — Questionnaire Scoring import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker as mticker
from scipy import stats
from typing import Optional , Dict , List , Tuple , Union
SCALE_RELIABILITY = {
"PHQ-9" : 0.84 ,
"GAD-7" : 0.83 ,
"PCL-5" : 0.82 ,
"BDI-II" : 0.93 ,
"SWLS" : 0.82 ,
}
SCALE_NORM_SD = {
"PHQ-9" : 7.1 ,
"GAD-7" : 5.6 ,
"PCL-5" : 22.0 ,
"BDI-II" : 12.7 ,
"SWLS" : 6.4 ,
}
SEVERITY_CUTOFFS = {
"PHQ-9" : [(4 , "minimal" ), (9 , "mild" ), (14 , "moderate" ), (27 , "severe" )],
"GAD-7" : [(4 , "minimal" ), (9 , "mild" ), (14 , "moderate" ), (21 , "severe" )],
"PCL-5" : [(32 , "below_threshold" ), (80 , "provisional_PTSD" )],
"BDI-II" : [(13 , "minimal" ), (19 , "mild" ), (28 , "moderate" ), (63 , "severe" )],
"SWLS" : [(9 , "extremely_dissatisfied" ), (14 , "dissatisfied" ),
(19 , "slightly_below_avg" ), (24 , "average" ),
(29 , "high" ), (34 , "very_high" ), (35 , "extremely_satisfied" )],
}
CLINICAL_CUTOFF = {
"PHQ-9" : 10 ,
"GAD-7" : 10 ,
"PCL-5" : 33 ,
"BDI-II" : 20 ,
"SWLS" : 20 ,
}
def apply_severity_cutoff (score: float , scale: str ) -> str :
"""Apply severity classification based on published cutoffs."""
cutoffs = SEVERITY_CUTOFFS.get(scale, [])
for max_val, label in cutoffs:
if score <= max_val:
return label
return "unknown"
def score_phq9 (
df: pd.DataFrame,
item_cols: Optional [List [str ]] = None ,
id_col: str = "participant_id" ,
allow_missing: int = 1 ,
) -> pd.DataFrame:
"""
Score PHQ-9 depression questionnaire.
Items are scored 0 (not at all) to 3 (nearly every day).
Prorated scoring: if ≤ allow_missing items are missing, impute with
the mean of valid items × 9.
Args:
df: DataFrame with one row per participant.
item_cols: List of 9 PHQ-9 item column names (in order).
Defaults to ['phq1',...,'phq9'].
id_col: Participant ID column.
allow_missing: Max missing items allowed for prorated scoring.
Returns:
DataFrame with PHQ-9 total, severity, and item-level flags.
"""
if item_cols is None :
item_cols = [f"phq{i} " for i in range (1 , 10 )]
assert len (item_cols) == 9 , "PHQ-9 requires exactly 9 item columns."
result = df[[id_col]].copy() if id_col in df.columns else df.iloc[:, :1 ].copy()
result.columns = [id_col]
scores = []
severities = []
n_missing_list = []
for _, row in df.iterrows():
item_vals = row[item_cols]
n_valid = item_vals.notna().sum ()
n_missing = 9 - n_valid
if n_missing > allow_missing:
total = np.nan
severity = "missing"
elif n_missing == 0 :
total = item_vals.sum ()
severity = apply_severity_cutoff(total, "PHQ-9" )
else :
total = round ((item_vals.sum () / n_valid) * 9 )
severity = apply_severity_cutoff(total, "PHQ-9" )
scores.append(total)
severities.append(severity)
n_missing_list.append(n_missing)
result["PHQ9_total" ] = scores
result["PHQ9_severity" ] = severities
result["PHQ9_n_missing" ] = n_missing_list
result["PHQ9_item9_suicidal" ] = df[item_cols[8 ]].values
return result
def score_gad7 (
df: pd.DataFrame,
item_cols: Optional [List [str ]] = None ,
id_col: str = "participant_id" ,
allow_missing: int = 1 ,
) -> pd.DataFrame:
"""
Score GAD-7 anxiety questionnaire (7 items, 0–3 each, range 0–21).
