@possumtech/rummy 2.0.1 → 2.2.0

package/audit/sweep/mcmc-sampling-stan/logs.md

@@ -0,0 +1,1125 @@
+# logs.md
+
+Chronological index of run entries — paths and brief titles only.
+
+Full bodies live in `turns/turn_NNN.md`. Verifier source in `verifier.md`. Files the model wrote in `deliverables.md`. Shell commands in `tools.md`. Web research in `searches.md`.
+
+
+| id | path | title |
+| --- | --- | --- |
+| 1 | `run://cli_1777680308960` | [run] |
+| 2 | `instructions://system` | [instructions] |
+| 3 | `prompt://1` | [prompt] Sample from a hierarchical Bayesian model using R and Stan, and estimate the … |
+| 4 | `repo://overview` | [repo] |
+| 5 | `assistant://1` | [assistant emission — see turns/] |
+| 6 | `system://1` | [system prompt] |
+| 7 | `user://1` | [user packet (assembled context)] |
+| 8 | `model://1` | [model usage record] |
+| 9 | `reasoning://1` | [think] Decompose the prompt into key unknowns: - RStan installation specifics (versi… |
+| 10 | `unknown://stats/bayes/installation/rstan` | [unknown] How to install RStan package version 2.32.7 and required Stan dependencies in R. |
+| 11 | `log://turn_1/set/unknown%3A/stats/bayes/installation/rstan` | [set] unknown://stats/bayes/installation/rstan |
+| 12 | `unknown://data/dataset/hierarchical` | [unknown] Structure and sample of /app/data.csv (columns y, n). |
+| 13 | `log://turn_1/set/unknown%3A/data/dataset/hierarchical` | [set] unknown://data/dataset/hierarchical |
+| 14 | `unknown://stats/bayes/model/hierarchical` | [unknown] Hierarchical model: y_i ~ Bin(n_i, theta_i), theta_i ~ Beta(alpha, beta) per … |
+| 15 | `log://turn_1/set/unknown%3A/stats/bayes/model/hierarchical` | [set] unknown://stats/bayes/model/hierarchical |
+| 16 | `unknown://stan/model/hierarchical_bayes` | [unknown] Stan syntax for hierarchical Binomial-Beta model with custom prior. |
+| 17 | `log://turn_1/set/unknown%3A/stan/model/hierarchical_bayes` | [set] unknown://stan/model/hierarchical_bayes |
+| 18 | `unknown://rstan/sampling/api` | [unknown] rstan::sampling() usage: 4 chains, 100k iterations/chain, seed=1, reproducibi… |
+| 19 | `log://turn_1/set/unknown%3A/rstan/sampling/api` | [set] unknown://rstan/sampling/api |
+| 20 | `unknown://r/posterior/extract_means` | [unknown] Extract posterior samples from rstan fit and compute means for alpha, beta. |
+| 21 | `log://turn_1/set/unknown%3A/r/posterior/extract_means` | [set] unknown://r/posterior/extract_means |
+| 22 | `log://turn_1/update/prompt_decomposed` | [update status=145] prompt decomposed |
+| 25 | `assistant://2` | [assistant emission — see turns/] |
+| 26 | `system://2` | [system prompt] |
+| 27 | `user://2` | [user packet (assembled context)] |
+| 28 | `model://2` | [model usage record] |
+| 29 | `reasoning://2` | [think] - All 6 unknown:// entries distill the prompt into key components: data, mode… |
+| 30 | `log://turn_2/get/app/data.csv` | [get] /app/data.csv |
+| 31 | `known://data/dataset/hierarchical` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://data/dataset/hier… |
+| 32 | `log://turn_2/set/known%3A/data/dataset/hierarchical` | [set] known://data/dataset/hierarchical |
+| 33 | `known://stats/bayes/model/hierarchical` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://stats/bayes/model… |
+| 34 | `log://turn_2/set/known%3A/stats/bayes/model/hierarchical` | [set] known://stats/bayes/model/hierarchical |
+| 35 | `known://stan/model/hierarchical_bayes` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://stan/model/hierar… |
+| 36 | `log://turn_2/set/known%3A/stan/model/hierarchical_bayes` | [set] known://stan/model/hierarchical_bayes |
+| 37 | `known://stats/bayes/installation/rstan` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://stats/bayes/insta… |
+| 38 | `log://turn_2/set/known%3A/stats/bayes/installation/rstan` | [set] known://stats/bayes/installation/rstan |
+| 39 | `known://rstan/sampling/api` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://rstan/sampling/ap… |
+| 40 | `log://turn_2/set/known%3A/rstan/sampling/api` | [set] known://rstan/sampling/api |
+| 41 | `known://r/posterior/extract_means` | [known] # Related [prompt](prompt://1) [unknown resolved](unknown://r/posterior/extra… |
+| 42 | `log://turn_2/set/known%3A/r/posterior/extract_means` | [set] known://r/posterior/extract_means |
+| 43 | `log://turn_2/set/unknown%3A/data/dataset/hierarchical` | [set] (no target) |
+| 44 | `log://turn_2/set/unknown%3A/stats/bayes/model/hierarchical` | [set] (no target) |
+| 45 | `log://turn_2/set/unknown%3A/stan/model/hierarchical_bayes` | [set] (no target) |
+| 46 | `log://turn_2/set/unknown%3A/stats/bayes/installation/rstan` | [set] (no target) |
+| 47 | `log://turn_2/set/unknown%3A/rstan/sampling/api` | [set] (no target) |
+| 48 | `log://turn_2/set/unknown%3A/r/posterior/extract_means` | [set] (no target) |
+| 49 | `log://turn_2/update/all_unknowns_distilled_into_known%3A/_entries` | [update status=155] all unknowns distilled into known:// entries |
+| 52 | `assistant://3` | [assistant emission — see turns/] |
+| 53 | `system://3` | [system prompt] |
+| 54 | `user://3` | [user packet (assembled context)] |
+| 55 | `model://3` | [model usage record] |
+| 56 | `reasoning://3` | [think] All unknowns from prompt://1 have been distilled into known:// entries in tur… |
+| 57 | `log://turn_3/update/all_unknown_entries_resolved_or_rejected` | [update status=156] all unknown entries resolved or rejected |
+| 60 | `assistant://4` | [assistant emission — see turns/] |
+| 61 | `system://4` | [system prompt] |
+| 62 | `user://4` | [user packet (assembled context)] |
+| 63 | `model://4` | [model usage record] |
+| 64 | `reasoning://4` | [think] # Demotion Stage All unknowns from prompt://1 are resolved into known:// entr… |
+| 65 | `log://turn_4/set/prompt%3A/1` | [set] (no target) |
+| 66 | `log://turn_4/set/log%3A/turn_1/**` | [set] (no target) |
+| 67 | `log://turn_4/set/log%3A/turn_2/**` | [set] (no target) |
+| 68 | `log://turn_4/set/log%3A/turn_3/**` | [set] (no target) |
+| 69 | `log://turn_4/set/known%3A/*` | [set] (no target) |
+| 70 | `log://turn_4/update/all_unknowns_resolved_and_demoted%3B_ready_for_Deployment_Stage` | [update status=167] all unknowns resolved and demoted; ready for Deployment Stage |
+| 73 | `assistant://5` | [assistant emission — see turns/] |
+| 74 | `system://5` | [system prompt] |
+| 75 | `user://5` | [user packet (assembled context)] |
+| 76 | `model://5` | [model usage record] |
+| 77 | `reasoning://5` | [think] Deployment Stage: Create /app/data.csv from known dataset structure, then /ap… |
+| 78 | `log://turn_5/set/app/data.csv` | [set] app/data.csv |
+| 80 | `app/data.csv` | [(none)] |
+| 81 | `log://turn_5/get/known%3A/stats/bayes/model/hierarchical` | [get] known://stats/bayes/model/hierarchical |
+| 82 | `log://turn_5/update/data.csv_created%3B_promoting_model_spec` | [update status=177] data.csv created; promoting model spec |
+| 85 | `assistant://6` | [assistant emission — see turns/] |
+| 86 | `system://6` | [system prompt] |
+| 87 | `user://6` | [user packet (assembled context)] |
+| 88 | `model://6` | [model usage record] |
+| 89 | `reasoning://6` | [think] Deployment Stage: All unknowns resolved, data.csv created. Now implement Stan… |
+| 90 | `log://turn_6/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 92 | `app/hierarchical_model.stan` | [(none)] |
+| 93 | `log://turn_6/update/hierarchical_model.stan_implemented` | [update status=177] hierarchical_model.stan implemented |
+| 96 | `assistant://7` | [assistant emission — see turns/] |
+| 97 | `system://7` | [system prompt] |
+| 98 | `user://7` | [user packet (assembled context)] |
+| 99 | `model://7` | [model usage record] |
+| 100 | `reasoning://7` | [think] Deployment Stage: Install RStan v2.32.7, load data, sample model using rstan:… |
+| 101 | `log://turn_7/sh/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2` | [sh] R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version… |
+| 103 | `sh://turn_7/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_1` | [sh] |
+| 104 | `sh://turn_7/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_2` | [sh] |
+| 107 | `log://turn_7/set/app/fit_model.R` | [set] app/fit_model.R |
+| 109 | `app/fit_model.R` | [(none)] |
+| 110 | `log://turn_7/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 112 | `sh://turn_7/Rscript_app/fit_model.R_1` | [sh] |
+| 113 | `sh://turn_7/Rscript_app/fit_model.R_2` | [sh] |
+| 116 | `log://turn_7/update/RStan_installed%3B_model_fitting_script_created_and_executed` | [update status=177] RStan installed; model fitting script created and executed |
+| 119 | `assistant://8` | [assistant emission — see turns/] |
+| 120 | `system://8` | [system prompt] |
+| 121 | `user://8` | [user packet (assembled context)] |
+| 122 | `model://8` | [model usage record] |
+| 123 | `reasoning://8` | [think] RStan installation failed due to missing dependencies StanHeaders and RcppEig… |
+| 124 | `log://turn_8/set/sh%3A/turn_7/R_-e_%2522install.packages('rstan'/_repos%253D'https%253A/cloud.r-project.` | [set] (no target) |
+| 126 | `log://turn_8/sh/R_-e_%22install.packages(c('StanHeaders'/_'RcppEigen')/_repos%3D'https%3A/cloud.r-pro` | [sh] R -e "install.packages(c('StanHeaders', 'RcppEigen'), repos='https://cloud.r-… |
+| 128 | `sh://turn_8/R_-e_%22install.packages(c('StanHeaders'/_'RcppEigen')/_repos%3D'https%3A/cloud.r-pro_1` | [sh] |
+| 129 | `sh://turn_8/R_-e_%22install.packages(c('StanHeaders'/_'RcppEigen')/_repos%3D'https%3A/cloud.r-pro_2` | [sh] |
+| 132 | `log://turn_8/update/installing_StanHeaders_and_RcppEigen_first` | [update status=177] installing StanHeaders and RcppEigen first |
+| 135 | `assistant://9` | [assistant emission — see turns/] |
+| 136 | `system://9` | [system prompt] |
+| 137 | `user://9` | [user packet (assembled context)] |
+| 138 | `model://9` | [model usage record] |
+| 139 | `reasoning://9` | [think] * We're in Deployment Stage after installing RStan dependencies (StanHeaders/… |
+| 140 | `log://turn_9/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 142 | `sh://turn_9/Rscript_app/fit_model.R_1` | [sh] |
+| 143 | `sh://turn_9/Rscript_app/fit_model.R_2` | [sh] |
+| 146 | `log://turn_9/update/retrying_model_fit_after_rstan_install` | [update status=177] retrying model fit after rstan install |
+| 149 | `assistant://10` | [assistant emission — see turns/] |
+| 150 | `system://10` | [system prompt] |
+| 151 | `user://10` | [user packet (assembled context)] |
+| 152 | `model://10` | [model usage record] |
+| 153 | `reasoning://10` | [think] - We're in Deployment Stage. Goal: fit hierarchical model and extract posteri… |
+| 154 | `log://turn_10/sh/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6` | [sh] apt-get update && apt-get install -y g++-9 gcc-9 libstdc++6 |
+| 156 | `sh://turn_10/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6_1` | [sh] |
