@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/bn-fit-modify/turns/turn_006.md

@@ -1,97 +0,0 @@
-# turn 006
-
-tokens: prompt=9597 cached=157 completion=323 reasoning=0 total=9920 cost=0
-created: 2026-05-02 00:12:44
-
-update: status=155 body=distilling dag_recovery sources; dataset archived
-
----
-
-## reasoning (think)
-
-```
-- In Distillation Stage: Resolve remaining unknowns: dag_recovery, dataset (still unresolved), intervention_sampling.
-- Dataset: Confirmed missing via ls /app/ and get attempts; already distilled known://project/dataset. Demote unknown://project/dataset.
-- Tools: R available with base packages (stats, MASS, etc.). No bnlearn (not in installed.packages()). Need to check for DAG learning capabilities in R base or discover methods.
-- dag_recovery: Promote R package output fully, prompt hints, search for R DAG structure learning methods using score-based/PC/ges with constraints (U root, 6 edges).
-- intervention_sampling: Later, after DAG.
-- Plan: 
-  1. <get> full R installed.packages() to confirm no BN pkgs.
-  2. <search> for R DAG learning from data (score-based, BIC, with root node constraint).
-  3. <get> relevant search results next turn to distill dag_recovery.
-  4. Demote dataset unknown (redundant).
-  5. Continue distillation (155).
-- Budget ok: R pkgs slice was 298t, full 714t < 1.7M free.
-```
-
-## assistant emission
-
-```
-<think>
-- In Distillation Stage: Resolve remaining unknowns: dag_recovery, dataset (still unresolved), intervention_sampling.
-- Dataset: Confirmed missing via ls /app/ and get attempts; already distilled known://project/dataset. Demote unknown://project/dataset.
-- Tools: R available with base packages (stats, MASS, etc.). No bnlearn (not in installed.packages()). Need to check for DAG learning capabilities in R base or discover methods.
-- dag_recovery: Promote R package output fully, prompt hints, search for R DAG structure learning methods using score-based/PC/ges with constraints (U root, 6 edges).
-- intervention_sampling: Later, after DAG.
-- Plan: 
-  1. <get> full R installed.packages() to confirm no BN pkgs.
-  2. <search> for R DAG learning from data (score-based, BIC, with root node constraint).
-  3. <get> relevant search results next turn to distill dag_recovery.
-  4. Demote dataset unknown (redundant).
-  5. Continue distillation (155).
-- Budget ok: R pkgs slice was 298t, full 714t < 1.7M free.
-</think>
-
-<get path="env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1"/>
-
-<search>R DAG structure learning from data score-based BIC root node constraint</search>
-
-<set path="unknown://project/dataset" visibility="archived"/>
-
-<update status="155">distilling dag_recovery sources; dataset archived</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_6/get/env%3A/turn_5/R_-e_%2522installed.packages()%255B/1%255D%2522_1`
-scheme=log action=get attrs={"path":"env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1","action":"get"}
-
-```
-env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1 promoted
-```
-
-### `log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint`
-scheme=log action=search attrs={"query":"R DAG structure learning from data score-based BIC root node constraint","action":"search"}
-
-```
-7 of 12 results for "R DAG structure learning from data score-based BIC root node constraint" (5 unreachable)
-* https://erdogant.github.io/bnlearn/pages/html/bnlearn.structure_learning.html — bnlearn.structure_learning — bnlearn bnlearn documentation (4558 tokens)
-  # Constraintsearch ‘pc’ or ‘cs’ or ‘constraintsearch’ # Score-Based ‘ex’ or ‘exhaustivesearch’ ‘hc’ or ‘hillclimbsearch’ (default) # Score-Based: Requires Root Node ‘cl’ or ‘chow-liu’ (requires setting root_node parameter) ‘nb’ or ‘naivebayes’ (requires &lt;root_node&gt;) ‘tan’ (requires &lt;root_node&gt; and &lt;class_node&gt; parameter) # Score-Based: For continuous and mixed datasets ‘direct-lingam’ ‘ica-lingam’
-* https://ermongroup.github.io/cs228-notes/learning/structure — Structure learning for Bayesian networks (4094 tokens)
-  <strong>The task of structure learning for Bayesian networks refers to learning the structure of the directed acyclic graph (DAG) from data</strong>. There are two major approaches for structure learning: score-based and constraint-based.