Args:
df: DataFrame with one row per participant.
item_cols: List of 7 GAD-7 item column names.
id_col: Participant ID column.
allow_missing: Max missing items for prorated scoring.
Returns:
DataFrame with GAD-7 total and severity classification.
"""
if item_cols is None :
item_cols = [f"gad{i} " for i in range (1 , 8 )]
assert len (item_cols) == 7
result = df[[id_col]].copy() if id_col in df.columns else df.iloc[:, :1 ].copy()
result.columns = [id_col]
scores, severities, n_missing_list = [], [], []
for _, row in df.iterrows():
vals = row[item_cols]
n_valid = vals.notna().sum ()
n_missing = 7 - n_valid
if n_missing > allow_missing:
total, severity = np.nan, "missing"
elif n_missing == 0 :
total = vals.sum ()
severity = apply_severity_cutoff(total, "GAD-7" )
else :
total = round ((vals.sum () / n_valid) * 7 )
severity = apply_severity_cutoff(total, "GAD-7" )
scores.append(total)
severities.append(severity)
n_missing_list.append(n_missing)
result["GAD7_total" ] = scores
result["GAD7_severity" ] = severities
result["GAD7_n_missing" ] = n_missing_list
return result
def score_pcl5 (
df: pd.DataFrame,
item_cols: Optional [List [str ]] = None ,
id_col: str = "participant_id" ,
) -> pd.DataFrame:
"""
Score PCL-5 PTSD checklist (20 items, 0–4 each, range 0–80).
Computes total score and DSM-5 cluster subscores (B/C/D/E).
Args:
df: DataFrame with one row per participant.
item_cols: List of 20 PCL-5 item column names.
id_col: Participant ID column.
Returns:
DataFrame with total, cluster subscores, and provisional PTSD flag.
"""
if item_cols is None :
item_cols = [f"pcl{i} " for i in range (1 , 21 )]
assert len (item_cols) == 20
result = df[[id_col]].copy() if id_col in df.columns else df.iloc[:, :1 ].copy()
result.columns = [id_col]
clusters = {
"B_intrusion" : item_cols[0 :5 ],
"C_avoidance" : item_cols[5 :7 ],
"D_neg_cognition" : item_cols[7 :14 ],
"E_hyperarousal" : item_cols[14 :20 ],
}
result["PCL5_total" ] = df[item_cols].sum (axis=1 )
for cluster_name, cols in clusters.items():
result[f"PCL5_{cluster_name} " ] = df[cols].sum (axis=1 )
result["PCL5_provisional_PTSD" ] = result["PCL5_total" ] >= 33
result["PCL5_severity" ] = result["PCL5_total" ].apply(
lambda x: apply_severity_cutoff(x, "PCL-5" )
)
return result
Step 2 — Reliable Change Index def compute_rci (
pre_scores: np.ndarray,
post_scores: np.ndarray,
scale: str ,
sd_pre: Optional [float ] = None ,
r_tt: Optional [float ] = None ,
clinical_cutoff: Optional [float ] = None ,
dysfunctional_above_cutoff: bool = True ,
) -> pd.DataFrame:
"""
Compute Reliable Change Index (RCI) for pre-post score pairs.
Classification (Jacobson & Truax, 1991):
Recovered: Reliable improvement AND crossed clinical cutoff
Improved: Reliable improvement only
Unchanged: No reliable change (|RCI| < 1.96)
Deteriorated: Reliable worsening (RCI <= -1.96)
Args:
pre_scores: Array of pre-treatment scores.
post_scores: Array of post-treatment scores.
scale: Scale name (e.g., 'PHQ-9') for default SD and r_tt lookup.
sd_pre: SD of pre-treatment scores (overrides norm SD if provided).
r_tt: Test-retest reliability (overrides default if provided).
clinical_cutoff: Score threshold for functional vs dysfunctional range.
dysfunctional_above_cutoff: True if high scores = clinical (PHQ-9, GAD-7);
False if low scores = clinical (SWLS).
Returns:
DataFrame with RCI, classification, and pre/post severity.