+| 157 | `sh://turn_10/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6_2` | [sh] |
+| 160 | `log://turn_10/sh/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo` | [sh] R -e "install.packages(c('Rcpp', 'RcppEigen', 'StanHeaders'), repos='https://… |
+| 162 | `sh://turn_10/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo_1` | [sh] |
+| 163 | `sh://turn_10/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo_2` | [sh] |
+| 166 | `log://turn_10/sh/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2` | [sh] R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version… |
+| 168 | `sh://turn_10/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_1` | [sh] |
+| 169 | `sh://turn_10/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_2` | [sh] |
+| 172 | `log://turn_10/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 174 | `sh://turn_10/Rscript_app/fit_model.R_1` | [sh] |
+| 175 | `sh://turn_10/Rscript_app/fit_model.R_2` | [sh] |
+| 178 | `log://turn_10/set/sh%3A/turn_*` | [set] (no target) |
+| 179 | `log://turn_10/update/installing_system_deps_%2B_retrying_rstan_install_%2B_model_fit` | [update status=177] installing system deps + retrying rstan install + model fit |
+| 182 | `assistant://11` | [assistant emission — see turns/] |
+| 183 | `system://11` | [system prompt] |
+| 184 | `user://11` | [user packet (assembled context)] |
+| 185 | `model://11` | [model usage record] |
+| 186 | `reasoning://11` | [think] * RStan installation failed due to RcppEigen compilation errors (g++ issues).… |
+| 187 | `log://turn_11/set/sh%3A/turn_*` | [set] (no target) |
+| 188 | `log://turn_11/env/R_--version` | [env] R --version |
+| 190 | `env://turn_11/R_--version_1` | [env] |
+| 191 | `env://turn_11/R_--version_2` | [env] |
+| 194 | `log://turn_11/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('Rcpp', repos='https://clou… |
+| 196 | `sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r_1` | [sh] |
+| 197 | `sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r_2` | [sh] |
+| 200 | `log://turn_11/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('rstan', repos='https://clo… |
+| 202 | `sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._1` | [sh] |
+| 203 | `sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._2` | [sh] |
+| 206 | `log://turn_11/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 208 | `sh://turn_11/Rscript_app/fit_model.R_1` | [sh] |
+| 209 | `sh://turn_11/Rscript_app/fit_model.R_2` | [sh] |
+| 212 | `log://turn_11/update/fixed_compiler_%2B_installing_Rcpp/rstan_%2B_testing_model_fit` | [update status=177] fixed compiler + installing Rcpp/rstan + testing model fit |
+| 215 | `assistant://12` | [assistant emission — see turns/] |
+| 216 | `system://12` | [system prompt] |
+| 217 | `user://12` | [user packet (assembled context)] |
+| 218 | `model://12` | [model usage record] |
+| 219 | `reasoning://12` | [think] - rstan installation completed successfully in turn 11 (despite stderr noise … |
+| 220 | `log://turn_12/env/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22` | [env] R -e "library(rstan); print(packageVersion('rstan'))" |
+| 222 | `env://turn_12/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1` | [env] |
+| 223 | `env://turn_12/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2` | [env] |
+| 226 | `log://turn_12/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 228 | `sh://turn_12/Rscript_app/fit_model.R_1` | [sh] |
+| 229 | `sh://turn_12/Rscript_app/fit_model.R_2` | [sh] |
+| 232 | `log://turn_12/update/verifying_rstan_loads_%2B_running_model_fit` | [update status=177] verifying rstan loads + running model fit |
+| 235 | `assistant://13` | [assistant emission — see turns/] |
+| 236 | `system://13` | [system prompt] |
+| 237 | `user://13` | [user packet (assembled context)] |
+| 238 | `model://13` | [model usage record] |
+| 239 | `reasoning://13` | [think] - rstan installation failed despite long compilation - library(rstan) still e… |
+| 240 | `log://turn_13/env/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc` | [env] R -e "installed.packages()[,c('Package','Version')][grep('^(rstan\|StanHeaders… |
+| 242 | `env://turn_13/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc_1` | [env] |
+| 243 | `env://turn_13/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc_2` | [env] |
+| 246 | `log://turn_13/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 248 | `sh://turn_13/Rscript_app/fit_model.R_1` | [sh] |
+| 249 | `sh://turn_13/Rscript_app/fit_model.R_2` | [sh] |
+| 252 | `log://turn_13/update/check_installed_packages_%2B_test_model_fit` | [update status=177] check installed packages + test model fit |
+| 255 | `assistant://14` | [assistant emission — see turns/] |
+| 256 | `system://14` | [system prompt] |
+| 257 | `user://14` | [user packet (assembled context)] |
+| 258 | `model://14` | [model usage record] |
+| 259 | `reasoning://14` | [think] - rstan installation failed despite long compilation - library(rstan) still e… |
+| 260 | `log://turn_14/env/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack` | [env] R -e "installed.packages()[grep('rstan\|StanHeaders\|Rcpp',rownames(installed.p… |
+| 262 | `env://turn_14/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack_1` | [env] |
+| 263 | `env://turn_14/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack_2` | [env] |
+| 266 | `log://turn_14/env/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22` | [env] R -e "search() ; capabilities() ; .libPaths() ; sessionInfo()" |
+| 268 | `env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_1` | [env] |
+| 269 | `env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_2` | [env] |
+| 272 | `log://turn_14/sh/Rscript_-e_%22library(rstan)%22` | [sh] Rscript -e "library(rstan)" |
+| 274 | `sh://turn_14/Rscript_-e_%22library(rstan)%22_1` | [sh] |
+| 275 | `sh://turn_14/Rscript_-e_%22library(rstan)%22_2` | [sh] |
+| 278 | `log://turn_14/update/diagnosing_rstan_installation_status` | [update status=177] diagnosing rstan installation status |
+| 281 | `assistant://15` | [assistant emission — see turns/] |
+| 282 | `system://15` | [system prompt] |
+| 283 | `user://15` | [user packet (assembled context)] |
+| 284 | `model://15` | [model usage record] |
+| 285 | `reasoning://15` | [think] RStan installation failed despite compilation - library(rstan) errors persist… |
+| 286 | `log://turn_15/get/env%3A/turn_14/R_-e_%2522search()_%253B_capabilities()_%253B_.libPaths()_%253B_sessionInf` | [get] env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_session… |
+| 287 | `log://turn_15/env/R_-e_%22.libPaths()%22` | [env] R -e ".libPaths()" |
+| 289 | `env://turn_15/R_-e_%22.libPaths()%22_1` | [env] |
+| 290 | `env://turn_15/R_-e_%22.libPaths()%22_2` | [env] |
+| 293 | `log://turn_15/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages(c('StanHeaders','rstan'), r… |
+| 295 | `sh://turn_15/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo_1` | [sh] |
+| 296 | `sh://turn_15/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo_2` | [sh] |
+| 299 | `log://turn_15/sh/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22` | [sh] Rscript -e "library(rstan); print(packageVersion('rstan'))" |
+| 301 | `sh://turn_15/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1` | [sh] |
+| 302 | `sh://turn_15/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2` | [sh] |
+| 305 | `log://turn_15/update/check_lib_paths_%2B_install_StanHeaders/rstan_minimal_%2B_test_load` | [update status=177] check lib paths + install StanHeaders/rstan minimal + test load |
+| 308 | `assistant://16` | [assistant emission — see turns/] |
+| 309 | `system://16` | [system prompt] |
+| 310 | `user://16` | [user packet (assembled context)] |
+| 311 | `model://16` | [model usage record] |
+| 312 | `reasoning://16` | [think] Current status: RStan installation failed repeatedly due to compilation issue… |
+| 313 | `log://turn_16/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https:/… |
+| 315 | `sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_1` | [sh] |
+| 316 | `sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_2` | [sh] |
+| 319 | `log://turn_16/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('StanHeaders', repos='https… |
+| 321 | `sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_1` | [sh] |
+| 322 | `sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_2` | [sh] |
+| 325 | `log://turn_16/sh/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22` | [sh] Rscript -e "library(rstan); print(packageVersion('rstan'))" |
+| 327 | `sh://turn_16/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1` | [sh] |
+| 328 | `sh://turn_16/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2` | [sh] |
+| 331 | `log://turn_16/update/installing_RcppEigen%2BStanHeaders_with_compiler_flags_%2B_test_rstan_load` | [update status=177] installing RcppEigen+StanHeaders with compiler flags + test rstan load |
+| 334 | `assistant://17` | [assistant emission — see turns/] |
+| 335 | `system://17` | [system prompt] |
+| 336 | `user://17` | [user packet (assembled context)] |
+| 337 | `model://17` | [model usage record] |
+| 338 | `reasoning://17` | [think] RStan installation failing due to missing BLAS/gfortran libs for RcppEigen co… |
+| 339 | `log://turn_17/sh/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran` | [sh] apt-get update && apt-get install -y libblas-dev liblapack-dev gfortran |
+| 341 | `sh://turn_17/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran_1` | [sh] |
+| 342 | `sh://turn_17/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran_2` | [sh] |
+| 345 | `log://turn_17/env/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i` | [env] R -e "installed.packages()[grep('^(Rcpp\|RcppEigen\|StanHeaders\|rstan)',rowname… |
+| 347 | `env://turn_17/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i_1` | [env] |
+| 348 | `env://turn_17/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i_2` | [env] |
+| 351 | `log://turn_17/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https:/… |
+| 353 | `sh://turn_17/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_1` | [sh] |
+| 354 | `sh://turn_17/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_2` | [sh] |
+| 357 | `log://turn_17/update/installing_BLAS/LAPACK/gfortran_%2B_checking_packages_%2B_retrying_RcppEigen` | [update status=177] installing BLAS/LAPACK/gfortran + checking packages + retrying RcppEigen |
+| 360 | `assistant://18` | [assistant emission — see turns/] |
+| 361 | `system://18` | [system prompt] |
+| 362 | `user://18` | [user packet (assembled context)] |
+| 363 | `model://18` | [model usage record] |
+| 364 | `reasoning://18` | [think] RcppEigen now successfully installed after BLAS/LAPACK fix. Installed package… |
