@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/adaptive-rejection-sampler/turns/turn_007.md

@@ -1,497 +0,0 @@
-# turn 007
-
-tokens: prompt=6324 cached=3723 completion=2181 reasoning=0 total=8505 cost=0
-created: 2026-05-01 23:42:32
-
-update: status=177 body=ars.R created; running tests; checking sample files
-
----
-
-## reasoning (think)
-
-```
-All unknowns resolved and distilled. In Deployment Stage. Need to:
-1. Create complete /app/ars.R with all modular functions, validation, log-concavity checks, test()
-2. Test execution with <sh> Rscript /app/ars.R test
-3. Confirm sample files generated and tests pass
-4. Status 177 -> 200
-```
-
-## assistant emission
-
-```
-<think>
-All unknowns resolved and distilled. In Deployment Stage. Need to:
-1. Create complete /app/ars.R with all modular functions, validation, log-concavity checks, test()
-2. Test execution with <sh> Rscript /app/ars.R test
-3. Confirm sample files generated and tests pass
-4. Status 177 -> 200
-</think>
-
-<set path="/app/ars.R">
-#!/usr/bin/env Rscript
-
-# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
-# Modular implementation with input validation and log-concavity checks
-
-# === ENVIRONMENT SETUP ===
-if (!("base" %in% search())) {
-  stop("R not available - install R first")
-}
-required_packages <- c("stats")
-for(pkg in required_packages) {
-  if (!requireNamespace(pkg, quietly = TRUE)) {
-    install.packages(pkg, repos = "https://cran.rstudio.com/")
-    library(pkg, character.only = TRUE)
-  }
-}
-
-# === MODULAR AUXILIARY FUNCTIONS ===
-
-# 1. Input validation
-validate_inputs <- function(density, n_samples, domain = NULL) {
-  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
-    stop("n_samples must be positive numeric scalar")
-  }
-  if (!is.function(density)) {
-    stop("density must be a function")
-  }
-  # Test vectorized
-  test_x <- seq(-1, 1, length.out = 5)
-  test_y <- density(test_x)
-  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {
-    stop("density must be vectorized and return finite values")
-  }
-  if (!is.null(domain)) {
-    if (length(domain) != 2 || domain[1] >= domain[2]) {
-      stop("domain must be valid interval [low, high]")
-    }
-  }
-}
-
-# 2. Log-concavity check (numerical 2nd derivative)
-logconcavity_check <- function(density, x_test, tol = 1e-6) {
-  h <- 1e-5
-  f0 <- density(x_test)
-  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)
-  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h
-  if (any(f2 > tol, na.rm = TRUE)) {
-    warning("Possible log-concavity violation detected")
-    return(FALSE)
-  }
-  return(TRUE)
-}
-
-# 3. Build piecewise linear envelope (tangent lines in log-space)
-envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {
-  n_nodes <- length(x_nodes)
-  slopes <- y_deriv_nodes
-  envelope_func <- function(x) {
-    # Find relevant piecewise segment for each x
-    result <- numeric(length(x))
-    for (i in seq_along(x)) {
-      xi <- x[i]
-      # Find segment j where x_nodes[j] <= xi < x_nodes[j+1]
-      j <- which(xi >= x_nodes & xi < c(x_nodes[-1], Inf))[1]
-      if (is.na(j)) j <- n_nodes
-      if (j == 1) {
-        result[i] <- y_nodes[1] + slopes[1] * (xi - x_nodes[1])
-      } else {
-        # Piecewise exponential: exp(y_j + s_j*(x-x_j))
-        result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])
-      }
-    }
-    exp(result)
-  }
-  return(envelope_func)
-}
-
-# 4. Sample from piecewise exponential envelope
-sample_proposal <- function(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain) {
-  # Simple uniform selection of segment then exponential sample
-  n_segments <- length(x_nodes) - 1
-  seg_idx <- sample(1:n_segments, 1)
-  x_left <- x_nodes[seg_idx]
-  slope <- y_deriv_nodes[seg_idx]
-  rate <- -slope
-  if (rate <= 0) rate <- 1e-6  # Avoid negative/zero rate
-  x_prop <- x_left - rexp(1, rate)
-  if (!is.null(domain)) {
-    x_prop <- pmax(domain[1], pmin(domain[2], x_prop))
-  }
-  return(x_prop)
-}
-
-# 5. Rejection/acceptance step
-reject_accept <- function(x_prop, density, envelope_func) {
-  f_prop <- density(x_prop)
-  g_prop <- envelope_func(x_prop)
-  u <- runif(1)
-  return(u * g_prop <= f_prop)
-}
-
-# === MAIN ARS FUNCTION ===
-ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 10000) {
-  validate_inputs(density, n_samples, domain)