-* https://link.springer.com/article/10.1007/s11704-020-0268-6 — BIC-based node order learning for improving Bayesian network structure learning (13720 tokens)
-  The relation between the subgraph number and the node number is analyzed. Thirdly, we provide the rules of orienting directions for all edges in UGC, which converts it into a directed acyclic graph (DAG). Further, we rank the DAG’s topology order and describe the BIC-based node order learning algorithm.
-* https://www.bnlearn.com/examples/custom-score — Using custom scores in structure learning (8212 tokens)
-  computing the (conditional) probability table associated with the node from the contingency table; ... computing the log-likelihood from the (conditional) probability table and subtracting the BIC penalty term. Again, we can match the output of the built-in BIC score. &gt; dag = model2network(&quot;[A][C][F][B|A][D|A:C][E|B:F]&quot;) &gt; &gt; my.bic = function(node, parents, data, args) { + n = nrow(data) + if (length(parents) == 0) { + counts = table(data[, node]) + nparams = dim(counts) - 1 + sum(counts * log(counts / n)) - nparams * log(n) / 2 + }#THEN + else { + counts = table(data[, node], configs(data[, parents, drop = FALSE])) + nparams = ncol(counts) * (nrow(counts) - 1) + sum(counts * log(prop.table(counts, 2))) - nparams * log(n) / 2 + }#ELSE + }#MY.BIC &gt; score(dag, learning.test, type = &quot;custom-score&quot;, fun = my.bic, by.node = TRUE)
-* https://arxiv.org/html/2509.21658 — Differentiable Structure Learning and Causal Discovery for General Binary Data (76226 tokens)
-  Constraint‐based algorithms (e.g. PC (Spirtes and Glymour, 1991), MMHC (Tsamardinos et al., 2003), Copula‐PC (Cui et al., 2016)) use conditional‐independence tests to infer edges. Score‐based approaches assign each candidate DAG a goodness‐of‐fit score (e.g. BIC, BDeu (Maxwell Chickering and Heckerman, 1997; Heckerman et al., 1995), generalized scores (Huang et al., 2018; Li and Shimizu, 2018)) and then search for the optimal structure.
-* https://erdogant.github.io/bnlearn/pages/html/Structure%20learning.html — Causation — bnlearn bnlearn documentation (12711 tokens)
-  The search space of DAGs becomes so-called super-exponential in the number of variables that maximize the score. This means that an exhaustive search is practically infeasible with a large number of nodes, and therefore, various greedy strategies have been proposed to browse DAG space. With optimization-based search approaches, it is possible to browse a larger DAG space. Such approaches require a scoring function and a search strategy. A common scoring function is the posterior probability of the structure given the training data, like the BIC or the BDeu.
-* https://link.springer.com/article/10.1007/s10994-018-5701-9 — Approximate structure learning for large Bayesian networks (42288 tokens)
-  2015), and thus we adopt it in all our experiments. The objective of structure optimization is to <strong>select the parent set of each node from its cache in order to maximize the score of the resulting DAG</strong>.
-```
-
-### `log://turn_6/set/unknown%3A/project/dataset`
-scheme=log action=set attrs={}
-
-```
-unknown://project/dataset set to archived
-```
-
-### `log://turn_6/update/distilling_dag_recovery_sources%3B_dataset_archived`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling dag_recovery sources; dataset archived
-```
-

package/audit/sweep/bn-fit-modify/turns/turn_007.md

@@ -1,170 +0,0 @@
-# turn 007
-
-tokens: prompt=11250 cached=2391 completion=602 reasoning=0 total=11852 cost=0
-created: 2026-05-02 00:12:59
-
-update: status=155 body=distilling dag_recovery R capabilities
-
----
-
-## reasoning (think)
-
-```
-- Current stage: Distillation. Focus: resolve remaining unknowns (dag_recovery, intervention_sampling).
-- R available with base packages: stats, MASS, Matrix, boot, cluster, rpart, mgcv, nnet, survival, etc. No bnlearn.
-- Search results point to bnlearn (not installed) but also base R methods like score-based BIC via hill-climb.
-- Need to distill dag_recovery: check if R base or installed pkgs can do DAG learning with BIC score, root node U constraint.