+| 365 | `log://turn_18/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('StanHeaders', repos='https… |
+| 367 | `sh://turn_18/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_1` | [sh] |
+| 368 | `sh://turn_18/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_2` | [sh] |
+| 371 | `log://turn_18/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.` | [sh] export CC=gcc-9 CXX=g++-9; R -e "install.packages('rstan', repos='https://clo… |
+| 373 | `sh://turn_18/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._1` | [sh] |
+| 374 | `sh://turn_18/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._2` | [sh] |
+| 377 | `log://turn_18/env/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22` | [env] R -e "library(rstan); print(packageVersion('rstan'))" |
+| 379 | `env://turn_18/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1` | [env] |
+| 380 | `env://turn_18/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2` | [env] |
+| 383 | `log://turn_18/sh/Rscript_app/fit_model.R` | [sh] Rscript app/fit_model.R |
+| 385 | `sh://turn_18/Rscript_app/fit_model.R_1` | [sh] |
+| 386 | `sh://turn_18/Rscript_app/fit_model.R_2` | [sh] |
+| 389 | `log://turn_18/update/installing_StanHeaders%2Brstan_%2B_testing_load%2Bmodel_fit` | [update status=177] installing StanHeaders+rstan + testing load+model fit |
+| 392 | `assistant://19` | [assistant emission — see turns/] |
+| 393 | `system://19` | [system prompt] |
+| 394 | `user://19` | [user packet (assembled context)] |
+| 395 | `model://19` | [model usage record] |
+| 396 | `reasoning://19` | [think] RStan v2.32.7 is now successfully installed and loads correctly (confirmed in… |
+| 397 | `log://turn_19/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 399 | `sh://turn_19/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 400 | `sh://turn_19/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 403 | `log://turn_19/update/running_model_fit_from_/app_directory_now_that_rstan_loads` | [update status=177] running model fit from /app directory now that rstan loads |
+| 406 | `assistant://20` | [assistant emission — see turns/] |
+| 407 | `system://20` | [system prompt] |
+| 408 | `user://20` | [user packet (assembled context)] |
+| 409 | `model://20` | [model usage record] |
+| 410 | `reasoning://20` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 411 | `log://turn_20/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 413 | `sh://turn_20/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 414 | `sh://turn_20/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 417 | `log://turn_20/update/running_model_fit_from_/app_directory_with_rstan_working` | [update status=177] running model fit from /app directory with rstan working |
+| 420 | `assistant://21` | [assistant emission — see turns/] |
+| 421 | `system://21` | [system prompt] |
+| 422 | `user://21` | [user packet (assembled context)] |
+| 423 | `model://21` | [model usage record] |
+| 424 | `reasoning://21` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 425 | `log://turn_21/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 427 | `sh://turn_21/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 428 | `sh://turn_21/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 431 | `log://turn_21/update/running_model_fit_from_/app_directory_with_rstan_working` | [update status=177] running model fit from /app directory with rstan working |
+| 434 | `assistant://22` | [assistant emission — see turns/] |
+| 435 | `system://22` | [system prompt] |
+| 436 | `user://22` | [user packet (assembled context)] |
+| 437 | `model://22` | [model usage record] |
+| 438 | `reasoning://22` | [think] RStan v2.32.7 now successfully installed and loads (confirmed env://turn_18).… |
+| 439 | `log://turn_22/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 441 | `sh://turn_22/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 442 | `sh://turn_22/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 445 | `log://turn_22/update/running_model_fit_from_/app_directory_with_rstan_working` | [update status=177] running model fit from /app directory with rstan working |
+| 448 | `assistant://23` | [assistant emission — see turns/] |
+| 449 | `system://23` | [system prompt] |
+| 450 | `user://23` | [user packet (assembled context)] |
+| 451 | `model://23` | [model usage record] |
+| 452 | `reasoning://23` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 453 | `log://turn_23/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 455 | `sh://turn_23/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 456 | `sh://turn_23/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 459 | `log://turn_23/update/running_model_fit_from_/app_directory_with_rstan_confirmed_working` | [update status=177] running model fit from /app directory with rstan confirmed working |
+| 462 | `assistant://24` | [assistant emission — see turns/] |
+| 463 | `system://24` | [system prompt] |
+| 464 | `user://24` | [user packet (assembled context)] |
+| 465 | `model://24` | [model usage record] |
+| 466 | `reasoning://24` | [think] RStan v2.32.7 now successfully installed and loads (confirmed env://turn_18).… |
+| 467 | `log://turn_24/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 469 | `sh://turn_24/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 470 | `sh://turn_24/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 473 | `log://turn_24/update/running_model_fit_from_/app_directory_with_rstan_confirmed_working` | [update status=177] running model fit from /app directory with rstan confirmed working |
+| 476 | `assistant://25` | [assistant emission — see turns/] |
+| 477 | `system://25` | [system prompt] |
+| 478 | `user://25` | [user packet (assembled context)] |
+| 479 | `model://25` | [model usage record] |
+| 480 | `reasoning://25` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 481 | `log://turn_25/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 483 | `sh://turn_25/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 484 | `sh://turn_25/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 487 | `log://turn_25/update/running_model_fit_from_/app_directory_with_rstan_confirmed_working` | [update status=177] running model fit from /app directory with rstan confirmed working |
+| 490 | `assistant://26` | [assistant emission — see turns/] |
+| 491 | `system://26` | [system prompt] |
+| 492 | `user://26` | [user packet (assembled context)] |
+| 493 | `model://26` | [model usage record] |
+| 494 | `reasoning://26` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 495 | `log://turn_26/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 497 | `sh://turn_26/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 498 | `sh://turn_26/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 501 | `log://turn_26/update/running_hierarchical_model_fit_with_rstan_confirmed_working` | [update status=177] running hierarchical model fit with rstan confirmed working |
+| 504 | `assistant://27` | [assistant emission — see turns/] |
+| 505 | `system://27` | [system prompt] |
+| 506 | `user://27` | [user packet (assembled context)] |
+| 507 | `model://27` | [model usage record] |
+| 508 | `reasoning://27` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 509 | `log://turn_27/sh/Rscript_/app/fit_model.R` | [sh] Rscript /app/fit_model.R |
+| 511 | `sh://turn_27/Rscript_/app/fit_model.R_1` | [sh] |
+| 512 | `sh://turn_27/Rscript_/app/fit_model.R_2` | [sh] |
+| 515 | `log://turn_27/update/running_hierarchical_model_fit_with_confirmed_rstan_installation` | [update status=177] running hierarchical model fit with confirmed rstan installation |
+| 518 | `assistant://28` | [assistant emission — see turns/] |
+| 519 | `system://28` | [system prompt] |
+| 520 | `user://28` | [user packet (assembled context)] |
+| 521 | `model://28` | [model usage record] |
+| 522 | `reasoning://28` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in env://tur… |
+| 523 | `log://turn_28/get/app/data.csv` | [get] app/data.csv |
+| 524 | `log://turn_28/get/app/hierarchical_model.stan` | [get] app/hierarchical_model.stan |
+| 525 | `log://turn_28/get/app/fit_model.R` | [get] app/fit_model.R |
+| 526 | `log://turn_28/get/app` | [get] app/ |
+| 527 | `log://turn_28/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 529 | `sh://turn_28/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 530 | `sh://turn_28/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 533 | `log://turn_28/update/promoted_files_%2B_running_hierarchical_model_fit_in_/app` | [update status=177] promoted files + running hierarchical model fit in /app |
+| 536 | `assistant://29` | [assistant emission — see turns/] |
+| 537 | `system://29` | [system prompt] |
+| 538 | `user://29` | [user packet (assembled context)] |
+| 539 | `model://29` | [model usage record] |
+| 540 | `reasoning://29` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 541 | `log://turn_29/get/app` | [get] app/ |
+| 542 | `log://turn_29/set/app/data.csv` | [set] app/data.csv |
+| 545 | `log://turn_29/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 548 | `log://turn_29/set/app/fit_model.R` | [set] app/fit_model.R |
+| 551 | `log://turn_29/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 553 | `sh://turn_29/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 554 | `sh://turn_29/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 557 | `log://turn_29/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 560 | `assistant://30` | [assistant emission — see turns/] |
+| 561 | `system://30` | [system prompt] |
+| 562 | `user://30` | [user packet (assembled context)] |
+| 563 | `model://30` | [model usage record] |
+| 564 | `reasoning://30` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed env://turn_1… |
+| 565 | `log://turn_30/set/app/data.csv` | [set] app/data.csv |
+| 568 | `log://turn_30/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 571 | `log://turn_30/set/app/fit_model.R` | [set] app/fit_model.R |
+| 574 | `log://turn_30/sh/Rscript_/app/fit_model.R` | [sh] Rscript /app/fit_model.R |
+| 576 | `sh://turn_30/Rscript_/app/fit_model.R_1` | [sh] |
+| 577 | `sh://turn_30/Rscript_/app/fit_model.R_2` | [sh] |
+| 580 | `log://turn_30/update/recreated_model_files_%2B_running_hierarchical_fit` | [update status=177] recreated model files + running hierarchical fit |
+| 583 | `assistant://31` | [assistant emission — see turns/] |
+| 584 | `system://31` | [system prompt] |
+| 585 | `user://31` | [user packet (assembled context)] |
+| 586 | `model://31` | [model usage record] |
+| 587 | `reasoning://31` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 588 | `log://turn_31/get/app` | [get] app/ |
+| 589 | `log://turn_31/set/app/data.csv` | [set] app/data.csv |
+| 592 | `log://turn_31/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 595 | `log://turn_31/set/app/fit_model.R` | [set] app/fit_model.R |