"""
sd = sd_pre if sd_pre is not None else SCALE_NORM_SD.get(scale, 10.0 )
rtt = r_tt if r_tt is not None else SCALE_RELIABILITY.get(scale, 0.85 )
cutoff = clinical_cutoff if clinical_cutoff is not None else CLINICAL_CUTOFF.get(scale, None )
se_diff = sd * np.sqrt(2 ) * np.sqrt(1 - rtt)
rci_values = (post_scores - pre_scores) / se_diff
classifications = []
for rci_val, pre, post in zip (rci_values, pre_scores, post_scores):
if rci_val <= -1.96 :
if cutoff is not None :
if dysfunctional_above_cutoff:
crossed = pre >= cutoff and post < cutoff
else :
crossed = pre < cutoff and post >= cutoff
cls = "Recovered" if crossed else "Improved"
else :
cls = "Improved"
elif rci_val >= 1.96 :
cls = "Deteriorated"
else :
cls = "Unchanged"
classifications.append(cls)
result_df = pd.DataFrame({
"pre_score" : pre_scores,
"post_score" : post_scores,
"change" : post_scores - pre_scores,
"RCI" : np.round (rci_values, 3 ),
"classification" : classifications,
"pre_severity" : [apply_severity_cutoff(s, scale) for s in pre_scores],
"post_severity" : [apply_severity_cutoff(s, scale) for s in post_scores],
})
class_counts = result_df["classification" ].value_counts()
n = len (result_df)
print (f"\nRCI Summary for {scale} (SE_diff = {se_diff:.2 f} , r_tt = {rtt} ):" )
for cls in ["Recovered" , "Improved" , "Unchanged" , "Deteriorated" ]:
count = class_counts.get(cls, 0 )
print (f" {cls:15s} : n = {count:3d} ({count/n:.1 %} )" )
return result_df
Step 3 — Longitudinal Visualization def plot_longitudinal_trajectories (
df_long: pd.DataFrame,
outcome_col: str ,
time_col: str ,
id_col: str ,
scale_name: str = "" ,
highlight_clinical_cutoff: Optional [float ] = None ,
output_path: Optional [str ] = None ,
n_highlight: int = 5 ,
) -> plt.Figure:
"""
Plot individual longitudinal trajectories with group mean overlay.
Args:
df_long: Long-format DataFrame (one row per person × time).
outcome_col: Score column.
time_col: Time point column (numeric or ordered categorical).
id_col: Participant ID column.
scale_name: Scale label for plot title and y-axis.
highlight_clinical_cutoff: Draw a horizontal reference line at this score.
output_path: Optional path to save figure.
n_highlight: Number of individual trajectories to highlight.
Returns:
Matplotlib Figure.
"""
time_points = sorted (df_long[time_col].unique())
persons = df_long[id_col].unique()
rng = np.random.default_rng(42 )
fig, ax = plt.subplots(figsize=(10 , 6 ))
for person in persons:
pdata = df_long[df_long[id_col] == person].sort_values(time_col)
ax.plot(pdata[time_col], pdata[outcome_col],
color="lightgray" , linewidth=0.8 , alpha=0.5 , zorder=1 )
highlighted = rng.choice(persons, min (n_highlight, len (persons)), replace=False )
colors = plt.cm.tab10(np.linspace(0 , 0.8 , len (highlighted)))
for person, color in zip (highlighted, colors):
pdata = df_long[df_long[id_col] == person].sort_values(time_col)
ax.plot(pdata[time_col], pdata[outcome_col],
color=color, linewidth=2.0 , alpha=0.9 , zorder=3 ,
label=f"{id_col} ={person} " )
group_mean = df_long.groupby(time_col)[outcome_col].agg(["mean" , "sem" ]).reset_index()
ax.plot(group_mean[time_col], group_mean["mean" ],
color="black" , linewidth=3 , zorder=4 , label="Group mean" )
ax.fill_between(
group_mean[time_col],
group_mean["mean" ] - 1.96 * group_mean["sem" ],
group_mean["mean" ] + 1.96 * group_mean["sem" ],
alpha=0.15 , color="black" , zorder=2 ,
)
if highlight_clinical_cutoff is not None :
ax.axhline(highlight_clinical_cutoff, color="crimson" , linestyle="--" ,
linewidth=1.5 , label=f"Clinical cutoff ({highlight_clinical_cutoff} )" )
ax.set_xlabel("Time Point" )
ax.set_ylabel(scale_name or outcome_col)
ax.set_title(f"Longitudinal Trajectories — {scale_name} " )
ax.legend(fontsize=8 , loc="upper right" )
ax.grid(alpha=0.3 )
fig.tight_layout()
if output_path:
fig.savefig(output_path, dpi=150 )
plt.show()
return fig
Advanced Usage
Batch Scoring with PHQ-9 + GAD-7 Combined def batch_score_all_scales (
df: pd.DataFrame,
id_col: str = "participant_id" ,
phq9_items: Optional [List [str ]] = None ,
gad7_items: Optional [List [str ]] = None ,
pcl5_items: Optional [List [str ]] = None ,
) -> pd.DataFrame:
"""
Score PHQ-9, GAD-7, and PCL-5 in one call and merge results.
