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time-dependent-roc Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, `risk_score` as the default marker unless `--marker_col` is provided, parameter validation, standardized output directories, AUC table export, ROC point export, and PDF figure generation.
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name time-dependent-roc description Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, `risk_score` as the default marker unless `--marker_col` is provided, parameter validation, standardized output directories, AUC table export, ROC point export, and PDF figure generation. license MIT author AIPOCH
Source : https://github.com/aipoch/medical-research-skills
Time-Dependent ROC Analysis
Use this skill to compute and plot time-dependent ROC curves for survival outcomes.
Use This Skill When
You have survival data with futime and fustat columns.
You need time-specific ROC curves and AUC values for a numeric risk marker.
You want a command-line workflow with parameter validation and standardized outputs.
Your file contains a numeric marker column named risk_score, or you will provide another marker explicitly with --marker_col.
Primary Command
Rscript scripts/main.R \
--data_file <input_file> \
--times <comma_separated_times> \
--output_dir <output_dir>
Prerequisites
Rscript is available in the shell.
Required R packages: optparse, timeROC, survival, ggplot2.
Optional package for Excel input: openxlsx.
Install missing packages with Rscript -e 'install.packages(c("optparse", "timeROC", "survival", "ggplot2", "openxlsx"), repos="https://cloud.r-project.org")'.
Core Arguments Argument Required Description --data_fileYes Input data file in CSV, TXT, TSV, TAB, XLS, or XLSX format --timesNo Prediction time points, comma-separated. Default 1,3,5 --marker_colNo Marker column name. Default risk_score; provide this option when your file uses a different marker --output_dirNo Output directory, default ./TimeROC_Results --time_unitNo Time unit label for plot/output: year, month, or day. Default year --auto_convert_daysNo If TRUE, convert large futime values from days to the selected unit when appropriate. Default TRUE --weightingNo IPCW weighting method: aalen, marginal, or cox. Default aalen --causeNo Event code treated as the outcome of interest. Default 1
Input Requirements
The input file must contain futime and fustat columns.
The selected marker column must exist and be numeric or coercible to numeric.
If --marker_col is omitted, the input file must contain risk_score.
futime must be numeric or coercible to numeric.fustat must be numeric or coercible to numeric.Rows with missing futime, fustat, or marker values are excluded.
At least 5 complete rows and at least 1 event for the requested cause are required.
id fustat futime risk_score risk_group GPR161 RIBC2
TCGA-C5-A1M5 1 5.6219 -1.1070 low 2.8252 5.3532
TCGA-EA-A5O9 0 2.1589 -0.8964 low 2.6046 4.4293
TCGA-C5-A3HL 0 1.7014 -0.9044 low 4.1248 4.9166
Minimal Workflow
Confirm the input file exists and includes futime, fustat, and risk_score, or plan to pass --marker_col.
Run scripts/main.R with the requested time points.
Check the output directory for the AUC table and PDF figure.
If you omit --data_file, the script exits with SKILL_MISSING_INPUT.
Outputs Expected output structure:
<output_dir>/
├── data/
│ └── time_roc_points.<csv|txt>
├── session_info.txt
├── figure/
│ └── time_roc.pdf
└── table/
└── time_roc_auc.<csv|txt>
data/time_roc_points.csv or data/time_roc_points.txttable/time_roc_auc.csv or table/time_roc_auc.txtfigure/time_roc.pdfsession_info.txt Exported result fields include:
timetime_unitaucmarker_coln_completen_events Exported ROC point fields include:
false_positive_ratesensitivitytimetime_unitauccurve_label
Read These Files When Needed Need File Statistical details and assumptions references/algorithm.mdMore CLI examples references/cli-guide.mdError diagnosis references/troubleshooting.mdMain execution entry point scripts/main.RSample test data tests/data/
Quick Examples Rscript scripts/main.R \
--data_file tests/data/time_roc_sample1.txt \
--times 1,3,5 \
--output_dir tests/output_basic
Specify marker column and plot styling:
Rscript scripts/main.R \
--data_file tests/data/time_roc_sample2.txt \
--marker_col GPR161 \
--times 1,2,4 \
--line_colors "#4DBBD5,#E64B35,#00A087" \
--legend_position bottom \
--output_dir tests/output_gpr161
Validation Rscript scripts/main.R --help
Rscript scripts/main.R \
--data_file tests/data/time_roc_sample1.txt \
--times 1,3,5 \
--output_dir tests/validation_output
After running analysis, verify that these files exist:
tests/validation_output/data/time_roc_points.csvtests/validation_output/table/time_roc_auc.csvtests/validation_output/figure/time_roc.pdftests/validation_output/session_info.txt
Common Errors
SKILL_FILE_NOT_FOUND: Input file path is wrong or inaccessible.SKILL_MISSING_COLUMNS: futime or fustat is missing.SKILL_INVALID_DATA: The marker column is non-numeric, no complete rows remain, event coding is unsuitable, or requested time points yield unusable AUC values.SKILL_INVALID_PARAMETER: An argument value is invalid.SKILL_INSUFFICIENT_DATA: Too few complete rows or no target events remain.SKILL_DEPENDENCY_MISSING: A required R package such as optparse, timeROC, survival, ggplot2, or openxlsx is unavailable. If the issue is not obvious, read references/troubleshooting.md.
