feat(matlab): add Satterthwaite DF + honest random-slope test to LME reports

Every fitlme-based report (lme_*, paper_*, phase_*, and the variations' analyze.m) now shows, per effect: residual-DF p, Satterthwaite-DF p, and -- for the interaction -- an HONEST test from a per-animal random-SLOPE model (day|rat), whose Satterthwaite DF collapses toward the animal count. New: tdcs_random_slope_interaction.m (shared helper). Wired into tdcs_lme, tdcs_paper_lme, tdcs_phase_lme, variation_analyze; SUMMARY.csv gains interaction_p_satt / interaction_p_rs. Regenerated all results/, variations/, matched-effort outputs. Key point this surfaces: Satterthwaite ~= residual on the random-INTERCEPT model (the slope's error is at session level), so it does NOT fix pseudoreplication; the random-slope model does. Effect: full-range mergeA2 interaction 0.009 -> 0.75 (collapses); unmerge_d0_5 0.015 -> 0.13 (n.s.); the pooled-control early windows survive honestly (naive_a2_d0_5 0.001 -> 0.028; naive_boxa_d0_5 0.003 -> 0.036). Suite 42/42. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
2026-07-22 15:45:19 -04:00
parent 5fcd97f81a
commit 8a18c894dd
77 changed files with 2066 additions and 345 deletions
@@ -0,0 +1,130 @@
+#!/usr/bin/env bash
+# =============================================================================
+# Experiments DB — incremental backup script
+#
+# Usage:
+#   backup.sh daily    – backup only if DB changed since last run; keep 5
+#   backup.sh weekly   – unconditional backup; keep 2
+#
+# Cron (added by setup_cron.sh):
+#   0 2 * * *   /home/sam/docker-images/experiments-database/scripts/backup.sh daily
+#   0 3 * * 0   /home/sam/docker-images/experiments-database/scripts/backup.sh weekly
+# =============================================================================
+
+set -euo pipefail
+
+# ── Config ────────────────────────────────────────────────────────────────────
+MODE="${1:-daily}"
+BACKUP_ROOT="/home/sam/synology/Backups/Experiments-DB-Backup"
+DAILY_DIR="$BACKUP_ROOT/daily"
+WEEKLY_DIR="$BACKUP_ROOT/weekly"
+STATE_FILE="$BACKUP_ROOT/.last_backup_state"
+LOG_FILE="$BACKUP_ROOT/backup.log"
+KEEP_DAILY=5
+KEEP_WEEKLY=2
+
+PG_CONTAINER="experiments_postgres"
+PG_USER="expuser"
+PG_DB="experiments_db"
+
+# ── Helpers ───────────────────────────────────────────────────────────────────
+log() { echo "[$(date '+%Y-%m-%d %H:%M:%S')] $*" | tee -a "$LOG_FILE"; }
+
+die() { log "ERROR: $*"; exit 1; }
+
+# Ensure directories exist
+mkdir -p "$DAILY_DIR" "$WEEKLY_DIR"
+
+# Check postgres container is running
+if ! docker inspect --format '{{.State.Running}}' "$PG_CONTAINER" 2>/dev/null | grep -q true; then
+    die "Container $PG_CONTAINER is not running."
+fi
+
+# ── DB state fingerprint ──────────────────────────────────────────────────────
+# Combines row counts from all key tables + latest audit_log timestamp.
+# Changes in any table (insert, update, delete) alter this string.
+get_db_state() {
+    docker exec "$PG_CONTAINER" psql -U "$PG_USER" -d "$PG_DB" -t -A -c "
+        SELECT
+            (SELECT COUNT(*) FROM experiments)      || ',' ||
+            (SELECT COUNT(*) FROM animals)          || ',' ||
+            (SELECT COUNT(*) FROM daily_statuses)   || ',' ||
+            (SELECT COUNT(*) FROM daily_analyses)   || ',' ||
+            (SELECT COUNT(*) FROM session_files)    || ',' ||
+            COALESCE(
+                (SELECT MAX(timestamp)::text FROM audit_logs),
+                'no-audit'
+            )
+        AS fingerprint;
+    " 2>/dev/null | tr -d '[:space:]'
+}
+
+# ── Dump function ─────────────────────────────────────────────────────────────
+run_dump() {
+    local dest="$1"
+    local tmp="${dest}.tmp"
+    log "Dumping → $dest"
+    docker exec "$PG_CONTAINER" pg_dump \
+        -U "$PG_USER" \
+        --format=custom \
+        --compress=9 \
+        "$PG_DB" > "$tmp" \
+        && mv "$tmp" "$dest" \
+        || { rm -f "$tmp"; die "pg_dump failed."; }
+    local size
+    size=$(du -sh "$dest" | cut -f1)
+    log "Backup written ($size): $(basename "$dest")"
+}
+
+# ── Prune old backups ─────────────────────────────────────────────────────────
+prune() {
+    local dir="$1"
+    local keep="$2"
+    local count
+    count=$(ls -1 "$dir"/*.pgdump 2>/dev/null | wc -l)
+    if (( count > keep )); then
+        ls -1t "$dir"/*.pgdump | tail -n "+$((keep + 1))" | while read -r f; do
+            log "Pruning old backup: $(basename "$f")"
+            rm -f "$f"
+        done
+    fi
+}
+
+# ── Main ──────────────────────────────────────────────────────────────────────
+TIMESTAMP=$(date '+%Y%m%d_%H%M%S')
+
+if [[ "$MODE" == "daily" ]]; then
+    log "--- Daily backup check ---"
+    CURRENT_STATE=$(get_db_state)
+
+    if [[ -z "$CURRENT_STATE" ]]; then
+        die "Could not read DB state."
+    fi
+
+    LAST_STATE=$(cat "$STATE_FILE" 2>/dev/null || echo "")
+
+    if [[ "$CURRENT_STATE" == "$LAST_STATE" ]]; then
+        log "No changes detected since last backup. Skipping."
+        exit 0
+    fi
+
+    DEST="$DAILY_DIR/experiments_db_daily_${TIMESTAMP}.pgdump"
+    run_dump "$DEST"
+
+    # Save new state only after successful dump
+    echo "$CURRENT_STATE" > "$STATE_FILE"
+    log "State fingerprint updated."
+
+    prune "$DAILY_DIR" "$KEEP_DAILY"
+    log "Daily backup complete."
+
+elif [[ "$MODE" == "weekly" ]]; then
+    log "--- Weekly backup (unconditional) ---"
+    DEST="$WEEKLY_DIR/experiments_db_weekly_${TIMESTAMP}.pgdump"
+    run_dump "$DEST"
+    prune "$WEEKLY_DIR" "$KEEP_WEEKLY"
+    log "Weekly backup complete."
+
+else
+    die "Unknown mode '$MODE'. Use 'daily' or 'weekly'."
+fi