Args:
df: Wide-format DataFrame.
id_col: Participant ID column.
phq9_items: PHQ-9 item columns (defaults to phq1–phq9).
gad7_items: GAD-7 item columns (defaults to gad1–gad7).
pcl5_items: PCL-5 item columns (defaults to pcl1–pcl20).
Returns:
DataFrame with all scale scores merged on id_col.
"""
phq9_df = score_phq9(df, item_cols=phq9_items, id_col=id_col)
gad7_df = score_gad7(df, item_cols=gad7_items, id_col=id_col)
pcl5_df = score_pcl5(df, item_cols=pcl5_items, id_col=id_col)
merged = phq9_df.merge(gad7_df, on=id_col).merge(pcl5_df, on=id_col)
merged["comorbid_dep_anx" ] = (
(merged["PHQ9_total" ] >= 10 ) & (merged["GAD7_total" ] >= 10 )
)
print (f"\nBatch scoring complete: {len (merged)} participants" )
print (f"PHQ-9 ≥ 10 (moderate+): {(merged['PHQ9_total' ] >= 10 ).sum ()} " )
print (f"GAD-7 ≥ 10 (moderate+): {(merged['GAD7_total' ] >= 10 ).sum ()} " )
print (f"PCL-5 ≥ 33 (provisional PTSD): {merged['PCL5_provisional_PTSD' ].sum ()} " )
print (f"Comorbid depression+anxiety: {merged['comorbid_dep_anx' ].sum ()} " )
return merged
Troubleshooting Problem Likely Cause Solution Negative RCI for "worsening" with PHQ-9 Convention: lower = better Check rci_val >= 1.96 means deterioration All classified as "Unchanged" SD too large or wrong scale Use clinical sample SD, not general population Prorated score unexpectedly high All non-missing items are high Expected behavior; flag if > 2 items missing PCL-5 cluster subscores don't sum to total Rounding or missing items Ensure no NaN; use sum(axis=1, min_count=20) Longitudinal plot illegible Too many participants Reduce n_highlight or use mean + CI only NaN in severity column Score is NaN (too many missing) Apply dropna() before severity lookup
External Resources
Kroenke, K., Spitzer, R. L., & Williams, J. B. W. (2001). The PHQ-9.
Journal of General Internal Medicine , 16(9), 606–613.
Spitzer, R. L., et al. (2006). A brief measure for assessing GAD. JAMA Internal Medicine.
Blevins, C. A., et al. (2015). PCL-5: Initial psychometric assessment.
Assessment , 22(5), 477–482.
Jacobson, N. S., & Truax, P. (1991). Clinical significance. Journal of Consulting
and Clinical Psychology , 59(1), 12–19.
Diener, E., et al. (1985). The Satisfaction with Life Scale. Journal of Personality
Assessment , 49(1), 71–75.
