Title: LTMLE Targeted Bootstrap Simulation Study
Domain: health_medicine — Economics & Quantitative Social Research

Summary: Reconstruct a six-script R simulation pipeline for a longitudinal LMTP variance study and reproduce the required summary and report outputs from the staged public materials.

Task prompt:
You are working on a Linux R biostatistics simulation benchmark.

Read these staged inputs first:
- `base/input/LTMLE_Targeted_Bootstrap_Task_INPUT/01_data_generation_longitudinal.R`
- `base/input/LTMLE_Targeted_Bootstrap_Task_INPUT/lmtp-bootstrap`
- `base/input/LTMLE_Targeted_Bootstrap_Task_INPUT/tmleVariance.pdf`
- `base/input/public_benchmark/README_output.md`
- `base/input/public_benchmark/reference_summary.csv`
- `base/input/public_benchmark/study_plan_public.json`

Your job is to reconstruct the missing longitudinal simulation pipeline and write the required deliverables under `base/output`.

Required pipeline files:
- `base/output/02_variance_methods_longitudinal.R`
- `base/output/03_simulation_runner_longitudinal.R`
- `base/output/04_analysis_functions_longitudinal.R`
- `base/output/05_run_full_simulation_longitudinal.R`
- `base/output/06_analyze_part2_results_longitudinal.R`
- `base/output/06b_analyze_by_sample_size.R`

Required generated outputs:
- `base/output/summary.csv`
- `base/output/report.pdf`

Requirements:
1. Use the bundled longitudinal DGP, the local `lmtp-bootstrap` source tree, the variance paper, and the public benchmark materials under `input/public_benchmark/`.
2. Cover the two public benchmark scenarios from `study_plan_public.json` and generate your own `summary.csv` plus `report.pdf` from a working pipeline.
3. The public benchmark summary is visible for orientation, but do not treat it as a file to relocate or copy into `output/`.
5. Write solver-created files only under `base/output`.


The agent must:
Read the staged longitudinal DGP, bundled `lmtp-bootstrap` source tree, variance paper, and public benchmark materials under `input/public_benchmark/`.
Reconstruct the missing six-file R pipeline for the standard LMTP, full-data targeting, and targeted-bootstrap inference workflows.
Run the required `n=200` and `n=1000` study settings from the public study plan.
Write the six R scripts plus `summary.csv` and `report.pdf` under `output/`.

Software: R
lmtp
SuperLearner

Input files:
name: Longitudinal DGP script
format: `.R`
path: input/LTMLE_Targeted_Bootstrap_Task_INPUT/01_data_generation_longitudinal.R
description: Defines the longitudinal data-generating process and Monte Carlo truth helper
name: Bundled lmtp source tree
format: directory
path: input/LTMLE_Targeted_Bootstrap_Task_INPUT/lmtp-bootstrap/
description: Local package source required for the task-specific LMTP methods
name: Variance paper
format: `.pdf`
path: input/LTMLE_Targeted_Bootstrap_Task_INPUT/tmleVariance.pdf
description: Public theory reference for the variance-estimation approaches
name: Public benchmark note
format: `.md`
path: input/public_benchmark/README_output.md
description: Explains the public benchmark surface and expected solve-time layout
name: Public benchmark summary
format: `.csv`
path: input/public_benchmark/reference_summary.csv
description: Visible benchmark summary for orientation
name: Public study plan
format: `.json`
path: input/public_benchmark/study_plan_public.json
description: Lists the two required public benchmark scenarios