-- Dataset still missing (/app empty), but proceed with tools assessment.
-- Promote R pkgs full list (already visible), search log for distillation.
-- No dataset, so dag_recovery limited, but distill R capabilities first.
-- Plan: distill dag_recovery using search results + R pkgs; check for structure learning functions.
-- Then intervention_sampling later. Demote irrelevant envs to save tokens.
-```
-
-## assistant emission
-
-```
-<think>
-- Current stage: Distillation. Focus: resolve remaining unknowns (dag_recovery, intervention_sampling).
-- R available with base packages: stats, MASS, Matrix, boot, cluster, rpart, mgcv, nnet, survival, etc. No bnlearn.
-- Search results point to bnlearn (not installed) but also base R methods like score-based BIC via hill-climb.
-- Need to distill dag_recovery: check if R base or installed pkgs can do DAG learning with BIC score, root node U constraint.
-- Dataset still missing (/app empty), but proceed with tools assessment.
-- Promote R pkgs full list (already visible), search log for distillation.
-- No dataset, so dag_recovery limited, but distill R capabilities first.
-- Plan: distill dag_recovery using search results + R pkgs; check for structure learning functions.
-- Then intervention_sampling later. Demote irrelevant envs to save tokens.
-</think>
-
-<get path="env://turn_5/R_-e_%22(.packages())%22_1" line="1" limit="50"/>
-<get path="log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint"/>
-
-<env>R -e "methods::code_search('structure', where=stats::stats); methods::code_search('dag', where=stats::stats)"</env>
-<env>R -e "methods::code_search('score', where=stats::stats); methods::code_search('bic', where=stats::stats)"</env>
-<env>R -e "search()"</env>
-
-<set path="known://project/r_bayesian_network" summary="r,packages,bn,dag,structure,learning,score,bic,root,constraint">
-# Related
-[prompt task](prompt://1)
-[unknown dag_recovery](unknown://project/dag_recovery)
-[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)
-[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)
-[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)
-
-# R Bayesian Network Capabilities
-Base R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.
-No bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).
-</set>
-
-<set path="env://turn_4/*" visibility="archived"/>
-<set path="env://turn_5/R_-e_%22(.packages())%22_*" visibility="summarized"/>
-<set path="env://turn_5/ls_/app_*" visibility="archived"/>
-
-<update status="155">distilling dag_recovery R capabilities</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_7/get/env%3A/turn_5/R_-e_%2522(.packages())%2522_1`
-scheme=log action=get attrs={"path":"env://turn_5/R_-e_%22(.packages())%22_1","lineStart":1,"lineEnd":23,"totalLines":23,"action":"get"}
-
-```
-env://turn_5/R_-e_%22(.packages())%22_1
-[lines 1–23 / 23 total]
-
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
-Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> (.packages())
-[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"  
-[7] "base"     
-> 
-> 
-
-```
-
-### `log://turn_7/get/log%3A/turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node`
-scheme=log action=get attrs={"path":"log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint","action":"get"}
-
-```
-log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint promoted
-```
-
-### `log://turn_7/env/R_-e_%22methods%3A%3Acode_search('structure'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_searc`
-scheme=log action=env attrs={"command":"R -e \"methods::code_search('structure', where=stats::stats); methods::code_search('dag', where=stats::stats)\"","summary":"R -e \"methods::code_search('structure', where=stats::stats); methods::code_search('dag', where=stats::stats)\"","action":"env"}
-
-```
-ran 'R -e "methods::code_search('structure', where=stats::stats); methods::code_search('dag', where=stats::stats)"', exit=1 (0s). Output: env://turn_7/R_-e_%22methods%3A%3Acode_search('structure'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_searc_1 (368 tokens), env://turn_7/R_-e_%22methods%3A%3Acode_search('structure'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_searc_2 (45 tokens)
-```
-
-### `log://turn_7/env/R_-e_%22methods%3A%3Acode_search('score'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_search('b`
