@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/adaptive-rejection-sampler/turns/turn_002.md

@@ -1,276 +0,0 @@
-# turn 002
-
-tokens: prompt=4354 cached=1749 completion=1028 reasoning=0 total=5382 cost=0
-created: 2026-05-01 23:41:42
-
-update: status=155 body=distilling ars design and structure
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage plan:
-1. All unknown://ars/* entries are already created from Decomposition (turn 1) - no new unknowns
-2. No external sources needed yet (no search/get for papers/code) - distill directly from unknowns/prompt into known://ars/*
-3. Create known://ars/main with full modular design, R code skeleton, file plan
-4. Create known://ars/implementation with detailed algorithm steps from unknown://ars/algorithm
-5. Create known://ars/test_suite with test details from unknown://ars/tests
-6. Reference prompt://1 and relevant unknowns in # Related sections
-7. Demote processed unknowns to summarized, keep known:// visible/summarized as needed
-8. Budget check: all small entries (<70 tokens), plenty free
-9. Continue Distillation for more detailed distillation (R code details next)
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage plan:
-1. All unknown://ars/* entries are already created from Decomposition (turn 1) - no new unknowns
-2. No external sources needed yet (no search/get for papers/code) - distill directly from unknowns/prompt into known://ars/*
-3. Create known://ars/main with full modular design, R code skeleton, file plan
-4. Create known://ars/implementation with detailed algorithm steps from unknown://ars/algorithm
-5. Create known://ars/test_suite with test details from unknown://ars/tests
-6. Reference prompt://1 and relevant unknowns in # Related sections
-7. Demote processed unknowns to summarized, keep known:// visible/summarized as needed
-8. Budget check: all small entries (<70 tokens), plenty free
-9. Continue Distillation for more detailed distillation (R code details next)
-</think>
-
-<get path="unknown://ars/*" manifest/>
-
-<set path="known://ars/main" visibility="visible" summary="ars.R,main,file,structure,modular,functions">
-# Related
-[prompt requirements](prompt://1)
-[ars algorithm](unknown://ars/algorithm)
-[ars files](unknown://ars/files)
-[ars modularity](unknown://ars/modularity)
-[ars inputs](unknown://ars/inputs)
-[ars tests](unknown://ars/tests)
-
-# /app/ars.R Main File Structure
-
-ʼ``r
-#!/usr/bin/env Rscript
-
-# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
-# Modular implementation with input validation and log-concavity checks
-
-# === MAIN FUNCTIONS ===
-ars <- function(density, n_samples = 1000, ...) {
-  # Primary interface: vectorized unnormalized log-density -> samples
-  # Inputs: density (function), n_samples (>0), optional domain
-  # Validates inputs, builds envelope, samples with adaptation
-}
-
-test <- function() {
-  # Formal testing suite: normal, exponential vs rnorm/rexp
-  # Stochastic tests: mean/sd/KS, PASS/FAIL output
-  # Generates /app/normal_samples.txt, /app/exponential_samples.txt
-}
-
-# === MODULAR AUXILIARIES ===
-envelope_build <- function(density, x_nodes, y_nodes) { ... }
-sample_proposal <- function(x_nodes, y_nodes, u) { ... }
-reject_accept <- function(x_prop, density, envelope) { ... }
-adapt_envelope <- function(x_nodes, y_nodes, rejects) { ... }
-logconcavity_check <- function(density, x_test) { ... }
-
-# === UTILITIES ===
-validate_inputs <- function(density, n_samples) { ... }
-
-# Run tests if called directly
-if (!interactive() && sys.nframe() == 0) test()
-ʼ``
-</set>
-
-<set path="known://ars/implementation" visibility="summarized" summary="algorithm,steps,gilks1992,envelope,rejection,adaptation">
-# Related
-[ars algorithm](unknown://ars/algorithm)
-[ars logconcavity](unknown://ars/logconcavity)
-
-# ARS Algorithm (Gilks 1992)
-
-1. **Initialize**: Pick 2-3 nodes in domain, evaluate log-density + derivatives
-2. **Build piecewise linear envelope** over nodes (tangent upper bounds)
-3. **Proposal**: Sample from exponential mixture (piecewise)
-4. **Reject/Accept**: u ~ Unif(0,1), accept if u * envelope(x) < density(x)
-5. **Adapt**: Add reject/accept points as new nodes, rebuild envelope
-6. **Log-concavity check**: Monitor derivative signs, reject if violated
-
-Core loop until n_samples collected.
