%% Experiments Report — main.tex
%% SOURCE: docs/working/experiments/campaigns/
%%         docs/working/experiments/02-experiments/
%% NOTE: R scripts generate figures/tables; include generated outputs from
%%       experiments/build/figures/ and experiments/build/tables/.
%%       Manual analysis and narrative are in docs/working/experiments/.
%%       DO NOT edit R scripts here — run them in docs/working/experiments/campaigns/.
%% TODO(bob): set version and date

\input{../common/preamble}

\title{StarForth Experimental Results\\[0.4em]
       \large Design of Experiments Campaigns and Analysis Reports}
\author{Robert A.\ James}
\date{%% TODO(bob): set report date — use campaign closure date
}

\begin{document}
\frontmatter
\maketitle
\tableofcontents

\mainmatter

%%────────────────────────────────────────────────
%% Part I — Design of Experiments Framework
%%────────────────────────────────────────────────
\part{Design of Experiments Framework}

\chapter{Experimental Design Overview}
%% SOURCE: docs/working/experiments/02-experiments/README.md
\input{../scraps/experiments/02-experiments/README}

\chapter{Null Hypothesis and Falsification Criteria}
%% SOURCE: docs/working/papers/NULL_HYPOTHESIS.md
\input{../scraps/papers/NULL_HYPOTHESIS}

\chapter{Negative Results and Sensitivity Analysis}
%% SOURCE: docs/working/papers/NEGATIVE_RESULTS.md
%%         docs/working/papers/SENSITIVITY_ANALYSIS.md
%% All claims checked against ANTI_CLAIMS.md before promotion.
\input{../scraps/papers/NEGATIVE_RESULTS}
\input{../scraps/papers/SENSITIVITY_ANALYSIS}

%%────────────────────────────────────────────────
%% Part II — 2\textsuperscript{7} Factorial Campaign
%%────────────────────────────────────────────────
\part{$2^7$ Factorial Campaign}

\chapter{Campaign Design}
%% SOURCE: docs/working/experiments/02-experiments/factorial-doe/guide.md
%%         docs/working/experiments/campaigns/doe_2x7/README.md
\input{../scraps/experiments/02-experiments/factorial-doe/guide}
\input{../scraps/experiments/02-experiments/factorial-doe/workflow}
\input{../scraps/experiments/02-experiments/factorial-doe/index}
\input{../scraps/experiments/campaigns/doe_2x7/README}
\input{../scraps/experiments/campaigns/shape_validation/README}

\chapter{Incompatible Configurations}
%% SOURCE: docs/working/experiments/02-experiments/factorial-doe/incompatible-configs.md
\input{../scraps/experiments/02-experiments/factorial-doe/incompatible-configs}

\chapter{Campaign Results — 90 Runs}
%% SOURCE: docs/working/experiments/campaigns/doe_2x7/results_30reps_RAJ_2025.11.22_1700hrs/
%%         R script: doe_full_report.R
%% TODO(bob): include R-generated tables and figures.
%% FIGURES: place generated PDFs/PNGs in experiments/figures/doe_2x7_90rep/
\begin{figure}[ht]
  \centering
  %% \includegraphics[width=\linewidth]{figures/doe_2x7_90rep_main_effects.pdf}
  %% TODO(bob): caption for main effects plot
  \caption{Main effects plot --- 90-run campaign (figure pending)}
  \label{fig:doe:90rep:main-effects}
\end{figure}

\chapter{Campaign Results — 300 Runs}
%% SOURCE: docs/working/experiments/campaigns/doe_2x7/results_300_reps_RAJ_2025.11.26.10:30hrs/
%%         R script: doe_full_report.R
%% TODO(bob): include R-generated tables and figures.
%% FIGURES: place generated PDFs/PNGs in experiments/figures/doe_2x7_300rep/
\begin{figure}[ht]
  \centering
  %% \includegraphics[width=\linewidth]{figures/doe_2x7_300rep_main_effects.pdf}
  %% TODO(bob): caption for 300-run main effects plot
  \caption{Main effects plot --- 300-run campaign (figure pending)}
  \label{fig:doe:300rep:main-effects}
\end{figure}

%%────────────────────────────────────────────────
%% Part III — L8 Attractor Map Campaign
%%────────────────────────────────────────────────
\part{L8 Attractor Map Campaign}

\chapter{Campaign Design and Execution}
%% SOURCE: docs/working/experiments/campaigns/l8_attractor_map/SESSION_REPORT_2025-12-10.md
\input{../scraps/experiments/campaigns/l8_attractor_map/SESSION_REPORT_2025-12-10}
\input{../scraps/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/TIDBITS}
\input{../scraps/experiments/campaigns/l8_validation/README}

\chapter{Mathematical Framework}
%% SOURCE: docs/working/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/mathematical_framework.md
\input{../scraps/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/mathematical_framework}

\chapter{Heartbeat Analysis}
%% SOURCE: docs/working/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/heartbeat_analysis.md
%%         R scripts: l8_analysis.R, l8_analysis_fixed.R
%% TODO(bob): include R-generated heartbeat analysis figures.
\input{../scraps/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/heartbeat_analysis}