-scheme=log action=env attrs={"command":"R -e \"methods::code_search('score', where=stats::stats); methods::code_search('bic', where=stats::stats)\"","summary":"R -e \"methods::code_search('score', where=stats::stats); methods::code_search('bic', where=stats::stats)\"","action":"env"}
-
-```
-ran 'R -e "methods::code_search('score', where=stats::stats); methods::code_search('bic', where=stats::stats)"', exit=1 (0s). Output: env://turn_7/R_-e_%22methods%3A%3Acode_search('score'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_search('b_1 (366 tokens), env://turn_7/R_-e_%22methods%3A%3Acode_search('score'/_where%3Dstats%3A%3Astats)%3B_methods%3A%3Acode_search('b_2 (45 tokens)
-```
-
-### `log://turn_7/env/R_-e_%22search()%22`
-scheme=log action=env attrs={"command":"R -e \"search()\"","summary":"R -e \"search()\"","action":"env"}
-
-```
-ran 'R -e "search()"', exit=0 (0s). Output: env://turn_7/R_-e_%22search()%22_1 (420 tokens), env://turn_7/R_-e_%22search()%22_2 (0 tokens)
-```
-
-### `log://turn_7/set/known%3A/project/r_bayesian_network`
-scheme=log action=set attrs={"path":"known://project/r_bayesian_network","patch":"===================================================================\n--- known://project/r_bayesian_network\told\t\n+++ known://project/r_bayesian_network\tnew\t\n@@ -0,0 +1,10 @@\n+# Related\n+[prompt task](prompt://1)\n+[unknown dag_recovery](unknown://project/dag_recovery)\n+[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)\n+[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)\n+[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)\n+\n+# R Bayesian Network Capabilities\n+Base R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.\n+No bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt task](prompt://1)\n[unknown dag_recovery](unknown://project/dag_recovery)\n[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)\n[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)\n[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)\n\n# R Bayesian Network Capabilities\nBase R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.\nNo bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":286,"summary":"r,packages,bn,dag,structure,learning,score,bic,root,constraint","action":"set"}
-
-```
-# Related
-[prompt task](prompt://1)
-[unknown dag_recovery](unknown://project/dag_recovery)
-[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)
-[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)
-[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)
-
-# R Bayesian Network Capabilities
-Base R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.
-No bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).
-```
-
-### `log://turn_7/set/env%3A/turn_4/*`
-scheme=log action=set attrs={}
-
-```
-env://turn_4/R_--version_1, env://turn_4/R_--version_2, env://turn_4/julia_--version_1, env://turn_4/julia_--version_2, env://turn_4/node_--version_1, env://turn_4/node_--version_2 set to archived
-```
-
-### `log://turn_7/set/env%3A/turn_5/R_-e_%2522(.packages())%2522_*`
-scheme=log action=set attrs={}
-
-```
-env://turn_5/R_-e_%22(.packages())%22_1, env://turn_5/R_-e_%22(.packages())%22_2 set to summarized
-```
-
-### `log://turn_7/set/env%3A/turn_5/ls_/app_*`
-scheme=log action=set attrs={}
-
-```
-env://turn_5/ls_/app_1, env://turn_5/ls_/app_2 set to archived
-```
-
-### `log://turn_7/update/distilling_dag_recovery_R_capabilities`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling dag_recovery R capabilities
-```
-

package/audit/sweep/bn-fit-modify/turns/turn_008.md

@@ -1,79 +0,0 @@
-# turn 008
-
-tokens: prompt=13760 cached=1747 completion=262 reasoning=0 total=14022 cost=0
-created: 2026-05-02 00:13:07
-
-update: status=155 body=discovering dataset & R bnlearn install capability
-
----
-
-## reasoning (think)
-
-```
-* In Distillation Stage: Focus on unknown://project/dag_recovery (visible, priority).
-* Base R lacks bnlearn; search results confirm bnlearn needed for score-based BIC/root node DAG learning.
-* Need to confirm dataset existence precisely and check for bnlearn install capability.
-* No data file found yet; /app empty per prior checks.
-* Plan: 
-  1. <env> ls -la /app/ (detailed check)
-  2. <env> R -e "install.packages('bnlearn', repos='https://cran.rstudio.com/')" (test install)
-  3. <get> dataset if found
-  4. Distill dag_recovery: Base R insufficient → need bnlearn.
-* Budget ok: small env commands.
-* Continue 155 after discovering sources.
-```
-
-## assistant emission
-
-```
-<think>
-* In Distillation Stage: Focus on unknown://project/dag_recovery (visible, priority).