-  
-  # Initial nodes (default [-10,0,10] or domain)
-  if (is.null(domain)) {
-    x_nodes <- c(-10, 0, 10)
-  } else {
-    x_nodes <- seq(domain[1], domain[2], length.out = 3)
-  }
-  
-  # Evaluate density and derivatives at nodes
-  y_nodes <- density(x_nodes)
-  if (any(!is.finite(y_nodes))) stop("Density evaluation failed at initial nodes")
-  
-  # Numerical derivatives
-  h <- 1e-5
-  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-  
-  # Check initial log-concavity
-  if (!logconcavity_check(density, x_nodes)) {
-    stop("Initial log-concavity check failed")
-  }
-  
-  samples <- numeric(n_samples)
-  n_collected <- 0
-  iter <- 0
-  
-  while (n_collected < n_samples && iter < max_iter) {
-    iter <- iter + 1
-    
-    # Build envelope
-    envelope_func <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
-    
-    # Propose sample
-    x_prop <- sample_proposal(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain)
-    
-    # Accept/reject
-    if (reject_accept(x_prop, density, envelope_func)) {
-      n_collected <- n_collected + 1
-      samples[n_collected] <- x_prop
-      
-      # Adapt: add acceptance point
-      insert_pos <- which(x_prop >= x_nodes)[1]
-      if (!is.na(insert_pos)) {
-        x_nodes <- sort(c(x_nodes, x_prop))
-        y_nodes <- density(x_nodes)
-        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-      }
-    } else {
-      # Adapt: add rejection point (less frequent)
-      if (runif(1) < 0.1) {  # 10% chance
-        x_nodes <- sort(c(x_nodes, x_prop))
-        y_nodes <- density(x_nodes)
-        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-      }
-    }
-    
-    # Periodic log-concavity check
-    if (iter %% 100 == 0) {
-      if (!logconcavity_check(density, x_nodes)) {
-        warning("Log-concavity violation during sampling")
-      }
-    }
-  }
-  
-  if (n_collected < n_samples) {
-    warning(sprintf("Only %d samples collected after %d iterations", n_collected, max_iter))
-  }
-  
-  return(samples[1:n_collected])
-}
-
-# === TEST FUNCTION ===
-test <- function(n_test = 10000, ks_alpha = 0.01) {
-  cat("Running ARS test suite...\n\n")
-  
-  # Normal test
-  cat("Testing normal distribution...\n")
-  ars_samples <- ars(dnorm, n_test)
-  truth <- rnorm(n_test)
-  ks_norm <- ks.test(ars_samples, truth)$p.value
-  mean_ars <- mean(ars_samples)
-  sd_ars <- sd(ars_samples)
-  normal_pass <- (abs(mean_ars) < 0.1) & (abs(sd_ars - 1) < 0.1) & (ks_norm > ks_alpha)
-  cat(sprintf("NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
-              ifelse(normal_pass, "PASS", "FAIL"), mean_ars, sd_ars, ks_norm))
-  writeLines(as.character(ars_samples), "/app/normal_samples.txt")
-  
-  # Exponential test
-  cat("\nTesting exponential distribution...\n")
-  ars_samples_exp <- ars(dexp, n_test)
-  truth_exp <- rexp(n_test)
-  ks_exp <- ks.test(ars_samples_exp, truth_exp)$p.value
-  mean_exp <- mean(ars_samples_exp)
-  sd_exp <- sd(ars_samples_exp)
-  exp_pass <- (abs(mean_exp - 1) < 0.1) & (abs(sd_exp - 1) < 0.2) & (ks_exp > ks_alpha)
-  cat(sprintf("EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
-              ifelse(exp_pass, "PASS", "FAIL"), mean_exp, sd_exp, ks_exp))
-  writeLines(as.character(ars_samples_exp), "/app/exponential_samples.txt")
-  
-  cat("\nTest complete. Samples saved to /app/normal_samples.txt and /app/exponential_samples.txt\n")
-}
-
-# === MAIN EXECUTION ===
-if (!interactive() && length(commandArgs(TRUE)) > 0) {
-  args <- commandArgs(TRUE)
-  if ("test" %in% args) {
-    test()
-  } else {
-    cat("Usage: Rscript /app/ars.R test\n")
-  }
-}
-</set>
-
-<sh>Rscript /app/ars.R test</sh>
-
-<get path="/app/" preview/>
-
-<update status="177">ars.R created; running tests; checking sample files</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_7/set/app/ars.R`