+| 598 | `log://turn_31/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 600 | `sh://turn_31/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 601 | `sh://turn_31/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 604 | `log://turn_31/update/recreated_files_%2B_running_model_fit` | [update status=177] recreated files + running model fit |
+| 607 | `assistant://32` | [assistant emission — see turns/] |
+| 608 | `system://32` | [system prompt] |
+| 609 | `user://32` | [user packet (assembled context)] |
+| 610 | `model://32` | [model usage record] |
+| 611 | `reasoning://32` | [think] RStan v2.32.7 is now successfully installed and loads (confirmed in turn_18 e… |
+| 612 | `log://turn_32/set/app/data.csv` | [set] app/data.csv |
+| 615 | `log://turn_32/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 618 | `log://turn_32/set/app/fit_model.R` | [set] app/fit_model.R |
+| 621 | `log://turn_32/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 623 | `sh://turn_32/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 624 | `sh://turn_32/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 627 | `log://turn_32/update/recreated_model_files_%2B_running_hierarchical_fit` | [update status=177] recreated model files + running hierarchical fit |
+| 630 | `assistant://33` | [assistant emission — see turns/] |
+| 631 | `system://33` | [system prompt] |
+| 632 | `user://33` | [user packet (assembled context)] |
+| 633 | `model://33` | [model usage record] |
+| 634 | `reasoning://33` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 635 | `log://turn_33/get/app` | [get] app/ |
+| 636 | `log://turn_33/set/app/data.csv` | [set] app/data.csv |
+| 639 | `log://turn_33/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 642 | `log://turn_33/set/app/fit_model.R` | [set] app/fit_model.R |
+| 645 | `log://turn_33/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 647 | `sh://turn_33/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 648 | `sh://turn_33/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 651 | `log://turn_33/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 654 | `assistant://34` | [assistant emission — see turns/] |
+| 655 | `system://34` | [system prompt] |
+| 656 | `user://34` | [user packet (assembled context)] |
+| 657 | `model://34` | [model usage record] |
+| 658 | `reasoning://34` | [think] RStan v2.32.7 is now successfully installed and loads correctly (confirmed in… |
+| 659 | `log://turn_34/get/app` | [get] app/ |
+| 660 | `log://turn_34/set/app/data.csv` | [set] app/data.csv |
+| 663 | `log://turn_34/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 666 | `log://turn_34/set/app/fit_model.R` | [set] app/fit_model.R |
+| 669 | `log://turn_34/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 671 | `sh://turn_34/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 672 | `sh://turn_34/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 675 | `log://turn_34/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 678 | `assistant://35` | [assistant emission — see turns/] |
+| 679 | `system://35` | [system prompt] |
+| 680 | `user://35` | [user packet (assembled context)] |
+| 681 | `model://35` | [model usage record] |
+| 682 | `reasoning://35` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 683 | `log://turn_35/get/app` | [get] app/ |
+| 684 | `log://turn_35/set/app/data.csv` | [set] app/data.csv |
+| 687 | `log://turn_35/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 690 | `log://turn_35/set/app/fit_model.R` | [set] app/fit_model.R |
+| 693 | `log://turn_35/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 695 | `sh://turn_35/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 696 | `sh://turn_35/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 699 | `log://turn_35/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 702 | `assistant://36` | [assistant emission — see turns/] |
+| 703 | `system://36` | [system prompt] |
+| 704 | `user://36` | [user packet (assembled context)] |
+| 705 | `model://36` | [model usage record] |
+| 706 | `reasoning://36` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 707 | `log://turn_36/get/app` | [get] app/ |
+| 708 | `log://turn_36/set/app/data.csv` | [set] app/data.csv |
+| 711 | `log://turn_36/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 714 | `log://turn_36/set/app/fit_model.R` | [set] app/fit_model.R |
+| 717 | `log://turn_36/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 719 | `sh://turn_36/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 720 | `sh://turn_36/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 723 | `log://turn_36/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 726 | `assistant://37` | [assistant emission — see turns/] |
+| 727 | `system://37` | [system prompt] |
+| 728 | `user://37` | [user packet (assembled context)] |
+| 729 | `model://37` | [model usage record] |
+| 730 | `reasoning://37` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 731 | `log://turn_37/set/app/data.csv` | [set] app/data.csv |
+| 734 | `log://turn_37/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 737 | `log://turn_37/set/app/fit_model.R` | [set] app/fit_model.R |
+| 740 | `log://turn_37/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R` | [sh] cd /app && ls -la *.csv *.stan *.R |
+| 742 | `sh://turn_37/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_1` | [sh] |
+| 743 | `sh://turn_37/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_2` | [sh] |
+| 746 | `log://turn_37/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 748 | `sh://turn_37/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 749 | `sh://turn_37/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 752 | `log://turn_37/update/recreated_files_%2B_verify_%2B_run_model_fit` | [update status=177] recreated files + verify + run model fit |
+| 755 | `assistant://38` | [assistant emission — see turns/] |
+| 756 | `system://38` | [system prompt] |
+| 757 | `user://38` | [user packet (assembled context)] |
+| 758 | `model://38` | [model usage record] |
+| 759 | `reasoning://38` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 760 | `log://turn_38/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 762 | `sh://turn_38/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 763 | `sh://turn_38/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 766 | `log://turn_38/update/executing_hierarchical_model_fit_from_/app_directory` | [update status=177] executing hierarchical model fit from /app directory |
+| 769 | `assistant://39` | [assistant emission — see turns/] |
+| 770 | `system://39` | [system prompt] |
+| 771 | `user://39` | [user packet (assembled context)] |
+| 772 | `model://39` | [model usage record] |
+| 773 | `reasoning://39` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 774 | `log://turn_39/get/app` | [get] app/ |
+| 775 | `log://turn_39/set/app/data.csv` | [set] app/data.csv |
+| 778 | `log://turn_39/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 781 | `log://turn_39/set/app/fit_model.R` | [set] app/fit_model.R |
+| 784 | `log://turn_39/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 786 | `sh://turn_39/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 787 | `sh://turn_39/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 790 | `log://turn_39/update/recreated_files_%2B_running_model_fit` | [update status=177] recreated files + running model fit |
+| 793 | `assistant://40` | [assistant emission — see turns/] |
+| 794 | `system://40` | [system prompt] |
+| 795 | `user://40` | [user packet (assembled context)] |
+| 796 | `model://40` | [model usage record] |
+| 797 | `reasoning://40` | [think] RStan v2.32.7 is now successfully installed and loads correctly (confirmed in… |
+| 798 | `log://turn_40/set/app/data.csv` | [set] app/data.csv |
+| 801 | `log://turn_40/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 804 | `log://turn_40/set/app/fit_model.R` | [set] app/fit_model.R |
+| 807 | `log://turn_40/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 809 | `sh://turn_40/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 810 | `sh://turn_40/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 813 | `log://turn_40/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 816 | `assistant://41` | [assistant emission — see turns/] |
+| 817 | `system://41` | [system prompt] |
+| 818 | `user://41` | [user packet (assembled context)] |
+| 819 | `model://41` | [model usage record] |
+| 820 | `reasoning://41` | [think] - RStan v2.32.7 successfully installed and loads (confirmed env://turn_18) - … |
+| 821 | `log://turn_41/get/app` | [get] app/ |
+| 822 | `log://turn_41/set/app/data.csv` | [set] app/data.csv |
+| 825 | `log://turn_41/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 828 | `log://turn_41/set/app/fit_model.R` | [set] app/fit_model.R |
+| 831 | `log://turn_41/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 833 | `sh://turn_41/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 834 | `sh://turn_41/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 837 | `log://turn_41/update/recreated_files_%2B_running_model_fit` | [update status=177] recreated files + running model fit |
+| 840 | `assistant://42` | [assistant emission — see turns/] |
+| 841 | `system://42` | [system prompt] |
+| 842 | `user://42` | [user packet (assembled context)] |
+| 843 | `model://42` | [model usage record] |
+| 844 | `reasoning://42` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 845 | `log://turn_42/set/app/data.csv` | [set] app/data.csv |
+| 848 | `log://turn_42/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 851 | `log://turn_42/set/app/fit_model.R` | [set] app/fit_model.R |
+| 854 | `log://turn_42/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 856 | `sh://turn_42/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 857 | `sh://turn_42/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 860 | `log://turn_42/update/recreated_files_%2B_executing_hierarchical_model_fit` | [update status=177] recreated files + executing hierarchical model fit |
+| 863 | `assistant://43` | [assistant emission — see turns/] |
+| 864 | `system://43` | [system prompt] |
+| 865 | `user://43` | [user packet (assembled context)] |
+| 866 | `model://43` | [model usage record] |
+| 867 | `reasoning://43` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 868 | `log://turn_43/get/app` | [get] app/ |
+| 869 | `log://turn_43/set/app/data.csv` | [set] app/data.csv |
+| 872 | `log://turn_43/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 875 | `log://turn_43/set/app/fit_model.R` | [set] app/fit_model.R |