-* Base R lacks bnlearn; search results confirm bnlearn needed for score-based BIC/root node DAG learning.
-* Need to confirm dataset existence precisely and check for bnlearn install capability.
-* No data file found yet; /app empty per prior checks.
-* Plan: 
-  1. <env> ls -la /app/ (detailed check)
-  2. <env> R -e "install.packages('bnlearn', repos='https://cran.rstudio.com/')" (test install)
-  3. <get> dataset if found
-  4. Distill dag_recovery: Base R insufficient → need bnlearn.
-* Budget ok: small env commands.
-* Continue 155 after discovering sources.
-</think>
-
-<env>ls -la /app/</env>
-<env>R -e "installed.packages('bnlearn', lib.loc=NULL)[,1] || 'bnlearn not installed'"</env>
-<env>R -e "if('bnlearn' %in% installed.packages()[,1]) 'installed' else capabilities('install.packages')"</env>
-
-<update status="155">discovering dataset & R bnlearn install capability</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_8/env/ls_-la_/app`
-scheme=log action=env attrs={"command":"ls -la /app/","summary":"ls -la /app/","action":"env"}
-
-```
-ran 'ls -la /app/', exit=0 (0s). Output: env://turn_8/ls_-la_/app_1 (81 tokens), env://turn_8/ls_-la_/app_2 (0 tokens)
-```
-
-### `log://turn_8/env/R_-e_%22installed.packages('bnlearn'/_lib.loc%3DNULL)%5B/1%5D_%7C%7C_'bnlearn_not_installed'`
-scheme=log action=env attrs={"command":"R -e \"installed.packages('bnlearn', lib.loc=NULL)[,1] || 'bnlearn not installed'\"","summary":"R -e \"installed.packages('bnlearn', lib.loc=NULL)[,1] || 'bnlearn not installed'\"","action":"env"}
-
-```
-ran 'R -e "installed.packages('bnlearn', lib.loc=NULL)[,1] || 'bnlearn not installed'"', exit=1 (0s). Output: env://turn_8/R_-e_%22installed.packages('bnlearn'/_lib.loc%3DNULL)%5B/1%5D_%7C%7C_'bnlearn_not_installed'_1 (354 tokens), env://turn_8/R_-e_%22installed.packages('bnlearn'/_lib.loc%3DNULL)%5B/1%5D_%7C%7C_'bnlearn_not_installed'_2 (69 tokens)
-```
-
-### `log://turn_8/env/R_-e_%22if('bnlearn'_%25in%25_installed.packages()%5B/1%5D)_'installed'_else_capabilities(`
-scheme=log action=env attrs={"command":"R -e \"if('bnlearn' %in% installed.packages()[,1]) 'installed' else capabilities('install.packages')\"","summary":"R -e \"if('bnlearn' %in% installed.packages()[,1]) 'installed' else capabilities('install.packages')\"","action":"env"}
-
-```
-ran 'R -e "if('bnlearn' %in% installed.packages()[,1]) 'installed' else capabilities('install.packages')"', exit=0 (0s). Output: env://turn_8/R_-e_%22if('bnlearn'_%25in%25_installed.packages()%5B/1%5D)_'installed'_else_capabilities(_1 (375 tokens), env://turn_8/R_-e_%22if('bnlearn'_%25in%25_installed.packages()%5B/1%5D)_'installed'_else_capabilities(_2 (0 tokens)
-```
-
-### `log://turn_8/update/discovering_dataset_%26_R_bnlearn_install_capability`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-discovering dataset & R bnlearn install capability
-```
-

package/audit/sweep/bn-fit-modify/turns/turn_009.md

@@ -1,145 +0,0 @@
-# turn 009
-
-tokens: prompt=15360 cached=3469 completion=473 reasoning=0 total=15833 cost=0
-created: 2026-05-02 00:13:10
-
-update: status=155 body=distilled dataset (now available); discovering dag_recovery
-
----
-
-## reasoning (think)
-
-```
-1. Dataset now exists at /app/bn_sample_10k.csv (844kB) - update known://project/dataset
-2. bnlearn not installed; capabilities() check returned empty - cannot install (no write perms)
-3. Base R lacks bnlearn structure learning; need dataset details to assess manual recovery
-4. Promote dataset file and ls output, distill updated dataset entry resolving unknown://project/dataset
-5. Demote irrelevant R env logs to stay under budget
-6. Continue distillation for dag_recovery next
-```
-
-## assistant emission
-
-```
-<think>
-1. Dataset now exists at /app/bn_sample_10k.csv (844kB) - update known://project/dataset
-2. bnlearn not installed; capabilities() check returned empty - cannot install (no write perms)
-3. Base R lacks bnlearn structure learning; need dataset details to assess manual recovery
-4. Promote dataset file and ls output, distill updated dataset entry resolving unknown://project/dataset
-5. Demote irrelevant R env logs to stay under budget
-6. Continue distillation for dag_recovery next
-</think>
-
-<get path="env://turn_8/ls_-la_/app_1" line="1" limit="5"/>
-<get path="/app/bn_sample_10k.csv" preview/>
-
-<set path="known://project/dataset" visibility="visible">
-# Related
-[prompt task](prompt://1)
-[unknown resolved](unknown://project/dataset)
-[dataset file](/app/bn_sample_10k.csv)
-[app ls](env://turn_8/ls_-la_/app_1)
-
-# Dataset Assessment - NOW AVAILABLE
-/app/bn_sample_10k.csv exists (844kB). Ready for DAG recovery.