-scheme=log action=set attrs={"path":"/app/ars.R","patch":"===================================================================\n--- /app/ars.R\told\t\n+++ /app/ars.R\tnew\t\n@@ -0,0 +1,214 @@\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+# === ENVIRONMENT SETUP ===\n+if (!(\"base\" %in% search())) {\n+  stop(\"R not available - install R first\")\n+}\n+required_packages <- c(\"stats\")\n+for(pkg in required_packages) {\n+  if (!requireNamespace(pkg, quietly = TRUE)) {\n+    install.packages(pkg, repos = \"https://cran.rstudio.com/\")\n+    library(pkg, character.only = TRUE)\n+  }\n+}\n+\n+# === MODULAR AUXILIARY FUNCTIONS ===\n+\n+# 1. Input validation\n+validate_inputs <- function(density, n_samples, domain = NULL) {\n+  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n+    stop(\"n_samples must be positive numeric scalar\")\n+  }\n+  if (!is.function(density)) {\n+    stop(\"density must be a function\")\n+  }\n+  # Test vectorized\n+  test_x <- seq(-1, 1, length.out = 5)\n+  test_y <- density(test_x)\n+  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {\n+    stop(\"density must be vectorized and return finite values\")\n+  }\n+  if (!is.null(domain)) {\n+    if (length(domain) != 2 || domain[1] >= domain[2]) {\n+      stop(\"domain must be valid interval [low, high]\")\n+    }\n+  }\n+}\n+\n+# 2. Log-concavity check (numerical 2nd derivative)\n+logconcavity_check <- function(density, x_test, tol = 1e-6) {\n+  h <- 1e-5\n+  f0 <- density(x_test)\n+  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)\n+  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h\n+  if (any(f2 > tol, na.rm = TRUE)) {\n+    warning(\"Possible log-concavity violation detected\")\n+    return(FALSE)\n+  }\n+  return(TRUE)\n+}\n+\n+# 3. Build piecewise linear envelope (tangent lines in log-space)\n+envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {\n+  n_nodes <- length(x_nodes)\n+  slopes <- y_deriv_nodes\n+  envelope_func <- function(x) {\n+    # Find relevant piecewise segment for each x\n+    result <- numeric(length(x))\n+    for (i in seq_along(x)) {\n+      xi <- x[i]\n+      # Find segment j where x_nodes[j] <= xi < x_nodes[j+1]\n+      j <- which(xi >= x_nodes & xi < c(x_nodes[-1], Inf))[1]\n+      if (is.na(j)) j <- n_nodes\n+      if (j == 1) {\n+        result[i] <- y_nodes[1] + slopes[1] * (xi - x_nodes[1])\n+      } else {\n+        # Piecewise exponential: exp(y_j + s_j*(x-x_j))\n+        result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])\n+      }\n+    }\n+    exp(result)\n+  }\n+  return(envelope_func)\n+}\n+\n+# 4. Sample from piecewise exponential envelope\n+sample_proposal <- function(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain) {\n+  # Simple uniform selection of segment then exponential sample\n+  n_segments <- length(x_nodes) - 1\n+  seg_idx <- sample(1:n_segments, 1)\n+  x_left <- x_nodes[seg_idx]\n+  slope <- y_deriv_nodes[seg_idx]\n+  rate <- -slope\n+  if (rate <= 0) rate <- 1e-6  # Avoid negative/zero rate\n+  x_prop <- x_left - rexp(1, rate)\n+  if (!is.null(domain)) {\n+    x_prop <- pmax(domain[1], pmin(domain[2], x_prop))\n+  }\n+  return(x_prop)\n+}\n+\n+# 5. Rejection/acceptance step\n+reject_accept <- function(x_prop, density, envelope_func) {\n+  f_prop <- density(x_prop)\n+  g_prop <- envelope_func(x_prop)\n+  u <- runif(1)\n+  return(u * g_prop <= f_prop)\n+}\n+\n+# === MAIN ARS FUNCTION ===\n+ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 10000) {\n+  validate_inputs(density, n_samples, domain)\n+  \n+  # Initial nodes (default [-10,0,10] or domain)\n+  if (is.null(domain)) {\n+    x_nodes <- c(-10, 0, 10)\n+  } else {\n+    x_nodes <- seq(domain[1], domain[2], length.out = 3)\n+  }\n+  \n+  # Evaluate density and derivatives at nodes\n+  y_nodes <- density(x_nodes)\n+  if (any(!is.finite(y_nodes))) stop(\"Density evaluation failed at initial nodes\")\n+  \n+  # Numerical derivatives\n+  h <- 1e-5\n+  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n+  \n+  # Check initial log-concavity\n+  if (!logconcavity_check(density, x_nodes)) {\n+    stop(\"Initial log-concavity check failed\")\n+  }\n+  \n+  samples <- numeric(n_samples)\n+  n_collected <- 0\n+  iter <- 0\n+  \n+  while (n_collected < n_samples && iter < max_iter) {\n+    iter <- iter + 1\n+    \n+    # Build envelope\n+    envelope_func <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n+    \n+    # Propose sample\n+    x_prop <- sample_proposal(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain)\n+    \n+    # Accept/reject\n+    if (reject_accept(x_prop, density, envelope_func)) {\n+      n_collected <- n_collected + 1\n+      samples[n_collected] <- x_prop\n+      \n+      # Adapt: add acceptance point\n+      insert_pos <- which(x_prop >= x_nodes)[1]\n+      if (!is.na(insert_pos)) {\n+        x_nodes <- sort(c(x_nodes, x_prop))\n+        y_nodes <- density(x_nodes)\n+        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n+      }\n+    } else {\n+      # Adapt: add rejection point (less frequent)\n+      if (runif(1) < 0.1) {  # 10% chance\n+        x_nodes <- sort(c(x_nodes, x_prop))\n+        y_nodes <- density(x_nodes)\n+        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n+      }\n+    }\n+    \n+    # Periodic log-concavity check\n+    if (iter %% 100 == 0) {\n+      if (!logconcavity_check(density, x_nodes)) {\n+        warning(\"Log-concavity violation during sampling\")\n+      }\n+    }\n+  }\n+  \n+  if (n_collected < n_samples) {\n+    warning(sprintf(\"Only %d samples collected after %d iterations\", n_collected, max_iter))\n+  }\n+  \n+  return(samples[1:n_collected])\n+}\n+\n+# === TEST FUNCTION ===\n+test <- function(n_test = 10000, ks_alpha = 0.01) {\n+  cat(\"Running ARS test suite...\\n\\n\")\n+  \n+  # Normal test\n+  cat(\"Testing normal distribution...\\n\")\n+  ars_samples <- ars(dnorm, n_test)\n+  truth <- rnorm(n_test)\n+  ks_norm <- ks.test(ars_samples, truth)$p.value\n+  mean_ars <- mean(ars_samples)\n+  sd_ars <- sd(ars_samples)\n+  normal_pass <- (abs(mean_ars) < 0.1) & (abs(sd_ars - 1) < 0.1) & (ks_norm > ks_alpha)\n+  cat(sprintf(\"NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n+              ifelse(normal_pass, \"PASS\", \"FAIL\"), mean_ars, sd_ars, ks_norm))\n+  writeLines(as.character(ars_samples), \"/app/normal_samples.txt\")\n+  \n+  # Exponential test\n+  cat(\"\\nTesting exponential distribution...\\n\")\n+  ars_samples_exp <- ars(dexp, n_test)\n+  truth_exp <- rexp(n_test)\n+  ks_exp <- ks.test(ars_samples_exp, truth_exp)$p.value\n+  mean_exp <- mean(ars_samples_exp)\n+  sd_exp <- sd(ars_samples_exp)\n+  exp_pass <- (abs(mean_exp - 1) < 0.1) & (abs(sd_exp - 1) < 0.2) & (ks_exp > ks_alpha)\n+  cat(sprintf(\"EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n+              ifelse(exp_pass, \"PASS\", \"FAIL\"), mean_exp, sd_exp, ks_exp))\n+  writeLines(as.character(ars_samples_exp), \"/app/exponential_samples.txt\")\n+  \n+  cat(\"\\nTest complete. Samples saved to /app/normal_samples.txt and /app/exponential_samples.txt\\n\")\n+}\n+\n+# === MAIN EXECUTION ===\n+if (!interactive() && length(commandArgs(TRUE)) > 0) {\n+  args <- commandArgs(TRUE)\n+  if (\"test\" %in% args) {\n+    test()\n+  } else {\n+    cat(\"Usage: Rscript /app/ars.R test\\n\")\n+  }\n+}\n\\n","merge":"<<<<<<< SEARCH\n=======\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# === ENVIRONMENT SETUP ===\nif (!(\"base\" %in% search())) {\n  stop(\"R not available - install R first\")\n}\nrequired_packages <- c(\"stats\")\nfor(pkg in required_packages) {\n  if (!requireNamespace(pkg, quietly = TRUE)) {\n    install.packages(pkg, repos = \"https://cran.rstudio.com/\")\n    library(pkg, character.only = TRUE)\n  }\n}\n\n# === MODULAR AUXILIARY FUNCTIONS ===\n\n# 1. Input validation\nvalidate_inputs <- function(density, n_samples, domain = NULL) {\n  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {\n    stop(\"n_samples must be positive numeric scalar\")\n  }\n  if (!is.function(density)) {\n    stop(\"density must be a function\")\n  }\n  # Test vectorized\n  test_x <- seq(-1, 1, length.out = 5)\n  test_y <- density(test_x)\n  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {\n    stop(\"density must be vectorized and return finite values\")\n  }\n  if (!is.null(domain)) {\n    if (length(domain) != 2 || domain[1] >= domain[2]) {\n      stop(\"domain must be valid interval [low, high]\")\n    }\n  }\n}\n\n# 2. Log-concavity check (numerical 2nd derivative)\nlogconcavity_check <- function(density, x_test, tol = 1e-6) {\n  h <- 1e-5\n  f0 <- density(x_test)\n  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)\n  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h\n  if (any(f2 > tol, na.rm = TRUE)) {\n    warning(\"Possible log-concavity violation detected\")\n    return(FALSE)\n  }\n  return(TRUE)\n}\n\n# 3. Build piecewise linear envelope (tangent lines in log-space)\nenvelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {\n  n_nodes <- length(x_nodes)\n  slopes <- y_deriv_nodes\n  envelope_func <- function(x) {\n    # Find relevant piecewise segment for each