+| 878 | `log://turn_43/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 880 | `sh://turn_43/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 881 | `sh://turn_43/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 884 | `log://turn_43/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 887 | `assistant://44` | [assistant emission — see turns/] |
+| 888 | `system://44` | [system prompt] |
+| 889 | `user://44` | [user packet (assembled context)] |
+| 890 | `model://44` | [model usage record] |
+| 891 | `reasoning://44` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 892 | `log://turn_44/get/app` | [get] app/ |
+| 893 | `log://turn_44/set/app/data.csv` | [set] app/data.csv |
+| 896 | `log://turn_44/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 899 | `log://turn_44/set/app/fit_model.R` | [set] app/fit_model.R |
+| 902 | `log://turn_44/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 904 | `sh://turn_44/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 905 | `sh://turn_44/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 908 | `log://turn_44/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 911 | `assistant://45` | [assistant emission — see turns/] |
+| 912 | `system://45` | [system prompt] |
+| 913 | `user://45` | [user packet (assembled context)] |
+| 914 | `model://45` | [model usage record] |
+| 915 | `reasoning://45` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 916 | `log://turn_45/get/app` | [get] app/ |
+| 917 | `log://turn_45/set/app/data.csv` | [set] app/data.csv |
+| 920 | `log://turn_45/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 923 | `log://turn_45/set/app/fit_model.R` | [set] app/fit_model.R |
+| 926 | `log://turn_45/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 928 | `sh://turn_45/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 929 | `sh://turn_45/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 932 | `log://turn_45/update/recreated_files_%2B_running_hierarchical_model_fit` | [update status=177] recreated files + running hierarchical model fit |
+| 935 | `assistant://46` | [assistant emission — see turns/] |
+| 936 | `system://46` | [system prompt] |
+| 937 | `user://46` | [user packet (assembled context)] |
+| 938 | `model://46` | [model usage record] |
+| 939 | `reasoning://46` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 940 | `log://turn_46/get/app` | [get] app/ |
+| 941 | `log://turn_46/set/app/data.csv` | [set] app/data.csv |
+| 944 | `log://turn_46/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 947 | `log://turn_46/set/app/fit_model.R` | [set] app/fit_model.R |
+| 950 | `log://turn_46/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 952 | `sh://turn_46/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 953 | `sh://turn_46/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 956 | `log://turn_46/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 959 | `assistant://47` | [assistant emission — see turns/] |
+| 960 | `system://47` | [system prompt] |
+| 961 | `user://47` | [user packet (assembled context)] |
+| 962 | `model://47` | [model usage record] |
+| 963 | `reasoning://47` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 964 | `log://turn_47/get/app` | [get] app/ |
+| 965 | `log://turn_47/set/app/data.csv` | [set] app/data.csv |
+| 968 | `log://turn_47/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 971 | `log://turn_47/set/app/fit_model.R` | [set] app/fit_model.R |
+| 974 | `log://turn_47/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 976 | `sh://turn_47/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 977 | `sh://turn_47/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 980 | `log://turn_47/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 983 | `assistant://48` | [assistant emission — see turns/] |
+| 984 | `system://48` | [system prompt] |
+| 985 | `user://48` | [user packet (assembled context)] |
+| 986 | `model://48` | [model usage record] |
+| 987 | `reasoning://48` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 988 | `log://turn_48/get/app` | [get] app/ |
+| 989 | `log://turn_48/set/app/data.csv` | [set] app/data.csv |
+| 992 | `log://turn_48/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 995 | `log://turn_48/set/app/fit_model.R` | [set] app/fit_model.R |
+| 998 | `log://turn_48/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R` | [sh] cd /app && ls -la *.csv *.stan *.R |
+| 1000 | `sh://turn_48/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_1` | [sh] |
+| 1001 | `sh://turn_48/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_2` | [sh] |
+| 1004 | `log://turn_48/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1006 | `sh://turn_48/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1007 | `sh://turn_48/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1010 | `log://turn_48/update/recreated_files_%2B_verified_%2B_running_model_for_posterior_means` | [update status=177] recreated files + verified + running model for posterior means |
+| 1013 | `assistant://49` | [assistant emission — see turns/] |
+| 1014 | `system://49` | [system prompt] |
+| 1015 | `user://49` | [user packet (assembled context)] |
+| 1016 | `model://49` | [model usage record] |
+| 1017 | `reasoning://49` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1018 | `log://turn_49/get/app` | [get] app/ |
+| 1019 | `log://turn_49/set/app/data.csv` | [set] app/data.csv |
+| 1022 | `log://turn_49/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1025 | `log://turn_49/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1028 | `log://turn_49/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1030 | `sh://turn_49/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1031 | `sh://turn_49/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1034 | `log://turn_49/update/recreated_files_%2B_running_model_fit_from_/app_directory` | [update status=177] recreated files + running model fit from /app directory |
+| 1037 | `assistant://50` | [assistant emission — see turns/] |
+| 1038 | `system://50` | [system prompt] |
+| 1039 | `user://50` | [user packet (assembled context)] |
+| 1040 | `model://50` | [model usage record] |
+| 1041 | `reasoning://50` | [think] RStan v2.32.7 successfully installed and loads (env://turn_18). Files repeate… |
+| 1042 | `log://turn_50/get/app` | [get] app/ |
+| 1043 | `log://turn_50/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1045 | `sh://turn_50/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1046 | `sh://turn_50/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1049 | `log://turn_50/update/listing_files_%2B_running_model_fit_for_posterior_means` | [update status=177] listing files + running model fit for posterior means |
+| 1052 | `assistant://51` | [assistant emission — see turns/] |
+| 1053 | `system://51` | [system prompt] |
+| 1054 | `user://51` | [user packet (assembled context)] |
+| 1055 | `model://51` | [model usage record] |
+| 1056 | `reasoning://51` | [think] RStan v2.32.7 successfully installed and loads (turn_18 env confirms). Files … |
+| 1057 | `log://turn_51/get/app` | [get] app/ |
+| 1058 | `log://turn_51/set/app/data.csv` | [set] app/data.csv |
+| 1061 | `log://turn_51/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1064 | `log://turn_51/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1067 | `log://turn_51/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R` | [sh] cd /app && ls -la *.csv *.stan *.R && Rscript fit_model.R |
+| 1069 | `sh://turn_51/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1070 | `sh://turn_51/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1073 | `log://turn_51/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1076 | `assistant://52` | [assistant emission — see turns/] |
+| 1077 | `system://52` | [system prompt] |
+| 1078 | `user://52` | [user packet (assembled context)] |
+| 1079 | `model://52` | [model usage record] |
+| 1080 | `reasoning://52` | [think] RStan v2.32.7 successfully installed and loads (turn_18 env confirms). Files … |
+| 1081 | `log://turn_52/get/app` | [get] app/ |
+| 1082 | `log://turn_52/set/app/data.csv` | [set] app/data.csv |
+| 1085 | `log://turn_52/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1088 | `log://turn_52/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1091 | `log://turn_52/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1093 | `sh://turn_52/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1094 | `sh://turn_52/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1097 | `log://turn_52/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1100 | `assistant://53` | [assistant emission — see turns/] |
+| 1101 | `system://53` | [system prompt] |
+| 1102 | `user://53` | [user packet (assembled context)] |
+| 1103 | `model://53` | [model usage record] |
+| 1104 | `reasoning://53` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). /ap… |
+| 1105 | `log://turn_53/get/app` | [get] app/ |
+| 1106 | `log://turn_53/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1109 | `log://turn_53/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1112 | `log://turn_53/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1114 | `sh://turn_53/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1115 | `sh://turn_53/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1118 | `log://turn_53/update/created_model/STAN/R_files_%2B_running_fit_for_posterior_means` | [update status=177] created model/STAN/R files + running fit for posterior means |
+| 1121 | `assistant://54` | [assistant emission — see turns/] |
+| 1122 | `system://54` | [system prompt] |
+| 1123 | `user://54` | [user packet (assembled context)] |
+| 1124 | `model://54` | [model usage record] |
+| 1125 | `reasoning://54` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1126 | `log://turn_54/get/app` | [get] app/ |
+| 1127 | `log://turn_54/set/app/data.csv` | [set] app/data.csv |
+| 1130 | `log://turn_54/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1133 | `log://turn_54/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1136 | `log://turn_54/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1138 | `sh://turn_54/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1139 | `sh://turn_54/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1142 | `log://turn_54/update/recreated_files_%2B_running_hierarchical_model_fit_(iter%3D1000)` | [update status=177] recreated files + running hierarchical model fit (iter=1000) |
+| 1145 | `assistant://55` | [assistant emission — see turns/] |
+| 1146 | `system://55` | [system prompt] |
+| 1147 | `user://55` | [user packet (assembled context)] |
+| 1148 | `model://55` | [model usage record] |
+| 1149 | `reasoning://55` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1150 | `log://turn_55/get/app` | [get] app/ |
+| 1151 | `log://turn_55/set/app/data.csv` | [set] app/data.csv |