-</set>
-
-<set path="known://ars/test_suite" visibility="summarized" summary="tests,normal,exponential,ks,test,statistics">
-# Related
-[ars tests](unknown://ars/tests)
-[prompt](prompt://1)
-
-# test() Suite
-
-- **Normal**: ars(dnorm, 10000) vs rnorm() → mean≈0, sd≈1, KS p>0.01
-- **Exponential**: ars(dexp, 10000) vs rexp() → mean≈1, KS p>0.01
-- Output: "NORMAL_TEST: PASS (mean=0.02, sd=0.99, KS=0.03)" or FAIL
-- Save samples: writeLines(as.character(samples), "/app/normal_samples.txt")
-</set>
-
-<set path="unknown://ars/algorithm" visibility="summarized"/>
-<set path="unknown://ars/files" visibility="summarized"/>
-<set path="unknown://ars/inputs" visibility="summarized"/>
-<set path="unknown://ars/logconcavity" visibility="summarized"/>
-<set path="unknown://ars/modularity" visibility="summarized"/>
-<set path="unknown://ars/tests" visibility="summarized"/>
-
-<update status="155">distilling ars design and structure</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_2/get/unknown%3A/ars/*`
-scheme=log action=get attrs={"path":"unknown://ars/*","action":"get"}
-
-```
-MANIFEST get path="unknown://ars/*": 7 matched (287 tokens)
-unknown://ars/algorithm (70)
-unknown://ars/files (27)
-unknown://ars/inputs (36)
-unknown://ars/logconcavity (50)
-unknown://ars/modularity (42)
-unknown://ars/r_environment (27)
-unknown://ars/tests (35)
-```
-
-### `log://turn_2/set/known%3A/ars/main`
-scheme=log action=set attrs={"path":"known://ars/main","patch":"===================================================================\n--- known://ars/main\told\t\n+++ known://ars/main\tnew\t\n@@ -0,0 +1,42 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[ars algorithm](unknown://ars/algorithm)\n+[ars files](unknown://ars/files)\n+[ars modularity](unknown://ars/modularity)\n+[ars inputs](unknown://ars/inputs)\n+[ars tests](unknown://ars/tests)\n+\n+# /app/ars.R Main File Structure\n+\n+```r\n+#!/usr/bin/env Rscript\n+\n+# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)\n+# Modular implementation with input validation and log-concavity checks\n+\n+# === MAIN FUNCTIONS ===\n+ars <- function(density, n_samples = 1000, ...) {\n+  # Primary interface: vectorized unnormalized log-density -> samples\n+  # Inputs: density (function), n_samples (>0), optional domain\n+  # Validates inputs, builds envelope, samples with adaptation\n+}\n+\n+test <- function() {\n+  # Formal testing suite: normal, exponential vs rnorm/rexp\n+  # Stochastic tests: mean/sd/KS, PASS/FAIL output\n+  # Generates /app/normal_samples.txt, /app/exponential_samples.txt\n+}\n+\n+# === MODULAR AUXILIARIES ===\n+envelope_build <- function(density, x_nodes, y_nodes) { ... }\n+sample_proposal <- function(x_nodes, y_nodes, u) { ... }\n+reject_accept <- function(x_prop, density, envelope) { ... }\n+adapt_envelope <- function(x_nodes, y_nodes, rejects) { ... }\n+logconcavity_check <- function(density, x_test) { ... }\n+\n+# === UTILITIES ===\n+validate_inputs <- function(density, n_samples) { ... }\n+\n+# Run tests if called directly\n+if (!interactive() && sys.nframe() == 0) test()\n+```\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[ars algorithm](unknown://ars/algorithm)\n[ars files](unknown://ars/files)\n[ars modularity](unknown://ars/modularity)\n[ars inputs](unknown://ars/inputs)\n[ars tests](unknown://ars/tests)\n\n# /app/ars.R Main File Structure\n\n```r\n#!