-Columns, node names (expect U,A-Z,Y), data types, sample rows needed for analysis.
-</set>
-
-<set path="known://project/r_bayesian_network" visibility="summarized">
-# Related
-[prompt task](prompt://1)
-[unknown dag_recovery](unknown://project/dag_recovery)
-[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)
-[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)
-
-# R BN Status
-No bnlearn. Base R (stats,rpart,etc.) lacks structure learning. Manual DAG recovery from data required.
-</set>
-
-<!-- Demote old/irrelevant R logs -->
-<set path="env://turn_7/*" visibility="archived"/>
-<set path="env://turn_8/R_*" visibility="archived"/>
-<set path="env://turn_5/R_*" visibility="summarized"/>
-
-<update status="155">distilled dataset (now available); discovering dag_recovery</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_9/get/env%3A/turn_8/ls_-la_/app_1`
-scheme=log action=get attrs={"path":"env://turn_8/ls_-la_/app_1","lineStart":1,"lineEnd":5,"totalLines":5,"action":"get"}
-
-```
-env://turn_8/ls_-la_/app_1
-[lines 1–5 / 5 total]
-total 836
-drwxr-xr-x 1 root root   4096 Oct 31  2025 .
-drwxr-xr-x 1 root root   4096 May  2 00:11 ..
--rw-r--r-- 1 root root 844949 Oct 31  2025 bn_sample_10k.csv
-
-```
-
-### `log://turn_9/get/app/bn_sample_10k.csv`
-scheme=log action=get attrs={"path":"/app/bn_sample_10k.csv","action":"get"}
-
-```
-/app/bn_sample_10k.csv not found
-```
-
-### `log://turn_9/set/known%3A/project/dataset`
-scheme=log action=set attrs={"path":"known://project/dataset","patch":"===================================================================\n--- known://project/dataset\told\t\n+++ known://project/dataset\tnew\t\n@@ -1,10 +1,9 @@\n # Related\n [prompt task](prompt://1)\n [unknown resolved](unknown://project/dataset)\n-[dataset searches](log://turn_2/get/app/bn_sample_10k.csv)\n-[repo overview](repo://overview)\n-[app dir check](log://turn_2/get/app)\n+[dataset file](/app/bn_sample_10k.csv)\n+[app ls](env://turn_8/ls_-la_/app_1)\n \n-# Dataset Assessment\n-/app/bn_sample_10k.csv not found. /app directory empty (0 files).\n-No data available for DAG recovery or BN learning.\n\\n+# Dataset Assessment - NOW AVAILABLE\n+/app/bn_sample_10k.csv exists (844kB). Ready for DAG recovery.\n+Columns, node names (expect U,A-Z,Y), data types, sample rows needed for analysis.\n\\n","merge":"<<<<<<< SEARCH\n# Related\n[prompt task](prompt://1)\n[unknown resolved](unknown://project/dataset)\n[dataset searches](log://turn_2/get/app/bn_sample_10k.csv)\n[repo overview](repo://overview)\n[app dir check](log://turn_2/get/app)\n\n# Dataset Assessment\n/app/bn_sample_10k.csv not found. /app directory empty (0 files).\nNo data available for DAG recovery or BN learning.\n=======\n# Related\n[prompt task](prompt://1)\n[unknown resolved](unknown://project/dataset)\n[dataset file](/app/bn_sample_10k.csv)\n[app ls](env://turn_8/ls_-la_/app_1)\n\n# Dataset Assessment - NOW AVAILABLE\n/app/bn_sample_10k.csv exists (844kB). Ready for DAG recovery.\nColumns, node names (expect U,A-Z,Y), data types, sample rows needed for analysis.\n>>>>>>> REPLACE","beforeTokens":175,"afterTokens":171,"summary":null,"action":"set"}
-
-```
-# Related
-[prompt task](prompt://1)
-[unknown resolved](unknown://project/dataset)
-[dataset file](/app/bn_sample_10k.csv)
-[app ls](env://turn_8/ls_-la_/app_1)
-
-# Dataset Assessment - NOW AVAILABLE
-/app/bn_sample_10k.csv exists (844kB). Ready for DAG recovery.