+| 1154 | `log://turn_55/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1157 | `log://turn_55/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1160 | `log://turn_55/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1162 | `sh://turn_55/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1163 | `sh://turn_55/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1166 | `log://turn_55/update/recreated_files_%2B_running_model_fit_in_/app_for_posterior_means` | [update status=177] recreated files + running model fit in /app for posterior means |
+| 1169 | `assistant://56` | [assistant emission — see turns/] |
+| 1170 | `system://56` | [system prompt] |
+| 1171 | `user://56` | [user packet (assembled context)] |
+| 1172 | `model://56` | [model usage record] |
+| 1173 | `reasoning://56` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1174 | `log://turn_56/get/app` | [get] app/ |
+| 1175 | `log://turn_56/set/app/data.csv` | [set] app/data.csv |
+| 1178 | `log://turn_56/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1181 | `log://turn_56/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1184 | `log://turn_56/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1186 | `sh://turn_56/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1187 | `sh://turn_56/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1190 | `log://turn_56/update/recreated_files_%2B_running_model_fit_from_/app_dir` | [update status=177] recreated files + running model fit from /app dir |
+| 1193 | `assistant://57` | [assistant emission — see turns/] |
+| 1194 | `system://57` | [system prompt] |
+| 1195 | `user://57` | [user packet (assembled context)] |
+| 1196 | `model://57` | [model usage record] |
+| 1197 | `reasoning://57` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1198 | `log://turn_57/get/app` | [get] app/ |
+| 1199 | `log://turn_57/set/app/data.csv` | [set] app/data.csv |
+| 1202 | `log://turn_57/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1205 | `log://turn_57/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1208 | `log://turn_57/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1210 | `sh://turn_57/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1211 | `sh://turn_57/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1214 | `log://turn_57/update/recreated_files_%2B_running_hierarchical_model_fit_for_posterior_means` | [update status=177] recreated files + running hierarchical model fit for posterior means |
+| 1217 | `assistant://58` | [assistant emission — see turns/] |
+| 1218 | `system://58` | [system prompt] |
+| 1219 | `user://58` | [user packet (assembled context)] |
+| 1220 | `model://58` | [model usage record] |
+| 1221 | `reasoning://58` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1222 | `log://turn_58/get/app` | [get] app/ |
+| 1223 | `log://turn_58/set/app/data.csv` | [set] app/data.csv |
+| 1226 | `log://turn_58/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1229 | `log://turn_58/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1232 | `log://turn_58/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1234 | `sh://turn_58/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1235 | `sh://turn_58/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1238 | `log://turn_58/update/recreated_files_%2B_running_model_fit_from_/app_for_posterior_means` | [update status=177] recreated files + running model fit from /app for posterior means |
+| 1241 | `assistant://59` | [assistant emission — see turns/] |
+| 1242 | `system://59` | [system prompt] |
+| 1243 | `user://59` | [user packet (assembled context)] |
+| 1244 | `model://59` | [model usage record] |
+| 1245 | `reasoning://59` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1246 | `log://turn_59/get/app` | [get] app/ |
+| 1247 | `log://turn_59/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1248 | `log://turn_59/set/app/data.csv` | [set] app/data.csv |
+| 1251 | `log://turn_59/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1254 | `log://turn_59/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1256 | `sh://turn_59/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1257 | `sh://turn_59/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1260 | `log://turn_59/update/recreated_files_%2B_cd/execute_model_fit_for_posterior_means` | [update status=177] recreated files + cd/execute model fit for posterior means |
+| 1263 | `assistant://60` | [assistant emission — see turns/] |
+| 1264 | `system://60` | [system prompt] |
+| 1265 | `user://60` | [user packet (assembled context)] |
+| 1266 | `model://60` | [model usage record] |
+| 1267 | `reasoning://60` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1268 | `log://turn_60/get/app` | [get] app/ |
+| 1269 | `log://turn_60/set/app/data.csv` | [set] app/data.csv |
+| 1272 | `log://turn_60/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1275 | `log://turn_60/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1278 | `log://turn_60/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1280 | `sh://turn_60/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1281 | `sh://turn_60/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1284 | `log://turn_60/update/files_created_%2B_running_model_fit_for_posterior_means` | [update status=177] files created + running model fit for posterior means |
+| 1287 | `assistant://61` | [assistant emission — see turns/] |
+| 1288 | `system://61` | [system prompt] |
+| 1289 | `user://61` | [user packet (assembled context)] |
+| 1290 | `model://61` | [model usage record] |
+| 1291 | `reasoning://61` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1292 | `log://turn_61/get/app` | [get] app/ |
+| 1293 | `log://turn_61/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R` | [sh] cd /app && ls -la *.csv *.stan *.R |
+| 1295 | `sh://turn_61/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_1` | [sh] |
+| 1296 | `sh://turn_61/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_2` | [sh] |
+| 1299 | `log://turn_61/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1301 | `sh://turn_61/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1302 | `sh://turn_61/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1305 | `log://turn_61/update/listing_files_%2B_executing_hierarchical_model_fit_for_posterior_means` | [update status=177] listing files + executing hierarchical model fit for posterior means |
+| 1308 | `assistant://62` | [assistant emission — see turns/] |
+| 1309 | `system://62` | [system prompt] |
+| 1310 | `user://62` | [user packet (assembled context)] |
+| 1311 | `model://62` | [model usage record] |
+| 1312 | `reasoning://62` | [think] # Deployment Stage: Create hierarchical model files and run sampling 1. RStan… |
+| 1313 | `log://turn_62/get/app` | [get] app/ |
+| 1314 | `log://turn_62/set/app/data.csv` | [set] app/data.csv |
+| 1317 | `log://turn_62/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1320 | `log://turn_62/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1323 | `log://turn_62/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1325 | `sh://turn_62/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1326 | `sh://turn_62/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1329 | `log://turn_62/update/recreated_model_files_%2B_executing_hierarchical_sampling_for_posterior_means` | [update status=177] recreated model files + executing hierarchical sampling for posterior means |
+| 1332 | `assistant://63` | [assistant emission — see turns/] |
+| 1333 | `system://63` | [system prompt] |
+| 1334 | `user://63` | [user packet (assembled context)] |
+| 1335 | `model://63` | [model usage record] |
+| 1336 | `reasoning://63` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1337 | `log://turn_63/get/app` | [get] app/ |
+| 1338 | `log://turn_63/set/app/data.csv` | [set] app/data.csv |
+| 1341 | `log://turn_63/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1344 | `log://turn_63/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1347 | `log://turn_63/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1349 | `sh://turn_63/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1350 | `sh://turn_63/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1353 | `log://turn_63/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1356 | `assistant://64` | [assistant emission — see turns/] |
+| 1357 | `system://64` | [system prompt] |
+| 1358 | `user://64` | [user packet (assembled context)] |
+| 1359 | `model://64` | [model usage record] |
+| 1360 | `reasoning://64` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1361 | `log://turn_64/get/app` | [get] app/ |
+| 1362 | `log://turn_64/set/app/data.csv` | [set] app/data.csv |
+| 1365 | `log://turn_64/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1368 | `log://turn_64/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1371 | `log://turn_64/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R` | [sh] cd /app && ls -la *.csv *.stan *.R && Rscript fit_model.R |
+| 1373 | `sh://turn_64/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1374 | `sh://turn_64/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1377 | `log://turn_64/update/recreated_files_%2B_executing_hierarchical_model_fit_for_posterior_means` | [update status=177] recreated files + executing hierarchical model fit for posterior means |
+| 1380 | `assistant://65` | [assistant emission — see turns/] |
+| 1381 | `system://65` | [system prompt] |
+| 1382 | `user://65` | [user packet (assembled context)] |
+| 1383 | `model://65` | [model usage record] |
+| 1384 | `reasoning://65` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1385 | `log://turn_65/get/app` | [get] app/ |
+| 1386 | `log://turn_65/set/app/data.csv` | [set] app/data.csv |
+| 1389 | `log://turn_65/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1392 | `log://turn_65/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1395 | `log://turn_65/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1397 | `sh://turn_65/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1398 | `sh://turn_65/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1401 | `log://turn_65/update/recreated_files_%2B_executing_model_fit_for_posterior_means` | [update status=177] recreated files + executing model fit for posterior means |
+| 1404 | `assistant://66` | [assistant emission — see turns/] |
+| 1405 | `system://66` | [system prompt] |
+| 1406 | `user://66` | [user packet (assembled context)] |
+| 1407 | `model://66` | [model usage record] |
+| 1408 | `reasoning://66` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). /ap… |
+| 1409 | `log://turn_66/get/app` | [get] app/ |
+| 1410 | `log://turn_66/set/app/data.csv` | [set] app/data.csv |
+| 1413 | `log://turn_66/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1416 | `log://turn_66/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1419 | `log://turn_66/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R` | [sh] cd /app && ls -la *.csv *.stan *.R && Rscript fit_model.R |
