Phase 3: Optimize Duplicate Detection (1.25-1.76× Speedup)

[dshkol]

Summary

This PR optimizes duplicate detection in GIS conversion functions by replacing a double-scan approach with a single-pass algorithm, achieving 1.25-1.76× speedup depending on input characteristics.

Problem

The previous implementation scanned input twice to detect and remove duplicates:

if (anyDuplicated(gh) > 0L) {        # Scan 1: Check for duplicates
  idx = which(duplicated(gh))        # Scan 2: Find duplicate indices
  gh = gh[-idx]
}

This double-scan is wasteful since duplicated() already identifies all duplicates.

Solution

Single-pass approach:

dup_idx = duplicated(gh)             # Single scan: Find duplicates
if (any(dup_idx)) {
  gh = gh[!dup_idx]
}

Applied to three functions:

• gh_to_sp
• gh_to_spdf.default
• gh_to_spdf.data.frame

Performance Results

Comprehensive benchmarks across varying:

• Input sizes: 100, 1K, 10K, 100K geohashes
• Duplicate ratios: 0%, 10%, 50%, 90%

Summary Statistics

• Median speedup: 1.44×
• Mean speedup: 1.48×
• Best case: 1.76× (small inputs)
• Large inputs: 1.25-1.48×

By Duplicate Ratio

Duplicates	Median Speedup
0%	1.38×
10%	1.36×
50%	1.44×
90%	1.51×

Higher duplicate ratios show better relative performance (more work saved).

Testing

✅ All 48 GIS tests pass
✅ No breaking changes to API or behavior
✅ Same output, same warnings, just faster
✅ Benchmark script and plots included

Visualizations

The PR includes:

• benchmarks/dedup_speedup.png - Speedup factor across test cases
• benchmarks/dedup_absolute.png - Absolute performance comparison
• benchmarks/dedup_benchmark.R - Reproducible benchmark script

Changes

• R/gis_tools.R: Updated duplicate detection in 3 functions
• NEWS.md: Documented performance improvement
• benchmarks/: Added microbenchmark analysis

Verification

# Run benchmarks yourself
source("benchmarks/dedup_benchmark.R")

# Run tests
devtools::test(filter = "gis")

Series Progress

• ✅ Phase 1: Quick fixes and code quality (#43)
• ✅ Phase 2: gh_covering optimization - 2-3× speedup (#44)
• ✅ Phase 3: Duplicate detection optimization (this PR)
• 🔜 Phase 4: CI/CD modernization (GitHub Actions)

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