-Columns, node names (expect U,A-Z,Y), data types, sample rows needed for analysis.
-```
-
-### `log://turn_9/set/known%3A/project/r_bayesian_network`
-scheme=log action=set attrs={"path":"known://project/r_bayesian_network","patch":"===================================================================\n--- known://project/r_bayesian_network\told\t\n+++ known://project/r_bayesian_network\tnew\t\n@@ -3,8 +3,6 @@\n [unknown dag_recovery](unknown://project/dag_recovery)\n [R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)\n [R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)\n-[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)\n \n-# R Bayesian Network Capabilities\n-Base R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.\n-No bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).\n\\n+# R BN Status\n+No bnlearn. Base R (stats,rpart,etc.) lacks structure learning. Manual DAG recovery from data required.\n\\n","merge":"<<<<<<< SEARCH\n# Related\n[prompt task](prompt://1)\n[unknown dag_recovery](unknown://project/dag_recovery)\n[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)\n[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)\n[R loaded pkgs](env://turn_5/R_-e_%22(.packages())%22_1)\n\n# R Bayesian Network Capabilities\nBase R (4.3.3) with packages: stats, MASS, Matrix, rpart, mgcv, nnet, survival, etc.\nNo bnlearn detected. Need to assess if base pkgs support DAG structure learning (score-based BIC, root node U constraint).\n=======\n# Related\n[prompt task](prompt://1)\n[unknown dag_recovery](unknown://project/dag_recovery)\n[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)\n[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)\n\n# R BN Status\nNo bnlearn. Base R (stats,rpart,etc.) lacks structure learning. Manual DAG recovery from data required.\n>>>>>>> REPLACE","beforeTokens":286,"afterTokens":196,"summary":null,"action":"set"}
-
-```
-# Related
-[prompt task](prompt://1)
-[unknown dag_recovery](unknown://project/dag_recovery)
-[R pkgs list](env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1)
-[R search DAG BIC](log://turn_6/search/R_DAG_structure_learning_from_data_score-based_BIC_root_node_constraint)
-
-# R BN Status
-No bnlearn. Base R (stats,rpart,etc.) lacks structure learning. Manual DAG recovery from data required.
-```
-
-### `log://turn_9/set/env%3A/turn_7/*`
-scheme=log action=set attrs={}
-
-```
-env://turn_7/R_-e_%22search()%22_1, env://turn_7/R_-e_%22search()%22_2 set to archived
-```
-
-### `log://turn_9/set/env%3A/turn_8/R_*`
-scheme=log action=set attrs={}
-
-```
-env://turn_8/R_* not found
-```
-
-### `log://turn_9/set/env%3A/turn_5/R_*`
-scheme=log action=set attrs={}
-
-```
-env://turn_5/R_-e_%22(.packages())%22_1, env://turn_5/R_-e_%22(.packages())%22_2 set to summarized
-```
-
-### `log://turn_9/update/distilled_dataset_(now_available)%3B_discovering_dag_recovery`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilled dataset (now available); discovering dag_recovery
-```
-

package/audit/sweep/bn-fit-modify/turns/turn_010.md

@@ -1,95 +0,0 @@
-# turn 010
-
-tokens: prompt=15744 cached=3239 completion=304 reasoning=0 total=16048 cost=0
-created: 2026-05-02 00:13:14
-
-update: status=155 body=discovering dataset structure for dag_recovery
-
----
-
-## reasoning (think)
-
-```
-* Distillation stage: Resolve remaining unknowns (dag_recovery, intervention_sampling).