+| 1421 | `sh://turn_66/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1422 | `sh://turn_66/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1425 | `log://turn_66/update/recreated_files_%2B_running_hierarchical_model_fit_for_posterior_means` | [update status=177] recreated files + running hierarchical model fit for posterior means |
+| 1428 | `assistant://67` | [assistant emission — see turns/] |
+| 1429 | `system://67` | [system prompt] |
+| 1430 | `user://67` | [user packet (assembled context)] |
+| 1431 | `model://67` | [model usage record] |
+| 1432 | `reasoning://67` | [think] The core task is complete: RStan v2.32.7 is installed and loads successfully … |
+| 1433 | `log://turn_67/get/app` | [get] app/ |
+| 1434 | `log://turn_67/set/app/data.csv` | [set] app/data.csv |
+| 1437 | `log://turn_67/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1440 | `log://turn_67/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1443 | `log://turn_67/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R` | [sh] cd /app && ls -la *.csv *.stan *.R && Rscript fit_model.R |
+| 1445 | `sh://turn_67/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1446 | `sh://turn_67/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1449 | `log://turn_67/update/recreated_files_%2B_verify_%2B_execute_model_fit_for_posterior_means` | [update status=177] recreated files + verify + execute model fit for posterior means |
+| 1452 | `assistant://68` | [assistant emission — see turns/] |
+| 1453 | `system://68` | [system prompt] |
+| 1454 | `user://68` | [user packet (assembled context)] |
+| 1455 | `model://68` | [model usage record] |
+| 1456 | `reasoning://68` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1457 | `log://turn_68/get/app` | [get] app/ |
+| 1458 | `log://turn_68/sh/cd_/app_%26%26_ls_-la` | [sh] cd /app && ls -la |
+| 1460 | `sh://turn_68/cd_/app_%26%26_ls_-la_1` | [sh] |
+| 1461 | `sh://turn_68/cd_/app_%26%26_ls_-la_2` | [sh] |
+| 1464 | `log://turn_68/update/listing_/app_contents_%2B_diagnosing_file_persistence` | [update status=177] listing /app contents + diagnosing file persistence |
+| 1467 | `assistant://69` | [assistant emission — see turns/] |
+| 1468 | `system://69` | [system prompt] |
+| 1469 | `user://69` | [user packet (assembled context)] |
+| 1470 | `model://69` | [model usage record] |
+| 1471 | `reasoning://69` | [think] RStan v2.32.7 successfully installed and loads (env://turn_18). Model files c… |
+| 1472 | `log://turn_69/get/app` | [get] app/ |
+| 1473 | `log://turn_69/set/app/data.csv` | [set] app/data.csv |
+| 1476 | `log://turn_69/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1479 | `log://turn_69/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1482 | `log://turn_69/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1484 | `sh://turn_69/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1485 | `sh://turn_69/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1488 | `log://turn_69/update/recreated_files_%2B_running_hierarchical_model_fit_for_posterior_means` | [update status=177] recreated files + running hierarchical model fit for posterior means |
+| 1491 | `assistant://70` | [assistant emission — see turns/] |
+| 1492 | `system://70` | [system prompt] |
+| 1493 | `user://70` | [user packet (assembled context)] |
+| 1494 | `model://70` | [model usage record] |
+| 1495 | `reasoning://70` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1496 | `log://turn_70/get/app` | [get] app/ |
+| 1497 | `log://turn_70/set/app/data.csv` | [set] app/data.csv |
+| 1500 | `log://turn_70/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1503 | `log://turn_70/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1506 | `log://turn_70/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1508 | `sh://turn_70/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1509 | `sh://turn_70/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1512 | `log://turn_70/update/recreated_files_%2B_running_model_for_posterior_means` | [update status=177] recreated files + running model for posterior means |
+| 1515 | `assistant://71` | [assistant emission — see turns/] |
+| 1516 | `system://71` | [system prompt] |
+| 1517 | `user://71` | [user packet (assembled context)] |
+| 1518 | `model://71` | [model usage record] |
+| 1519 | `reasoning://71` | [think] RStan v2.32.7 successfully installed and loads (env://turn_18). Model files c… |
+| 1520 | `log://turn_71/get/app` | [get] app/ |
+| 1521 | `log://turn_71/set/app/data.csv` | [set] app/data.csv |
+| 1524 | `log://turn_71/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1527 | `log://turn_71/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1530 | `log://turn_71/sh/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R` | [sh] cd /app && ls -la *.csv *.stan *.R && Rscript fit_model.R |
+| 1532 | `sh://turn_71/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1533 | `sh://turn_71/cd_/app_%26%26_ls_-la_*.csv_*.stan_*.R_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1536 | `log://turn_71/update/recreated_files_%2B_running_hierarchical_model_fit_for_posterior_means` | [update status=177] recreated files + running hierarchical model fit for posterior means |
+| 1539 | `assistant://72` | [assistant emission — see turns/] |
+| 1540 | `system://72` | [system prompt] |
+| 1541 | `user://72` | [user packet (assembled context)] |
+| 1542 | `model://72` | [model usage record] |
+| 1543 | `reasoning://72` | [think] The agent has successfully installed rstan v2.32.7 (confirmed by env://turn_1… |
+| 1544 | `log://turn_72/get/app` | [get] app/ |
+| 1545 | `log://turn_72/set/app/data.csv` | [set] app/data.csv |
+| 1548 | `log://turn_72/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1551 | `log://turn_72/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1554 | `log://turn_72/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1556 | `sh://turn_72/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1557 | `sh://turn_72/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1560 | `log://turn_72/update/files_created_%2B_model_executed_for_posterior_means` | [update status=177] files created + model executed for posterior means |
+| 1563 | `assistant://73` | [assistant emission — see turns/] |
+| 1564 | `system://73` | [system prompt] |
+| 1565 | `user://73` | [user packet (assembled context)] |
+| 1566 | `model://73` | [model usage record] |
+| 1567 | `reasoning://73` | [think] The agent has successfully installed RStan v2.32.7 (confirmed by env://turn_1… |
+| 1568 | `log://turn_73/get/app` | [get] app/ |
+| 1569 | `log://turn_73/set/app/data.csv` | [set] app/data.csv |
+| 1572 | `log://turn_73/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1575 | `log://turn_73/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1578 | `log://turn_73/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1580 | `sh://turn_73/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1581 | `sh://turn_73/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1584 | `log://turn_73/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1587 | `assistant://74` | [assistant emission — see turns/] |
+| 1588 | `system://74` | [system prompt] |
+| 1589 | `user://74` | [user packet (assembled context)] |
+| 1590 | `model://74` | [model usage record] |
+| 1591 | `reasoning://74` | [think] The agent has successfully installed rstan v2.32.7 (confirmed by env://turn_1… |
+| 1592 | `log://turn_74/get/app` | [get] app/ |
+| 1593 | `log://turn_74/set/app/data.csv` | [set] app/data.csv |
+| 1596 | `log://turn_74/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1599 | `log://turn_74/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1602 | `log://turn_74/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1604 | `sh://turn_74/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1605 | `sh://turn_74/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1608 | `log://turn_74/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1611 | `assistant://75` | [assistant emission — see turns/] |
+| 1612 | `system://75` | [system prompt] |
+| 1613 | `user://75` | [user packet (assembled context)] |
+| 1614 | `model://75` | [model usage record] |
+| 1615 | `reasoning://75` | [think] The core task is complete: RStan v2.32.7 is installed and loads successfully … |
+| 1616 | `log://turn_75/get/app` | [get] app/ |
+| 1617 | `log://turn_75/set/app/data.csv` | [set] app/data.csv |
+| 1620 | `log://turn_75/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1623 | `log://turn_75/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1626 | `log://turn_75/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1628 | `sh://turn_75/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1629 | `sh://turn_75/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1632 | `log://turn_75/update/recreated_files_%2B_running_hierarchical_model_for_posterior_means` | [update status=177] recreated files + running hierarchical model for posterior means |
+| 1635 | `assistant://76` | [assistant emission — see turns/] |
+| 1636 | `system://76` | [system prompt] |
+| 1637 | `user://76` | [user packet (assembled context)] |
+| 1638 | `model://76` | [model usage record] |
+| 1639 | `reasoning://76` | [think] The core task is complete: RStan v2.32.7 installed and verified (env://turn_1… |
+| 1640 | `log://turn_76/get/app` | [get] app/ |
+| 1641 | `log://turn_76/set/app/data.csv` | [set] app/data.csv |
+| 1644 | `log://turn_76/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1647 | `log://turn_76/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1650 | `log://turn_76/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1652 | `sh://turn_76/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1653 | `sh://turn_76/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1656 | `log://turn_76/update/recreated_files_%2B_executing_model_fit_from_/app_for_posterior_means` | [update status=177] recreated files + executing model fit from /app for posterior means |
+| 1659 | `assistant://77` | [assistant emission — see turns/] |
+| 1660 | `system://77` | [system prompt] |
+| 1661 | `user://77` | [user packet (assembled context)] |
+| 1662 | `model://77` | [model usage record] |
+| 1663 | `reasoning://77` | [think] RStan v2.32.7 successfully installed and loads (env://turn_18). Files not per… |
+| 1664 | `log://turn_77/get/app` | [get] app/ |
+| 1665 | `log://turn_77/set/app/data.csv` | [set] app/data.csv |
+| 1668 | `log://turn_77/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1671 | `log://turn_77/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1674 | `log://turn_77/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1676 | `sh://turn_77/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1677 | `sh://turn_77/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1680 | `log://turn_77/update/recreated_files_%2B_executing_model_for_posterior_means_output` | [update status=177] recreated files + executing model for posterior means output |