/usr/bin/env Rscript\n\n# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)\n# Modular implementation with input validation and log-concavity checks\n\n# === MAIN FUNCTIONS ===\nars <- function(density, n_samples = 1000, ...) {\n  # Primary interface: vectorized unnormalized log-density -> samples\n  # Inputs: density (function), n_samples (>0), optional domain\n  # Validates inputs, builds envelope, samples with adaptation\n}\n\ntest <- function() {\n  # Formal testing suite: normal, exponential vs rnorm/rexp\n  # Stochastic tests: mean/sd/KS, PASS/FAIL output\n  # Generates /app/normal_samples.txt, /app/exponential_samples.txt\n}\n\n# === MODULAR AUXILIARIES ===\nenvelope_build <- function(density, x_nodes, y_nodes) { ... }\nsample_proposal <- function(x_nodes, y_nodes, u) { ... }\nreject_accept <- function(x_prop, density, envelope) { ... }\nadapt_envelope <- function(x_nodes, y_nodes, rejects) { ... }\nlogconcavity_check <- function(density, x_test) { ... }\n\n# === UTILITIES ===\nvalidate_inputs <- function(density, n_samples) { ... }\n\n# Run tests if called directly\nif (!interactive() && sys.nframe() == 0) test()\n```\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":695,"summary":"ars.R,main,file,structure,modular,functions","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[ars algorithm](unknown://ars/algorithm)
-[ars files](unknown://ars/files)
-[ars modularity](unknown://ars/modularity)
-[ars inputs](unknown://ars/inputs)
-[ars tests](unknown://ars/tests)
-
-# /app/ars.R Main File Structure
-
-ʼ``r
-#!/usr/bin/env Rscript
-
-# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
-# Modular implementation with input validation and log-concavity checks
-
-# === MAIN FUNCTIONS ===
-ars <- function(density, n_samples = 1000, ...) {
-  # Primary interface: vectorized unnormalized log-density -> samples
-  # Inputs: density (function), n_samples (>0), optional domain
-  # Validates inputs, builds envelope, samples with adaptation
-}
-
-test <- function() {
-  # Formal testing suite: normal, exponential vs rnorm/rexp
-  # Stochastic tests: mean/sd/KS, PASS/FAIL output
-  # Generates /app/normal_samples.txt, /app/exponential_samples.txt
-}
-
-# === MODULAR AUXILIARIES ===
-envelope_build <- function(density, x_nodes, y_nodes) { ... }
-sample_proposal <- function(x_nodes, y_nodes, u) { ... }
-reject_accept <- function(x_prop, density, envelope) { ... }
-adapt_envelope <- function(x_nodes, y_nodes, rejects) { ... }
-logconcavity_check <- function(density, x_test) { ... }
-
-# === UTILITIES ===
-validate_inputs <- function(density, n_samples) { ... }
-
-# Run tests if called directly
-if (!interactive() && sys.nframe() == 0) test()
-ʼ``
-```
-
-### `log://turn_2/set/known%3A/ars/implementation`
-scheme=log action=set attrs={"path":"known://ars/implementation","patch":"===================================================================\n--- known://ars/implementation\told\t\n+++ known://ars/implementation\tnew\t\n@@ -0,0 +1,14 @@\n+# Related\n+[ars algorithm](unknown://ars/algorithm)\n+[ars logconcavity](unknown://ars/logconcavity)\n+\n+# ARS Algorithm (Gilks 1992)\n+\n+1. **Initialize**: Pick 2-3 nodes in domain, evaluate log-density + derivatives\n+2. **Build piecewise linear envelope** over nodes (tangent upper bounds)\n+3. **Proposal**: Sample from exponential mixture (piecewise)\n+4. **Reject/Accept**: u ~ Unif(0,1), accept if u * envelope(x) < density(x)\n+5. **Adapt**: Add reject/accept points as new nodes, rebuild envelope\n+6. **Log-concavity check**: Monitor derivative signs, reject if violated\n+\n+Core loop until n_samples collected.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[ars algorithm](unknown://ars/algorithm)\n[ars logconcavity](unknown://ars/logconcavity)\n\n# ARS Algorithm (Gilks 1992)\n\n1. **Initialize**: Pick 2-3 nodes in domain, evaluate log-density + derivatives\n2. **Build piecewise linear envelope** over nodes (tangent upper bounds)\n3. **Proposal**: Sample from exponential mixture (piecewise)\n4. **Reject/Accept**: u ~ Unif(0,1), accept if u * envelope(x) < density(x)\n5. **Adapt**: Add reject/accept points as new nodes, rebuild envelope\n6. **Log-concavity check**: Monitor derivative signs, reject if violated\n\nCore loop until n_samples collected.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":300,"summary":"algorithm,steps,gilks1992,envelope,rejection,adaptation","action":"set"}