Examples
Example 1 — Batch PHQ-9 + GAD-7 Scoring with Cutoff Classification import pandas as pd
import numpy as np
rng = np.random.default_rng(0 )
n = 80
data = {
"participant_id" : [f"P{i:03d} " for i in range (1 , n + 1 )],
}
for i in range (1 , 10 ):
data[f"phq{i} " ] = rng.integers(0 , 4 , n)
for i in range (1 , 8 ):
data[f"gad{i} " ] = rng.integers(0 , 4 , n)
for i in range (1 , 21 ):
data[f"pcl{i} " ] = rng.integers(0 , 5 , n)
data["phq3" ][5 ] = np.nan
data["gad2" ][12 ] = np.nan
df_raw = pd.DataFrame(data)
df_scored = batch_score_all_scales(
df_raw,
id_col="participant_id" ,
phq9_items=[f"phq{i} " for i in range (1 , 10 )],
gad7_items=[f"gad{i} " for i in range (1 , 8 )],
pcl5_items=[f"pcl{i} " for i in range (1 , 21 )],
)
print ("\nSample of scored data:" )
print (df_scored[["participant_id" , "PHQ9_total" , "PHQ9_severity" ,
"GAD7_total" , "GAD7_severity" , "PCL5_total" ]].head(10 ))
fig, axes = plt.subplots(1 , 3 , figsize=(14 , 5 ))
for ax, (col, title) in zip (axes, [
("PHQ9_severity" , "PHQ-9 Severity" ),
("GAD7_severity" , "GAD-7 Severity" ),
("PCL5_severity" , "PCL-5 Severity" ),
]):
counts = df_scored[col].value_counts()
ax.bar(counts.index, counts.values, color="steelblue" , edgecolor="white" )
ax.set_title(title)
ax.set_ylabel("Frequency" )
ax.tick_params(axis="x" , rotation=30 )
fig.tight_layout()
plt.savefig("severity_distributions.png" , dpi=150 )
plt.show()
Example 2 — RCI and Clinical Significance Classification
rng = np.random.default_rng(1 )
n_pts = 60
pre = rng.normal(16 , 6 , n_pts).clip(0 , 27 ).round ()
post = (pre - rng.normal(5 , 4 , n_pts)).clip(0 , 27 ).round ()
rci_df = compute_rci(
pre_scores=pre,
post_scores=post,
scale="PHQ-9" ,
clinical_cutoff=10 ,
dysfunctional_above_cutoff=True ,
)
print ("\nRCI results sample:" )
print (rci_df.head(10 ).to_string())
class_counts = rci_df["classification" ].value_counts()
fig, axes = plt.subplots(1 , 2 , figsize=(12 , 5 ))
colors_map = {"Recovered" : "#2ecc71" , "Improved" : "#3498db" ,
"Unchanged" : "#f39c12" , "Deteriorated" : "#e74c3c" }
bars = axes[0 ].bar(class_counts.index,
class_counts.values,
color=[colors_map.get(c, "gray" ) for c in class_counts.index])
axes[0 ].set_title("Treatment Response Classification" )
axes[0 ].set_ylabel("Number of Participants" )
for bar, count in zip (bars, class_counts.values):
axes[0 ].text(bar.get_x() + bar.get_width() / 2 , bar.get_height() + 0.5 ,
str (count), ha="center" , va="bottom" , fontsize=10 )
scatter_colors = [colors_map.get(c, "gray" ) for c in rci_df["classification" ]]
axes[1 ].scatter(rci_df["pre_score" ], rci_df["post_score" ],
c=scatter_colors, alpha=0.7 , s=40 )
axes[1 ].plot([0 , 27 ], [0 , 27 ], "k--" , linewidth=1 , label="No change" )
axes[1 ].axhline(10 , color="crimson" , linestyle=":" , linewidth=1 , label="Cutoff post" )
axes[1 ].axvline(10 , color="crimson" , linestyle=":" , linewidth=1 , label="Cutoff pre" )
axes[1 ].set_xlabel("Pre-treatment PHQ-9" )
axes[1 ].set_ylabel("Post-treatment PHQ-9" )
axes[1 ].set_title("RCI Scatter Plot" )
legend_patches = [mpatches.Patch(color=c, label=l) for l, c in colors_map.items()]
axes[1 ].legend(handles=legend_patches, fontsize=8 )
import matplotlib.patches as mpatches
fig.tight_layout()
plt.savefig("rci_analysis.png" , dpi=150 )
plt.show()
print ("Clinical assessment analysis complete." )
Changelog Version Date Change 1.0.0 2026-03-18 Initial release — PHQ-9/GAD-7/PCL-5 scoring, RCI, clinical significance, longitudinal plots