\chapter{Comprehensive Results}
%% SOURCE: docs/working/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/comprehensive_report.md
\input{../scraps/experiments/campaigns/l8_attractor_map/results_20251209_145907/analysis_output/report/comprehensive_report}

\chapter{Binary 2-Cycle Analysis}
%% SOURCE: docs/working/experiments/campaigns/l8_attractor_map/results_20251209_145907/binary_2cycle_analysis_report.md
\input{../scraps/experiments/campaigns/l8_attractor_map/results_20251209_145907/binary_2cycle_analysis_report}

%%────────────────────────────────────────────────
%% Part IV — Window Scaling Campaign
%%────────────────────────────────────────────────
\part{Window Scaling Campaign}

\chapter{Campaign Design}
%% SOURCE: docs/working/experiments/campaigns/window_scaling/README.md
%%         docs/working/experiments/campaigns/window_scaling/QUICK_START.md
\input{../scraps/experiments/campaigns/window_scaling/README}
\input{../scraps/experiments/campaigns/window_scaling/QUICK_START}

\chapter{Results and Analysis}
%% SOURCE: R scripts: analyze_results.R, generate_run_matrix.R
%% TODO(bob): include R-generated window scaling figures and tables.

%%────────────────────────────────────────────────
%% Part V — James Law Protocol
%%────────────────────────────────────────────────
\part{James Law Protocol}

\chapter{Protocol Definition}
%% SOURCE: docs/working/experiments/02-experiments/james-law/protocol.md
%% NOTE: "James Law" is a registered proper noun — do not rename.
\input{../scraps/experiments/02-experiments/james-law/protocol}

%%────────────────────────────────────────────────
%% Part VI — Heartbeat and Physics Optimization Campaigns
%%────────────────────────────────────────────────
\part{Supplementary Campaigns}

\chapter{Heartbeat DoE}
%% SOURCE: docs/working/experiments/02-experiments/heartbeat-doe/design.md
%%         docs/working/experiments/02-experiments/heartbeat-doe/corrected-design.md
\input{../scraps/experiments/02-experiments/heartbeat-doe/design}
\input{../scraps/experiments/02-experiments/heartbeat-doe/corrected-design}
\input{../scraps/experiments/02-experiments/heartbeat-doe/implementation-summary}
\input{../scraps/experiments/02-experiments/heartbeat-doe/phase2-corrected}
\input{../scraps/experiments/02-experiments/heartbeat-doe/execution-guide}

\chapter{Physics Optimization DoE}
%% SOURCE: docs/working/experiments/02-experiments/physics-optimization/doe-guide.md
%%         docs/working/experiments/02-experiments/physics-optimization/reproduce.md
\input{../scraps/experiments/02-experiments/physics-optimization/doe-guide}
\input{../scraps/experiments/02-experiments/physics-optimization/execution-guide}
\input{../scraps/experiments/02-experiments/physics-optimization/hotwords-cache}
\input{../scraps/experiments/02-experiments/physics-optimization/proposals}
\input{../scraps/experiments/02-experiments/physics-optimization/reproduce}

\chapter{L8 Wiring}
\input{../scraps/experiments/02-experiments/L8_WIRING_PLAN}
\input{../scraps/experiments/02-experiments/L8_WIRING_IMPLEMENTATION_SUMMARY}
\input{../scraps/experiments/02-experiments/L8_WIRING_CODE_REVIEW_GUIDE}

\chapter{L8 Validation}
%% SOURCE: docs/working/experiments/campaigns/l8_validation/README.md
%% (already included in L8 Attractor Map chapter above)

\chapter{Shape Validation}
%% SOURCE: docs/working/experiments/campaigns/shape_validation/README.md
%% (already included in Campaign Design chapter above)

%%────────────────────────────────────────────────
%% Appendices
%%────────────────────────────────────────────────
\appendix

\chapter{Reproducibility Protocol}
%% SOURCE: docs/working/papers/REPRODUCIBILITY.md
\input{../scraps/papers/REPRODUCIBILITY}

\chapter{Replication Invitation}
%% SOURCE: docs/working/papers/REPLICATION_INVITE.md
\input{../scraps/papers/REPLICATION_INVITE}

\chapter{DoE Metrics Schema}
\input{../scraps/archive/research/doe-metrics-schema}

\chapter{Methodology Record}
\input{../scraps/archive/legacy/phase-1/Reference/physics_experiment/PEER_REVIEW_SUBMISSION/06_ASCIIDOC/03-experimental-methodology}
\input{../scraps/archive/legacy/phase-1/Reference/physics_experiment/PEER_REVIEW_SUBMISSION/06_ASCIIDOC/04-variance-analysis}

\chapter{Session Logs}
\input{../scraps/archive/session-logs/experimental-addendum}
\input{../scraps/archive/session-logs/experimental-iteration-usage}

\chapter{R Script Inventory}
%% TODO(bob): table of all R scripts, their inputs, outputs, and campaign association.
%% Scripts live in docs/working/experiments/campaigns/*/scripts/ and campaigns/*/R files.

\backmatter
\bibliographystyle{plainnat}
\bibliography{../common/starship}

\end{document}