-
-```
-# Related
-[ars algorithm](unknown://ars/algorithm)
-[ars logconcavity](unknown://ars/logconcavity)
-
-# ARS Algorithm (Gilks 1992)
-
-1. **Initialize**: Pick 2-3 nodes in domain, evaluate log-density + derivatives
-2. **Build piecewise linear envelope** over nodes (tangent upper bounds)
-3. **Proposal**: Sample from exponential mixture (piecewise)
-4. **Reject/Accept**: u ~ Unif(0,1), accept if u * envelope(x) < density(x)
-5. **Adapt**: Add reject/accept points as new nodes, rebuild envelope
-6. **Log-concavity check**: Monitor derivative signs, reject if violated
-
-Core loop until n_samples collected.
-```
-
-### `log://turn_2/set/known%3A/ars/test_suite`
-scheme=log action=set attrs={"path":"known://ars/test_suite","patch":"===================================================================\n--- known://ars/test_suite\told\t\n+++ known://ars/test_suite\tnew\t\n@@ -0,0 +1,10 @@\n+# Related\n+[ars tests](unknown://ars/tests)\n+[prompt](prompt://1)\n+\n+# test() Suite\n+\n+- **Normal**: ars(dnorm, 10000) vs rnorm() → mean≈0, sd≈1, KS p>0.01\n+- **Exponential**: ars(dexp, 10000) vs rexp() → mean≈1, KS p>0.01\n+- Output: \"NORMAL_TEST: PASS (mean=0.02, sd=0.99, KS=0.03)\" or FAIL\n+- Save samples: writeLines(as.character(samples), \"/app/normal_samples.txt\")\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[ars tests](unknown://ars/tests)\n[prompt](prompt://1)\n\n# test() Suite\n\n- **Normal**: ars(dnorm, 10000) vs rnorm() → mean≈0, sd≈1, KS p>0.01\n- **Exponential**: ars(dexp, 10000) vs rexp() → mean≈1, KS p>0.01\n- Output: \"NORMAL_TEST: PASS (mean=0.02, sd=0.99, KS=0.03)\" or FAIL\n- Save samples: writeLines(as.character(samples), \"/app/normal_samples.txt\")\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":180,"summary":"tests,normal,exponential,ks,test,statistics","action":"set"}
-
-```
-# Related
-[ars tests](unknown://ars/tests)
-[prompt](prompt://1)
-
-# test() Suite
-
-- **Normal**: ars(dnorm, 10000) vs rnorm() → mean≈0, sd≈1, KS p>0.01
-- **Exponential**: ars(dexp, 10000) vs rexp() → mean≈1, KS p>0.01
-- Output: "NORMAL_TEST: PASS (mean=0.02, sd=0.99, KS=0.03)" or FAIL
-- Save samples: writeLines(as.character(samples), "/app/normal_samples.txt")
-```
-
-### `log://turn_2/set/unknown%3A/ars/algorithm`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/algorithm set to summarized
-```
-
-### `log://turn_2/set/unknown%3A/ars/files`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/files set to summarized
-```
-
-### `log://turn_2/set/unknown%3A/ars/inputs`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/inputs set to summarized
-```
-
-### `log://turn_2/set/unknown%3A/ars/logconcavity`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/logconcavity set to summarized
-```
-
-### `log://turn_2/set/unknown%3A/ars/modularity`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/modularity set to summarized
-```
-
-### `log://turn_2/set/unknown%3A/ars/tests`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/tests set to summarized
-```
-
-### `log://turn_2/update/distilling_ars_design_and_structure`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling ars design and structure
-```
-

package/audit/sweep/adaptive-rejection-sampler/turns/turn_003.md

@@ -1,304 +0,0 @@
-# turn 003
-
-tokens: prompt=6316 cached=1745 completion=989 reasoning=0 total=7305 cost=0
-created: 2026-05-01 23:41:58
-
-update: status=155 body=distilling ars inputs, modularity, r_env
-
----
-
-## reasoning (think)
-
-```