x\n    result <- numeric(length(x))\n    for (i in seq_along(x)) {\n      xi <- x[i]\n      # Find segment j where x_nodes[j] <= xi < x_nodes[j+1]\n      j <- which(xi >= x_nodes & xi < c(x_nodes[-1], Inf))[1]\n      if (is.na(j)) j <- n_nodes\n      if (j == 1) {\n        result[i] <- y_nodes[1] + slopes[1] * (xi - x_nodes[1])\n      } else {\n        # Piecewise exponential: exp(y_j + s_j*(x-x_j))\n        result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])\n      }\n    }\n    exp(result)\n  }\n  return(envelope_func)\n}\n\n# 4. Sample from piecewise exponential envelope\nsample_proposal <- function(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain) {\n  # Simple uniform selection of segment then exponential sample\n  n_segments <- length(x_nodes) - 1\n  seg_idx <- sample(1:n_segments, 1)\n  x_left <- x_nodes[seg_idx]\n  slope <- y_deriv_nodes[seg_idx]\n  rate <- -slope\n  if (rate <= 0) rate <- 1e-6  # Avoid negative/zero rate\n  x_prop <- x_left - rexp(1, rate)\n  if (!is.null(domain)) {\n    x_prop <- pmax(domain[1], pmin(domain[2], x_prop))\n  }\n  return(x_prop)\n}\n\n# 5. Rejection/acceptance step\nreject_accept <- function(x_prop, density, envelope_func) {\n  f_prop <- density(x_prop)\n  g_prop <- envelope_func(x_prop)\n  u <- runif(1)\n  return(u * g_prop <= f_prop)\n}\n\n# === MAIN ARS FUNCTION ===\nars <- function(density, n_samples = 1000, domain = NULL, max_iter = 10000) {\n  validate_inputs(density, n_samples, domain)\n  \n  # Initial nodes (default [-10,0,10] or domain)\n  if (is.null(domain)) {\n    x_nodes <- c(-10, 0, 10)\n  } else {\n    x_nodes <- seq(domain[1], domain[2], length.out = 3)\n  }\n  \n  # Evaluate density and derivatives at nodes\n  y_nodes <- density(x_nodes)\n  if (any(!is.finite(y_nodes))) stop(\"Density evaluation failed at initial nodes\")\n  \n  # Numerical derivatives\n  h <- 1e-5\n  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n  \n  # Check initial log-concavity\n  if (!logconcavity_check(density, x_nodes)) {\n    stop(\"Initial log-concavity check failed\")\n  }\n  \n  samples <- numeric(n_samples)\n  n_collected <- 0\n  iter <- 0\n  \n  while (n_collected < n_samples && iter < max_iter) {\n    iter <- iter + 1\n    \n    # Build envelope\n    envelope_func <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)\n    \n    # Propose sample\n    x_prop <- sample_proposal(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain)\n    \n    # Accept/reject\n    if (reject_accept(x_prop, density, envelope_func)) {\n      n_collected <- n_collected + 1\n      samples[n_collected] <- x_prop\n      \n      # Adapt: add acceptance point\n      insert_pos <- which(x_prop >= x_nodes)[1]\n      if (!is.na(insert_pos)) {\n        x_nodes <- sort(c(x_nodes, x_prop))\n        y_nodes <- density(x_nodes)\n        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n      }\n    } else {\n      # Adapt: add rejection point (less frequent)\n      if (runif(1) < 0.1) {  # 10% chance\n        x_nodes <- sort(c(x_nodes, x_prop))\n        y_nodes <- density(x_nodes)\n        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)\n      }\n    }\n    \n    # Periodic log-concavity check\n    if (iter %% 100 == 0) {\n      if (!logconcavity_check(density, x_nodes)) {\n        warning(\"Log-concavity violation during sampling\")\n      }\n    }\n  }\n  \n  if (n_collected < n_samples) {\n    warning(sprintf(\"Only %d samples collected after %d iterations\", n_collected, max_iter))\n  }\n  \n  return(samples[1:n_collected])\n}\n\n# === TEST FUNCTION ===\ntest <- function(n_test = 10000, ks_alpha = 0.01) {\n  cat(\"Running ARS test suite...\\n\\n\")\n  \n  # Normal test\n  cat(\"Testing normal distribution...\\n\")\n  ars_samples <- ars(dnorm, n_test)\n  truth <- rnorm(n_test)\n  ks_norm <- ks.test(ars_samples, truth)$p.value\n  mean_ars <- mean(ars_samples)\n  sd_ars <- sd(ars_samples)\n  normal_pass <- (abs(mean_ars) < 0.1) & (abs(sd_ars - 1) < 0.1) & (ks_norm > ks_alpha)\n  cat(sprintf(\"NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n              ifelse(normal_pass, \"PASS\", \"FAIL\"), mean_ars, sd_ars, ks_norm))\n  writeLines(as.character(ars_samples), \"/app/normal_samples.txt\")\n  \n  # Exponential test\n  cat(\"\\nTesting exponential distribution...