--- 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](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 ```bash Rscript scripts/main.R \ --data_file \ --times \ --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_file` | Yes | Input data file in CSV, TXT, TSV, TAB, XLS, or XLSX format | | `--times` | No | Prediction time points, comma-separated. Default `1,3,5` | | `--marker_col` | No | Marker column name. Default `risk_score`; provide this option when your file uses a different marker | | `--output_dir` | No | Output directory, default `./TimeROC_Results` | | `--time_unit` | No | Time unit label for plot/output: `year`, `month`, or `day`. Default `year` | | `--auto_convert_days` | No | If `TRUE`, convert large `futime` values from days to the selected unit when appropriate. Default `TRUE` | | `--weighting` | No | IPCW weighting method: `aalen`, `marginal`, or `cox`. Default `aalen` | | `--cause` | No | 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. Example input: ```text 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 1. Confirm the input file exists and includes `futime`, `fustat`, and `risk_score`, or plan to pass `--marker_col`. 2. Run `scripts/main.R` with the requested time points. 3. 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: ```text / ├── data/ │ └── time_roc_points. ├── session_info.txt ├── figure/ │ └── time_roc.pdf └── table/ └── time_roc_auc. ``` Primary output files: - `data/time_roc_points.csv` or `data/time_roc_points.txt` - `table/time_roc_auc.csv` or `table/time_roc_auc.txt` - `figure/time_roc.pdf` - `session_info.txt` Exported result fields include: - `time` - `time_unit` - `auc` - `marker_col` - `n_complete` - `n_events` Exported ROC point fields include: - `false_positive_rate` - `sensitivity` - `time` - `time_unit` - `auc` - `curve_label` ## Read These Files When Needed | Need | File | |------|------| | Statistical details and assumptions | `references/algorithm.md` | | More CLI examples | `references/cli-guide.md` | | Error diagnosis | `references/troubleshooting.md` | | Main execution entry point | `scripts/main.R` | | Sample test data | `tests/data/` | ## Quick Examples Basic analysis: ```bash 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: ```bash 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 ```bash Rscript scripts/main.R --help ``` ```bash 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.csv` - `tests/validation_output/table/time_roc_auc.csv` - `tests/validation_output/figure/time_roc.pdf` - `tests/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`. --- Source attribution: aipoch Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/awesome-med-research-skills/Data%20Analysis/time-dependent-roc/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 AIpoch Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: aipoch Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/awesome-med-research-skills/Data%20Analysis/time-dependent-roc/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics Roles: Business Intelligence Analyst, Data Scientist, Market Research Analyst Specialties: API Tools: R, Openxlsx Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: d40f27d6982acfb7af58b98ab422babec4de97a7d2ab0e322bfdf8d4519bd5e2