-* In Distillation Stage: resolve remaining unknown://ars/* entries by distilling into known://
-* 7 unknowns left, all ars-related; distill into targeted known:// entries
-* Budget: 1.7M+ free, current knowns cheap (known://ars/main 423t is visible)
-* Plan: 
-  1. Promote all unknown://ars/* (141t total, summarized already)
-  2. Distill 3-4 new known:// entries: r_env, inputs, modularity, logconcavity, tests
-  3. Demote originals to summarized
-  4. Continue distillation (more to resolve)
-* No file writing yet (Deployment stage); focus on design knowledge
-```
-
-## assistant emission
-
-```
-<think>
-* In Distillation Stage: resolve remaining unknown://ars/* entries by distilling into known://
-* 7 unknowns left, all ars-related; distill into targeted known:// entries
-* Budget: 1.7M+ free, current knowns cheap (known://ars/main 423t is visible)
-* Plan: 
-  1. Promote all unknown://ars/* (141t total, summarized already)
-  2. Distill 3-4 new known:// entries: r_env, inputs, modularity, logconcavity, tests
-  3. Demote originals to summarized
-  4. Continue distillation (more to resolve)
-* No file writing yet (Deployment stage); focus on design knowledge
-</think>
-
-<get path="unknown://ars/*"/>
-
-<set path="known://ars/r_environment" summary="r,install,environment,runtime,check,shell" visibility="visible">
-# Related
-[prompt requirements](prompt://1)
-[ars r_environment](unknown://ars/r_environment)
-
-# R Runtime Environment Setup
-
-ʼ``r
-# Check R installation
-if (!("base" %in% search())) {
-  stop("R not available - install R first")
-}
-
-# Install packages if needed
-required_packages <- c("stats")  # base R has most needed
-for(pkg in required_packages) {
-  if (!requireNamespace(pkg, quietly = TRUE)) {
-    install.packages(pkg)
-    library(pkg, character.only = TRUE)
-  }
-}
-ʼ``
-</set>
-
-<set path="known://ars/inputs_validation" summary="inputs,validation,density,unnormalized,vectorized,sample_size,domain" visibility="visible">
-# Related
-[prompt requirements](prompt://1)
-[ars inputs](unknown://ars/inputs)
-
-# Input Validation for ars()
-
-ʼ``r
-validate_inputs <- function(density, n_samples, domain = NULL) {
-  # Check n_samples
-  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
-    stop("n_samples must be positive numeric scalar")
-  }
-  
-  # Check density function
-  if (!is.function(density)) {
-    stop("density must be a function")
-  }
-  
-  # Test vectorized: must handle vector input
-  test_x <- seq(-10, 10, length.out = 5)
-  tryCatch({
-    log_density_vals <- density(test_x)
-    if (length(log_density_vals) != length(test_x)) {
-      stop("density must be vectorized (accept vector input)")
-    }
-    if (any(!is.finite(log_density_vals))) {
-      warning("Some non-finite density values detected")
-    }
-  }, error = function(e) stop("density function failed: ", e$message))
-  
-  # Domain checks (optional)
-  if (!is.null(domain)) {
-    if (length(domain) != 2 || domain[1] >= domain[2]) {
-      stop("domain must be valid interval [lower, upper]")
-    }
-  }
-  
-  return(TRUE)
-}
-ʼ``
-</set>
-
-<set path="known://ars/modularity" summary="modularity,auxiliary,functions,envelope,sampling,rejection,adaptation" visibility="visible">
-# Related
-[prompt requirements](prompt://1)
-[ars modularity](unknown://ars/modularity)
-[ars algorithm](unknown://ars/algorithm)
-[known ars implementation](known://ars/implementation)
-
-# Modular Auxiliary Functions
-
-ʼ``r
-# 1. Build piecewise linear envelope (tangent lines)
-envelope_build <- function(density, x_nodes, y_nodes, slopes = NULL) {
-  # Construct upper bounding envelope using log-density tangents
-  # Returns: envelope function, piecewise exponentials
-}
-
-# 2. Sample from piecewise exponential proposal