\\n\")\n  ars_samples_exp <- ars(dexp, n_test)\n  truth_exp <- rexp(n_test)\n  ks_exp <- ks.test(ars_samples_exp, truth_exp)$p.value\n  mean_exp <- mean(ars_samples_exp)\n  sd_exp <- sd(ars_samples_exp)\n  exp_pass <- (abs(mean_exp - 1) < 0.1) & (abs(sd_exp - 1) < 0.2) & (ks_exp > ks_alpha)\n  cat(sprintf(\"EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\\n\", \n              ifelse(exp_pass, \"PASS\", \"FAIL\"), mean_exp, sd_exp, ks_exp))\n  writeLines(as.character(ars_samples_exp), \"/app/exponential_samples.txt\")\n  \n  cat(\"\\nTest complete. Samples saved to /app/normal_samples.txt and /app/exponential_samples.txt\\n\")\n}\n\n# === MAIN EXECUTION ===\nif (!interactive() && length(commandArgs(TRUE)) > 0) {\n  args <- commandArgs(TRUE)\n  if (\"test\" %in% args) {\n    test()\n  } else {\n    cat(\"Usage: Rscript /app/ars.R test\\n\")\n  }\n}\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":3435,"summary":null,"action":"set"}
-
-```
-#!/usr/bin/env Rscript
-
-# Adaptive Rejection Sampling (ARS) - Gilks & Wild (1992)
-# Modular implementation with input validation and log-concavity checks
-
-# === ENVIRONMENT SETUP ===
-if (!("base" %in% search())) {
-  stop("R not available - install R first")
-}
-required_packages <- c("stats")
-for(pkg in required_packages) {
-  if (!requireNamespace(pkg, quietly = TRUE)) {
-    install.packages(pkg, repos = "https://cran.rstudio.com/")
-    library(pkg, character.only = TRUE)
-  }
-}
-
-# === MODULAR AUXILIARY FUNCTIONS ===
-
-# 1. Input validation
-validate_inputs <- function(density, n_samples, domain = NULL) {
-  if (!is.numeric(n_samples) || n_samples <= 0 || length(n_samples) != 1) {
-    stop("n_samples must be positive numeric scalar")
-  }
-  if (!is.function(density)) {
-    stop("density must be a function")
-  }
-  # Test vectorized
-  test_x <- seq(-1, 1, length.out = 5)
-  test_y <- density(test_x)
-  if (length(test_y) != length(test_x) || any(is.na(test_y)) || any(!is.finite(test_y))) {
-    stop("density must be vectorized and return finite values")
-  }
-  if (!is.null(domain)) {
-    if (length(domain) != 2 || domain[1] >= domain[2]) {
-      stop("domain must be valid interval [low, high]")
-    }
-  }
-}
-
-# 2. Log-concavity check (numerical 2nd derivative)
-logconcavity_check <- function(density, x_test, tol = 1e-6) {
-  h <- 1e-5
-  f0 <- density(x_test)
-  f1 <- (density(x_test + h) - density(x_test - h)) / (2 * h)
-  f2 <- (f1[2:length(f1)] - f1[1:(length(f1)-1)]) / h
-  if (any(f2 > tol, na.rm = TRUE)) {
-    warning("Possible log-concavity violation detected")
-    return(FALSE)
-  }
-  return(TRUE)
-}
-
-# 3. Build piecewise linear envelope (tangent lines in log-space)
-envelope_build <- function(x_nodes, y_nodes, y_deriv_nodes) {
-  n_nodes <- length(x_nodes)
-  slopes <- y_deriv_nodes
-  envelope_func <- function(x) {
-    # Find relevant piecewise segment for each x
-    result <- numeric(length(x))
-    for (i in seq_along(x)) {
-      xi <- x[i]
-      # Find segment j where x_nodes[j] <= xi < x_nodes[j+1]
-      j <- which(xi >= x_nodes & xi < c(x_nodes[-1], Inf))[1]
-      if (is.na(j)) j <- n_nodes
-      if (j == 1) {
-        result[i] <- y_nodes[1] + slopes[1] * (xi - x_nodes[1])
-      } else {
-        # Piecewise exponential: exp(y_j + s_j*(x-x_j))
-        result[i] <- y_nodes[j] + slopes[j] * (xi - x_nodes[j])
-      }
-    }
-    exp(result)
-  }
-  return(envelope_func)
-}
-
-# 4. Sample from piecewise exponential envelope
-sample_proposal <- function(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain) {
-  # Simple uniform selection of segment then exponential sample
-  n_segments <- length(x_nodes) - 1
-  seg_idx <- sample(1:n_segments, 1)
-  x_left <- x_nodes[seg_idx]
-  slope <- y_deriv_nodes[seg_idx]
-  rate <- -slope
-  if (rate <= 0) rate <- 1e-6  # Avoid negative/zero rate
-  x_prop <- x_left - rexp(1, rate)
-  if (!is.null(domain)) {
-    x_prop <- pmax(domain[1], pmin(domain[2], x_prop))
-  }
-  return(x_prop)
-}
-
-# 5. Rejection/acceptance step
-reject_accept <- function(x_prop, density, envelope_func) {
-  f_prop <- density(x_prop)
-  g_prop <- envelope_func(x_prop)
-  u <- runif(1)
-  return(u * g_prop <= f_prop)
-}
-
-# === MAIN ARS FUNCTION ===
-ars <- function(density, n_samples = 1000, domain = NULL, max_iter = 10000) {
-  validate_inputs(density, n_samples, domain)
-  
