fix-implement-copy

Metadata

Description

Fix the failed map-copy-number task by implementing concrete parameter mapping from copy-number weighted gene counts to R phyper(q,m,n,k) parameters.

## Background
The research-r-phyper task successfully created comprehensive research documents:
- r_phyper_modifications_research.md  
- phyper_parameter_modification_analysis.md
- mathematical_framework_copy_weighted_ora.md

## Scope  
- Read existing research documents
- Implement concrete R function for parameter mapping
- Document parameter transformation logic
- Create validation examples

## Expected Output
- R function that maps (weighted_overlap, weighted_background, total_genes) → (q,m,n,k)
- Clear documentation of parameter relationships
- Example usage with copy-number weighted data

Depends on

• done .assign-fix-implement-copy

Required by

• done map-copy-number

Log

• 2026-04-01T15:32:01.893964785+00:00 Task unclaimed: agent 'agent-205' (PID 22880) process exited
• 2026-04-01T15:36:09.745007201+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:36:30.303908117+00:00 Reconciliation: task recovered from orphaned state (agent: agent-220)
• 2026-04-01T15:37:35.888442993+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:37:53.077651821+00:00 Reconciliation: task recovered from orphaned state (agent: agent-224)
• 2026-04-01T15:38:03.072256336+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:38:06.135665575+00:00 Task unclaimed: agent 'agent-224' (PID 32697) process exited
• 2026-04-01T15:38:25.616216297+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:38:34.734023727+00:00 Task unclaimed: agent 'agent-226' (PID 33045) process exited
• 2026-04-01T15:39:46.346284960+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:40:02.708886453+00:00 Reconciliation: task recovered from orphaned state (agent: agent-231)
• 2026-04-01T15:41:25.140618816+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:41:53.960390696+00:00 Reconciliation: task recovered from orphaned state (agent: agent-239)
• 2026-04-01T15:42:14.782640696+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:43:06.362893165+00:00 Task unclaimed: agent 'agent-243' (PID 39357) process exited
• 2026-04-01T15:45:14.982466275+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:45:35.540186557+00:00 Reconciliation: task recovered from orphaned state (agent: agent-255)
• 2026-04-01T15:45:35.761713350+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:45:54.606015314+00:00 Task unclaimed: agent 'agent-255' (PID 43641) process exited
• 2026-04-01T15:46:55.002478346+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:47:26.417593440+00:00 Task unclaimed: agent 'agent-263' (PID 44743) process exited
• 2026-04-01T15:49:02.313150218+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:49:23.358142080+00:00 Reconciliation: task recovered from orphaned state (agent: agent-268)
• 2026-04-01T15:49:23.568415730+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:49:45.297625218+00:00 Task unclaimed: agent 'agent-268' (PID 46721) process exited
• 2026-04-01T15:50:55.408420848+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:51:25.350806271+00:00 Reconciliation: task recovered from orphaned state (agent: agent-270)
• 2026-04-01T15:51:25.565228356+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:51:35.388445772+00:00 Task unclaimed: agent 'agent-270' (PID 47268) process exited
• 2026-04-01T15:52:51.169258413+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:53:12.446526579+00:00 Reconciliation: task recovered from orphaned state (agent: agent-273)
• 2026-04-01T15:53:12.684321783+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:54:12.444410058+00:00 Task unclaimed: agent 'agent-273' (PID 47964) process exited
• 2026-04-01T15:55:12.722001015+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:56:12.448731939+00:00 Task unclaimed: agent 'agent-278' (PID 48454) process exited
• 2026-04-01T15:57:12.623374898+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T15:58:12.446137163+00:00 Task unclaimed: agent 'agent-279' (PID 48720) process exited
• 2026-04-01T15:59:12.678762582+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T16:00:12.449805848+00:00 Task unclaimed: agent 'agent-281' (PID 48979) process exited
• 2026-04-01T16:01:12.695877265+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T16:01:17.823074293+00:00 Task marked as failed: Agent exited with code 1
• 2026-04-01T18:11:04.549636932+00:00 Task reset for retry (attempt #2)
• 2026-04-01T18:11:06.787084126+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T18:11:57.590483817+00:00 Task unclaimed: agent 'agent-312' (PID 23589) process exited
• 2026-04-01T18:12:31.583790813+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T18:12:51.951434805+00:00 Reconciliation: task recovered from orphaned state (agent: agent-315)
• 2026-04-01T18:12:52.185008946+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
• 2026-04-01T18:13:03.200920428+00:00 Task unclaimed: agent 'agent-315' (PID 25209) process exited
• 2026-04-01T18:14:02.199972654+00:00 Task abandoned
• 2026-04-01T18:14:07.129914293+00:00 Task marked as done