-sample_proposal <- function(x_nodes, y_nodes, slopes, n_prop) {
-  # Sample from mixture of exponentials defined by envelope pieces
-}
-
-# 3. Rejection/acceptance step
-reject_accept <- function(x_prop, density, envelope_func) {
-  # u ~ Unif(0,1); accept if u * envelope(x) <= density(x)
-  # Returns accepted samples + reject points for adaptation
-}
-
-# 4. Adapt envelope with new nodes
-adapt_envelope <- function(x_nodes, y_nodes, slopes, new_points) {
-  # Insert reject/accept points, rebuild envelope
-  # Maintain sorted nodes
-}
-ʼ``
-</set>
-
-<set path="unknown://ars/r_environment" visibility="summarized"/>
-<set path="unknown://ars/inputs" visibility="summarized"/>
-<set path="unknown://ars/modularity" visibility="summarized"/>
-
-<update status="155">distilling ars inputs, modularity, r_env</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_3/get/unknown%3A/ars/*`
-scheme=log action=get attrs={"path":"unknown://ars/*","action":"get"}
-
-```
-get path="unknown://ars/*": 7 matched (287 tokens)
-unknown://ars/algorithm (70)
-unknown://ars/files (27)
-unknown://ars/inputs (36)
-unknown://ars/logconcavity (50)
-unknown://ars/modularity (42)
-unknown://ars/r_environment (27)
-unknown://ars/tests (35)
-```
-
-### `log://turn_3/set/known%3A/ars/r_environment`
-scheme=log action=set attrs={"path":"known://ars/r_environment","patch":"===================================================================\n--- known://ars/r_environment\told\t\n+++ known://ars/r_environment\tnew\t\n@@ -0,0 +1,21 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[ars r_environment](unknown://ars/r_environment)\n+\n+# R Runtime Environment Setup\n+\n+```r\n+# Check R installation\n+if (!(\"base\" %in% search())) {\n+  stop(\"R not available - install R first\")\n+}\n+\n+# Install packages if needed\n+required_packages <- c(\"stats\")  # base R has most needed\n+for(pkg in required_packages) {\n+  if (!requireNamespace(pkg, quietly = TRUE)) {\n+    install.packages(pkg)\n+    library(pkg, character.only = TRUE)\n+  }\n+}\n+```\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[ars r_environment](unknown://ars/r_environment)\n\n# R Runtime Environment Setup\n\n```r\n# Check R installation\nif (!(\"base\" %in% search())) {\n  stop(\"R not available - install R first\")\n}\n\n# Install packages if needed\nrequired_packages <- c(\"stats\")  # base R has most needed\nfor(pkg in required_packages) {\n  if (!requireNamespace(pkg, quietly = TRUE)) {\n    install.packages(pkg)\n    library(pkg, character.only = TRUE)\n  }\n}\n```\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":237,"summary":"r,install,environment,runtime,check,shell","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[ars r_environment](unknown://ars/r_environment)
-
-# R Runtime Environment Setup
-
-ʼ``r
-# Check R installation
-if (!("base" %in% search())) {
-  stop("R not available - install R first")
-}
-
-# Install packages if needed
-required_packages <- c("stats")  # base R has most needed
-for(pkg in required_packages) {
-  if (!requireNamespace(pkg, quietly = TRUE)) {
-    install.packages(pkg)
-    library(pkg, character.only = TRUE)
-  }
-}
-ʼ``
-```
-
-### `log://turn_3/set/known%3A/ars/inputs_validation`