-  # Initial nodes (default [-10,0,10] or domain)
-  if (is.null(domain)) {
-    x_nodes <- c(-10, 0, 10)
-  } else {
-    x_nodes <- seq(domain[1], domain[2], length.out = 3)
-  }
-  
-  # Evaluate density and derivatives at nodes
-  y_nodes <- density(x_nodes)
-  if (any(!is.finite(y_nodes))) stop("Density evaluation failed at initial nodes")
-  
-  # Numerical derivatives
-  h <- 1e-5
-  y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-  
-  # Check initial log-concavity
-  if (!logconcavity_check(density, x_nodes)) {
-    stop("Initial log-concavity check failed")
-  }
-  
-  samples <- numeric(n_samples)
-  n_collected <- 0
-  iter <- 0
-  
-  while (n_collected < n_samples && iter < max_iter) {
-    iter <- iter + 1
-    
-    # Build envelope
-    envelope_func <- envelope_build(x_nodes, y_nodes, y_deriv_nodes)
-    
-    # Propose sample
-    x_prop <- sample_proposal(envelope_func, x_nodes, y_nodes, y_deriv_nodes, domain)
-    
-    # Accept/reject
-    if (reject_accept(x_prop, density, envelope_func)) {
-      n_collected <- n_collected + 1
-      samples[n_collected] <- x_prop
-      
-      # Adapt: add acceptance point
-      insert_pos <- which(x_prop >= x_nodes)[1]
-      if (!is.na(insert_pos)) {
-        x_nodes <- sort(c(x_nodes, x_prop))
-        y_nodes <- density(x_nodes)
-        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-      }
-    } else {
-      # Adapt: add rejection point (less frequent)
-      if (runif(1) < 0.1) {  # 10% chance
-        x_nodes <- sort(c(x_nodes, x_prop))
-        y_nodes <- density(x_nodes)
-        y_deriv_nodes <- (density(x_nodes + h) - density(x_nodes - h)) / (2 * h)
-      }
-    }
-    
-    # Periodic log-concavity check
-    if (iter %% 100 == 0) {
-      if (!logconcavity_check(density, x_nodes)) {
-        warning("Log-concavity violation during sampling")
-      }
-    }
-  }
-  
-  if (n_collected < n_samples) {
-    warning(sprintf("Only %d samples collected after %d iterations", n_collected, max_iter))
-  }
-  
-  return(samples[1:n_collected])
-}
-
-# === TEST FUNCTION ===
-test <- function(n_test = 10000, ks_alpha = 0.01) {
-  cat("Running ARS test suite...\n\n")
-  
-  # Normal test
-  cat("Testing normal distribution...\n")
-  ars_samples <- ars(dnorm, n_test)
-  truth <- rnorm(n_test)
-  ks_norm <- ks.test(ars_samples, truth)$p.value
-  mean_ars <- mean(ars_samples)
-  sd_ars <- sd(ars_samples)
-  normal_pass <- (abs(mean_ars) < 0.1) & (abs(sd_ars - 1) < 0.1) & (ks_norm > ks_alpha)
-  cat(sprintf("NORMAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
-              ifelse(normal_pass, "PASS", "FAIL"), mean_ars, sd_ars, ks_norm))
-  writeLines(as.character(ars_samples), "/app/normal_samples.txt")
-  
-  # Exponential test
-  cat("\nTesting exponential distribution...\n")
-  ars_samples_exp <- ars(dexp, n_test)
-  truth_exp <- rexp(n_test)
-  ks_exp <- ks.test(ars_samples_exp, truth_exp)$p.value
-  mean_exp <- mean(ars_samples_exp)
-  sd_exp <- sd(ars_samples_exp)
-  exp_pass <- (abs(mean_exp - 1) < 0.1) & (abs(sd_exp - 1) < 0.2) & (ks_exp > ks_alpha)
-  cat(sprintf("EXPONENTIAL_TEST: %s (mean=%.2f, sd=%.2f, KS=%.3f)\n", 
-              ifelse(exp_pass, "PASS", "FAIL"), mean_exp, sd_exp, ks_exp))
-  writeLines(as.character(ars_samples_exp), "/app/exponential_samples.txt")
-  
-  cat("\nTest complete. Samples saved to /app/normal_samples.txt and /app/exponential_samples.txt\n")
-}
-
-# === MAIN EXECUTION ===
-if (!interactive() && length(commandArgs(TRUE)) > 0) {
-  args <- commandArgs(TRUE)
-  if ("test" %in% args) {
-    test()
-  } else {
-    cat("Usage: Rscript /app/ars.R test\n")
-  }
-}
-```
-
-### `log://turn_7/sh/Rscript_/app/ars.R_test`
-scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
-
-```
-ran 'Rscript /app/ars.R test', exit=127 (0s). Output: sh://turn_7/Rscript_/app/ars.R_test_1 (0 tokens), sh://turn_7/Rscript_/app/ars.R_test_2 (21 tokens)
-```
-
-### `log://turn_7/get/app`
-scheme=log action=get attrs={"path":"/app/","action":"get"}
-
-```
-/app/ promoted
-```
-
-### `log://turn_7/update/ars.R_created%3B_running_tests%3B_checking_sample_files`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-ars.R created; running tests; checking sample files
-```
-

package/audit/sweep/adaptive-rejection-sampler/turns/turn_008.md

@@ -1,72 +0,0 @@
-# turn 008
-