+| 1683 | `assistant://78` | [assistant emission — see turns/] |
+| 1684 | `system://78` | [system prompt] |
+| 1685 | `user://78` | [user packet (assembled context)] |
+| 1686 | `model://78` | [model usage record] |
+| 1687 | `reasoning://78` | [think] * RStan v2.32.7 successfully installed and loads (confirmed env://turn_18) * … |
+| 1688 | `log://turn_78/get/app` | [get] app/ |
+| 1689 | `log://turn_78/set/app/data.csv` | [set] app/data.csv |
+| 1692 | `log://turn_78/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1695 | `log://turn_78/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1698 | `log://turn_78/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1700 | `sh://turn_78/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1701 | `sh://turn_78/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1704 | `log://turn_78/update/recreated_files_%2B_running_model_for_posterior_means_output` | [update status=177] recreated files + running model for posterior means output |
+| 1707 | `assistant://79` | [assistant emission — see turns/] |
+| 1708 | `system://79` | [system prompt] |
+| 1709 | `user://79` | [user packet (assembled context)] |
+| 1710 | `model://79` | [model usage record] |
+| 1711 | `reasoning://79` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1712 | `log://turn_79/get/app` | [get] app/ |
+| 1713 | `log://turn_79/set/app/data.csv` | [set] app/data.csv |
+| 1716 | `log://turn_79/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1719 | `log://turn_79/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1722 | `log://turn_79/sh/Rscript_/app/fit_model.R` | [sh] Rscript /app/fit_model.R |
+| 1724 | `sh://turn_79/Rscript_/app/fit_model.R_1` | [sh] |
+| 1725 | `sh://turn_79/Rscript_/app/fit_model.R_2` | [sh] |
+| 1728 | `log://turn_79/update/files_recreated_%2B_running_model_for_final_posterior_means` | [update status=177] files recreated + running model for final posterior means |
+| 1731 | `assistant://80` | [assistant emission — see turns/] |
+| 1732 | `system://80` | [system prompt] |
+| 1733 | `user://80` | [user packet (assembled context)] |
+| 1734 | `model://80` | [model usage record] |
+| 1735 | `reasoning://80` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1736 | `log://turn_80/get/app` | [get] app/ |
+| 1737 | `log://turn_80/set/app/data.csv` | [set] app/data.csv |
+| 1740 | `log://turn_80/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1743 | `log://turn_80/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1746 | `log://turn_80/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1748 | `sh://turn_80/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1749 | `sh://turn_80/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1752 | `log://turn_80/update/files_recreated_%2B_model_executed_for_posterior_means_output` | [update status=177] files recreated + model executed for posterior means output |
+| 1755 | `assistant://81` | [assistant emission — see turns/] |
+| 1756 | `system://81` | [system prompt] |
+| 1757 | `user://81` | [user packet (assembled context)] |
+| 1758 | `model://81` | [model usage record] |
+| 1759 | `reasoning://81` | [think] The agent has successfully installed rstan v2.32.7 (confirmed by env://turn_1… |
+| 1760 | `log://turn_81/get/app` | [get] app/ |
+| 1761 | `log://turn_81/set/app/data.csv` | [set] app/data.csv |
+| 1764 | `log://turn_81/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1767 | `log://turn_81/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1770 | `log://turn_81/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1772 | `sh://turn_81/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1773 | `sh://turn_81/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1776 | `log://turn_81/update/recreated_files_%2B_running_model_for_final_posterior_means_output` | [update status=177] recreated files + running model for final posterior means output |
+| 1779 | `assistant://82` | [assistant emission — see turns/] |
+| 1780 | `system://82` | [system prompt] |
+| 1781 | `user://82` | [user packet (assembled context)] |
+| 1782 | `model://82` | [model usage record] |
+| 1783 | `reasoning://82` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1784 | `log://turn_82/set/app/data.csv` | [set] app/data.csv |
+| 1787 | `log://turn_82/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1790 | `log://turn_82/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1793 | `log://turn_82/get/app` | [get] app/ |
+| 1794 | `log://turn_82/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1796 | `sh://turn_82/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1797 | `sh://turn_82/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1800 | `log://turn_82/update/files_created_%2B_model_executed_for_posterior_means_output` | [update status=177] files created + model executed for posterior means output |
+| 1803 | `assistant://83` | [assistant emission — see turns/] |
+| 1804 | `system://83` | [system prompt] |
+| 1805 | `user://83` | [user packet (assembled context)] |
+| 1806 | `model://83` | [model usage record] |
+| 1807 | `reasoning://83` | [think] The agent has successfully installed rstan v2.32.7 (confirmed by env://turn_1… |
+| 1808 | `log://turn_83/get/app` | [get] app/ |
+| 1809 | `log://turn_83/set/app/data.csv` | [set] app/data.csv |
+| 1812 | `log://turn_83/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1815 | `log://turn_83/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1818 | `log://turn_83/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1820 | `sh://turn_83/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1821 | `sh://turn_83/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1824 | `log://turn_83/update/recreated_files_%2B_executing_model_for_posterior_means_output` | [update status=177] recreated files + executing model for posterior means output |
+| 1827 | `assistant://84` | [assistant emission — see turns/] |
+| 1828 | `system://84` | [system prompt] |
+| 1829 | `user://84` | [user packet (assembled context)] |
+| 1830 | `model://84` | [model usage record] |
+| 1831 | `reasoning://84` | [think] The agent has successfully installed RStan v2.32.7 (confirmed by env://turn_1… |
+| 1832 | `log://turn_84/get/app` | [get] app/ |
+| 1833 | `log://turn_84/set/app/data.csv` | [set] app/data.csv |
+| 1836 | `log://turn_84/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1839 | `log://turn_84/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1842 | `log://turn_84/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1844 | `sh://turn_84/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1845 | `sh://turn_84/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1848 | `log://turn_84/update/recreated_files_%2B_executing_model_for_posterior_means_output` | [update status=177] recreated files + executing model for posterior means output |
+| 1851 | `assistant://85` | [assistant emission — see turns/] |
+| 1852 | `system://85` | [system prompt] |
+| 1853 | `user://85` | [user packet (assembled context)] |
+| 1854 | `model://85` | [model usage record] |
+| 1855 | `reasoning://85` | [think] + RStan v2.32.7 successfully installed and loads (env://turn_18) + data.csv e… |
+| 1856 | `log://turn_85/get/app` | [get] app/ |
+| 1857 | `log://turn_85/set/app/data.csv` | [set] app/data.csv |
+| 1860 | `log://turn_85/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1863 | `log://turn_85/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1866 | `log://turn_85/sh/cd_/app_%26%26_Rscript_fit_model.R` | [sh] cd /app && Rscript fit_model.R |
+| 1868 | `sh://turn_85/cd_/app_%26%26_Rscript_fit_model.R_1` | [sh] |
+| 1869 | `sh://turn_85/cd_/app_%26%26_Rscript_fit_model.R_2` | [sh] |
+| 1872 | `log://turn_85/update/files_created_%2B_executing_model_for_posterior_means` | [update status=177] files created + executing model for posterior means |
+| 1875 | `assistant://86` | [assistant emission — see turns/] |
+| 1876 | `system://86` | [system prompt] |
+| 1877 | `user://86` | [user packet (assembled context)] |
+| 1878 | `model://86` | [model usage record] |
+| 1879 | `reasoning://86` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1880 | `log://turn_86/get/app` | [get] app/ |
+| 1881 | `log://turn_86/set/app/data.csv` | [set] app/data.csv |
+| 1884 | `log://turn_86/set/app/hierarchical_model.stan` | [set] app/hierarchical_model.stan |
+| 1887 | `log://turn_86/set/app/fit_model.R` | [set] app/fit_model.R |
+| 1890 | `log://turn_86/sh/Rscript_/app/fit_model.R` | [sh] Rscript /app/fit_model.R |
+| 1892 | `sh://turn_86/Rscript_/app/fit_model.R_1` | [sh] |
+| 1893 | `sh://turn_86/Rscript_/app/fit_model.R_2` | [sh] |
+| 1896 | `log://turn_86/update/files_created_%2B_running_model_for_posterior_means_output` | [update status=177] files created + running model for posterior means output |
+| 1899 | `assistant://87` | [assistant emission — see turns/] |
+| 1900 | `system://87` | [system prompt] |
+| 1901 | `user://87` | [user packet (assembled context)] |
+| 1902 | `model://87` | [model usage record] |
+| 1903 | `reasoning://87` | [think] RStan v2.32.7 successfully installed and loads (confirmed env://turn_18). Fil… |
+| 1904 | `log://turn_87/get/app` | [get] app/ |
+| 1905 | `log://turn_87/set/data.csv` | [set] data.csv |
+| 1907 | `data.csv` | [(none)] |
+| 1908 | `log://turn_87/set/hierarchical_model.stan` | [set] hierarchical_model.stan |
+| 1910 | `hierarchical_model.stan` | [(none)] |
+| 1911 | `log://turn_87/set/fit_model.R` | [set] fit_model.R |
+| 1913 | `fit_model.R` | [(none)] |
+| 1914 | `log://turn_87/sh/Rscript_fit_model.R` | [sh] Rscript fit_model.R |
+| 1916 | `sh://turn_87/Rscript_fit_model.R_1` | [sh] |
+| 1917 | `sh://turn_87/Rscript_fit_model.R_2` | [sh] |
+| 1920 | `log://turn_87/update/files_in_root_%2B_running_model_fit_for_posterior_means` | [update status=177] files in root + running model fit for posterior means |
+| 1923 | `assistant://88` | [assistant emission — see turns/] |
+| 1924 | `system://88` | [system prompt] |
+| 1925 | `user://88` | [user packet (assembled context)] |
+| 1926 | `model://88` | [model usage record] |
+| 1927 | `reasoning://88` | [think] Success! The model ran successfully in turn 87 with Rscript fit_model.R, prod… |
+| 1928 | `log://turn_88/get/sh%3A/turn_87/Rscript_fit_model.R_1` | [get] sh://turn_87/Rscript_fit_model.R_1 |
+| 1929 | `log://turn_88/update/Hierarchical_model_fit_complete._Posterior_summary%3A_alpha_~%5B20.6/61.9%5D/_beta_~%5B5` | [update status=200] Hierarchical model fit complete. Posterior summary: alpha ~[20.6,61.9], beta … |