-scheme=log action=set attrs={"path":"known://ars/inputs_validation","patch":"===================================================================\n--- known://ars/inputs_validation\told\t\n+++ known://ars/inputs_validation\tnew\t\n@@ -0,0 +1,40 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[ars inputs](unknown://ars/inputs)\n+\n+# Input Validation for ars()\n+\n+```r\n+validate_inputs <- function(density, n_samples, domain = NULL) {\n+  # Check n_samples\n+  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n+    stop(\"n_samples must be positive numeric scalar\")\n+  }\n+  \n+  # Check density function\n+  if (!is.function(density)) {\n+    stop(\"density must be a function\")\n+  }\n+  \n+  # Test vectorized: must handle vector input\n+  test_x <- seq(-10, 10, length.out = 5)\n+  tryCatch({\n+    log_density_vals <- density(test_x)\n+    if (length(log_density_vals) != length(test_x)) {\n+      stop(\"density must be vectorized (accept vector input)\")\n+    }\n+    if (any(!is.finite(log_density_vals))) {\n+      warning(\"Some non-finite density values detected\")\n+    }\n+  }, error = function(e) stop(\"density function failed: \", e$message))\n+  \n+  # Domain checks (optional)\n+  if (!is.null(domain)) {\n+    if (length(domain) != 2 || domain[1] >= domain[2]) {\n+      stop(\"domain must be valid interval [lower, upper]\")\n+    }\n+  }\n+  \n+  return(TRUE)\n+}\n+```\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[ars inputs](unknown://ars/inputs)\n\n# Input Validation for ars()\n\n```r\nvalidate_inputs <- function(density, n_samples, domain = NULL) {\n  # Check n_samples\n  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n    stop(\"n_samples must be positive numeric scalar\")\n  }\n  \n  # Check density function\n  if (!is.function(density)) {\n    stop(\"density must be a function\")\n  }\n  \n  # Test vectorized: must handle vector input\n  test_x <- seq(-10, 10, length.out = 5)\n  tryCatch({\n    log_density_vals <- density(test_x)\n    if (length(log_density_vals) != length(test_x)) {\n      stop(\"density must be vectorized (accept vector input)\")\n    }\n    if (any(!is.finite(log_density_vals))) {\n      warning(\"Some non-finite density values detected\")\n    }\n  }, error = function(e) stop(\"density function failed: \", e$message))\n  \n  # Domain checks (optional)\n  if (!is.null(domain)) {\n    if (length(domain) != 2 || domain[1] >= domain[2]) {\n      stop(\"domain must be valid interval [lower, upper]\")\n    }\n  }\n  \n  return(TRUE)\n}\n```\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":545,"summary":"inputs,validation,density,unnormalized,vectorized,sample_size,domain","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[ars inputs](unknown://ars/inputs)
-
-# Input Validation for ars()
-
-ʼ``r
-validate_inputs <- function(density, n_samples, domain = NULL) {
-  # Check n_samples
-  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
-    stop("n_samples must be positive numeric scalar")
-  }
-  
-  # Check density function
-  if (!is.function(density)) {
-    stop("density must be a function")
-  }
-  
-  # Test vectorized: must handle vector input
-  test_x <- seq(-10, 10, length.out = 5)
-  tryCatch({
-    log_density_vals <- density(test_x)
-    if (length(log_density_vals) != length(test_x)) {
-      stop("density must be vectorized (accept vector input)")
-    }
-    if (any(!is.finite(log_density_vals))) {
-      warning("Some non-finite density values detected")
-    }
-  }, error = function(e) stop("density function failed: ", e$message))
-  
-  # Domain checks (optional)
-  if (!is.null(domain)) {
-    if (length(domain) != 2 || domain[1] >= domain[2]) {
-      stop("domain must be valid interval [lower, upper]")
-    }
-  }
-  
-  return(TRUE)
-}
-ʼ``
-```
-
-### `log://turn_3/set/known%3A/ars/modularity`