-* Priority: Examine dataset structure (columns, sample data) to inform DAG recovery.
-* unknown://project/dataset notes columns/node names needed; /app/bn_sample_10k.csv exists (844kB).
-* Use <get path="/app/bn_sample_10k.csv" line="1" limit="20"/> for header + sample rows (low token cost).
-* Also check full structure with preview or head command via <env>.
-* After dataset inspection, distill dag_recovery method (manual given no bnlearn, use hints: U root, 6 edges, alphabet rule).
-* Defer intervention_sampling until DAG recovered.
-* Demote irrelevant R package search logs to manage tokens.
-* Continue distillation after dataset promotion.
-```
-
-## assistant emission
-
-```
-<think>
-* Distillation stage: Resolve remaining unknowns (dag_recovery, intervention_sampling).
-* Priority: Examine dataset structure (columns, sample data) to inform DAG recovery.
-* unknown://project/dataset notes columns/node names needed; /app/bn_sample_10k.csv exists (844kB).
-* Use <get path="/app/bn_sample_10k.csv" line="1" limit="20"/> for header + sample rows (low token cost).
-* Also check full structure with preview or head command via <env>.
-* After dataset inspection, distill dag_recovery method (manual given no bnlearn, use hints: U root, 6 edges, alphabet rule).
-* Defer intervention_sampling until DAG recovered.
-* Demote irrelevant R package search logs to manage tokens.
-* Continue distillation after dataset promotion.
-</think>
-
-<get path="/app/bn_sample_10k.csv" line="1" limit="20"/>
-
-<env>head -n 20 /app/bn_sample_10k.csv</env>
-
-<env>wc -l /app/bn_sample_10k.csv</env>
-
-<set path="env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1" visibility="summarized"/>
-
-<set path="env://turn_5/R_-e_%22(.packages())%22_1" visibility="archived"/>
-
-<update status="155">discovering dataset structure for dag_recovery</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_10/get/app/bn_sample_10k.csv`
-scheme=log action=get attrs={"path":"/app/bn_sample_10k.csv","action":"get"}
-
-```
-/app/bn_sample_10k.csv not found
-```
-
-### `log://turn_10/env/head_-n_20_/app/bn_sample_10k.csv`
-scheme=log action=env attrs={"command":"head -n 20 /app/bn_sample_10k.csv","summary":"head -n 20 /app/bn_sample_10k.csv","action":"env"}
-
-```
-ran 'head -n 20 /app/bn_sample_10k.csv', exit=0 (0s). Output: env://turn_10/head_-n_20_/app/bn_sample_10k.csv_1 (814 tokens), env://turn_10/head_-n_20_/app/bn_sample_10k.csv_2 (0 tokens)
-```
-
-### `log://turn_10/env/wc_-l_/app/bn_sample_10k.csv`
-scheme=log action=env attrs={"command":"wc -l /app/bn_sample_10k.csv","summary":"wc -l /app/bn_sample_10k.csv","action":"env"}
-
-```
-ran 'wc -l /app/bn_sample_10k.csv', exit=0 (0s). Output: env://turn_10/wc_-l_/app/bn_sample_10k.csv_1 (15 tokens), env://turn_10/wc_-l_/app/bn_sample_10k.csv_2 (0 tokens)
-```
-
-### `log://turn_10/set/env%3A/turn_5/R_-e_%2522installed.packages()%255B/1%255D%2522_1`
-scheme=log action=set attrs={}
-
-```
-env://turn_5/R_-e_%22installed.packages()%5B/1%5D%22_1 set to summarized
-```
-
-### `log://turn_10/set/env%3A/turn_5/R_-e_%2522(.packages())%2522_1`
-scheme=log action=set attrs={}
-
-```
-env://turn_5/R_-e_%22(.packages())%22_1 set to archived
-```
-
-### `log://turn_10/update/discovering_dataset_structure_for_dag_recovery`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-discovering dataset structure for dag_recovery
-```
-