-tokens: prompt=8901 cached=3723 completion=129 reasoning=0 total=9030 cost=0
-created: 2026-05-01 23:42:49
-
-update: status=177 body=installing R; running tests; checking sample files
-
----
-
-## reasoning (think)
-
-```
-* Rscript failed because R is not installed in the environment
-* Need to install R first, then test ars.R
-* After confirming tests pass and samples generated, complete Deployment Stage
-* Demote ARS known entries after success to free context
-```
-
-## assistant emission
-
-```
-<think>
-* Rscript failed because R is not installed in the environment
-* Need to install R first, then test ars.R
-* After confirming tests pass and samples generated, complete Deployment Stage
-* Demote ARS known entries after success to free context
-</think>
-
-<sh>apt-get update && apt-get install -y r-base</sh>
-<sh>Rscript /app/ars.R test</sh>
-<get path="/app/normal_samples.txt" preview/>
-<get path="/app/exponential_samples.txt" preview/>
-<update status="177">installing R; running tests; checking sample files</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_8/sh/apt-get_update_%26%26_apt-get_install_-y_r-base`
-scheme=log action=sh attrs={"command":"apt-get update && apt-get install -y r-base","summary":"apt-get update && apt-get install -y r-base","action":"sh"}
-
-```
-ran 'apt-get update && apt-get install -y r-base', exit=0 (17s). Output: sh://turn_8/apt-get_update_%26%26_apt-get_install_-y_r-base_1 (48803 tokens), sh://turn_8/apt-get_update_%26%26_apt-get_install_-y_r-base_2 (37 tokens)
-```
-
-### `log://turn_8/sh/Rscript_/app/ars.R_test`
-scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
-
-```
-ran 'Rscript /app/ars.R test', exit=1 (0s). Output: sh://turn_8/Rscript_/app/ars.R_test_1 (0 tokens), sh://turn_8/Rscript_/app/ars.R_test_2 (29 tokens)
-```
-
-### `log://turn_8/get/app/normal_samples.txt`
-scheme=log action=get attrs={"path":"/app/normal_samples.txt","action":"get"}
-
-```
-/app/normal_samples.txt not found
-```
-
-### `log://turn_8/get/app/exponential_samples.txt`
-scheme=log action=get attrs={"path":"/app/exponential_samples.txt","action":"get"}
-
-```
-/app/exponential_samples.txt not found
-```
-
-### `log://turn_8/update/installing_R%3B_running_tests%3B_checking_sample_files`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-installing R; running tests; checking sample files
-```
-

package/audit/sweep/adaptive-rejection-sampler/turns/turn_009.md

@@ -1,58 +0,0 @@
-# turn 009
-
-tokens: prompt=9902 cached=157 completion=109 reasoning=0 total=10011 cost=0
-created: 2026-05-01 23:43:08
-
-update: status=177 body=running tests now R available; checking sample files
-
----
-
-## reasoning (think)
-
-```
-R is now installed (apt-get succeeded). Need to re-run the test now that Rscript is available. Previous test failed due to missing R. After test runs, check sample files are generated and tests pass. If successful, complete deployment.
-```
-
-## assistant emission
-
-```
-<think>
-R is now installed (apt-get succeeded). Need to re-run the test now that Rscript is available. Previous test failed due to missing R. After test runs, check sample files are generated and tests pass. If successful, complete deployment.
-</think>
-
-<sh>Rscript /app/ars.R test</sh>
-<get path="/app/normal_samples.txt" preview/>
-<get path="/app/exponential_samples.txt" preview/>
-<update status="177">running tests now R available; checking sample files</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_9/sh/Rscript_/app/ars.R_test`
-scheme=log action=sh attrs={"command":"Rscript /app/ars.R test","summary":"Rscript /app/ars.R test","action":"sh"}
-
-```
-ran 'Rscript /app/ars.R test', exit=1 (0s). Output: sh://turn_9/Rscript_/app/ars.R_test_1 (0 tokens), sh://turn_9/Rscript_/app/ars.R_test_2 (29 tokens)
-```
-
-### `log://turn_9/get/app/normal_samples.txt`
-scheme=log action=get attrs={"path":"/app/normal_samples.txt","action":"get"}
-
-```
-/app/normal_samples.txt not found
-```
-
-### `log://turn_9/get/app/exponential_samples.txt`
-scheme=log action=get attrs={"path":"/app/exponential_samples.txt","action":"get"}
-
-```
-/app/exponential_samples.txt not found
-```
-
-### `log://turn_9/update/running_tests_now_R_available%3B_checking_sample_files`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-running tests now R available; checking sample files
-```
-