-scheme=log action=set attrs={"path":"known://ars/modularity","patch":"===================================================================\n--- known://ars/modularity\told\t\n+++ known://ars/modularity\tnew\t\n@@ -0,0 +1,32 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[ars modularity](unknown://ars/modularity)\n+[ars algorithm](unknown://ars/algorithm)\n+[known ars implementation](known://ars/implementation)\n+\n+# Modular Auxiliary Functions\n+\n+```r\n+# 1. Build piecewise linear envelope (tangent lines)\n+envelope_build <- function(density, x_nodes, y_nodes, slopes = NULL) {\n+  # Construct upper bounding envelope using log-density tangents\n+  # Returns: envelope function, piecewise exponentials\n+}\n+\n+# 2. Sample from piecewise exponential proposal\n+sample_proposal <- function(x_nodes, y_nodes, slopes, n_prop) {\n+  # Sample from mixture of exponentials defined by envelope pieces\n+}\n+\n+# 3. Rejection/acceptance step\n+reject_accept <- function(x_prop, density, envelope_func) {\n+  # u ~ Unif(0,1); accept if u * envelope(x) <= density(x)\n+  # Returns accepted samples + reject points for adaptation\n+}\n+\n+# 4. Adapt envelope with new nodes\n+adapt_envelope <- function(x_nodes, y_nodes, slopes, new_points) {\n+  # Insert reject/accept points, rebuild envelope\n+  # Maintain sorted nodes\n+}\n+```\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[ars modularity](unknown://ars/modularity)\n[ars algorithm](unknown://ars/algorithm)\n[known ars implementation](known://ars/implementation)\n\n# Modular Auxiliary Functions\n\n```r\n# 1. Build piecewise linear envelope (tangent lines)\nenvelope_build <- function(density, x_nodes, y_nodes, slopes = NULL) {\n  # Construct upper bounding envelope using log-density tangents\n  # Returns: envelope function, piecewise exponentials\n}\n\n# 2. Sample from piecewise exponential proposal\nsample_proposal <- function(x_nodes, y_nodes, slopes, n_prop) {\n  # Sample from mixture of exponentials defined by envelope pieces\n}\n\n# 3. Rejection/acceptance step\nreject_accept <- function(x_prop, density, envelope_func) {\n  # u ~ Unif(0,1); accept if u * envelope(x) <= density(x)\n  # Returns accepted samples + reject points for adaptation\n}\n\n# 4. Adapt envelope with new nodes\nadapt_envelope <- function(x_nodes, y_nodes, slopes, new_points) {\n  # Insert reject/accept points, rebuild envelope\n  # Maintain sorted nodes\n}\n```\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":523,"summary":"modularity,auxiliary,functions,envelope,sampling,rejection,adaptation","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[ars modularity](unknown://ars/modularity)
-[ars algorithm](unknown://ars/algorithm)
-[known ars implementation](known://ars/implementation)
-
-# Modular Auxiliary Functions
-
-ʼ``r
-# 1. Build piecewise linear envelope (tangent lines)
-envelope_build <- function(density, x_nodes, y_nodes, slopes = NULL) {
-  # Construct upper bounding envelope using log-density tangents
-  # Returns: envelope function, piecewise exponentials
-}
-
-# 2. Sample from piecewise exponential proposal
-sample_proposal <- function(x_nodes, y_nodes, slopes, n_prop) {
-  # Sample from mixture of exponentials defined by envelope pieces
-}
-
-# 3. Rejection/acceptance step
-reject_accept <- function(x_prop, density, envelope_func) {
-  # u ~ Unif(0,1); accept if u * envelope(x) <= density(x)
-  # Returns accepted samples + reject points for adaptation
-}
-
-# 4. Adapt envelope with new nodes
-adapt_envelope <- function(x_nodes, y_nodes, slopes, new_points) {
-  # Insert reject/accept points, rebuild envelope
-  # Maintain sorted nodes
-}
-ʼ``
-```
-
-### `log://turn_3/set/unknown%3A/ars/r_environment`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/r_environment set to summarized
-```
-
-### `log://turn_3/set/unknown%3A/ars/inputs`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/inputs set to summarized
-```
-
-### `log://turn_3/set/unknown%3A/ars/modularity`
-scheme=log action=set attrs={}
-
-```
-unknown://ars/modularity set to summarized
-```
-
-### `log://turn_3/update/distilling_ars_inputs/_modularity/_r_env`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling ars inputs, modularity, r_env
-```
-