---
title: "Troubleshooting Guide"
author: "Gilles Colling"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Troubleshooting Guide}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  error = TRUE
)
library(couplr)
library(dplyr)
```

## Overview
This vignette provides solutions to common issues encountered when using couplr. Each section describes a problem, explains why it occurs, and provides step-by-step solutions.

**Quick reference:**

| Issue | Jump to Section |
|-------|-----------------|
| No valid pairs found | [Infeasible Problems](#infeasible-problems) |
| Poor balance after matching | [Poor Balance](#poor-balance-despite-matching) |
| Matching is too slow | [Performance Issues](#performance-issues) |
| Memory errors | [Memory Errors](#memory-errors) |
| Different results with different methods | [Non-Determinism](#different-results-with-different-methods) |
| Unexpected NA in results | [Missing Values](#missing-values-in-data) |
| C++ compilation errors | [Installation Issues](#installation-issues) |

---

## Infeasible Problems

### Symptom

```{r, error=TRUE}
# This fails: all assignments have Inf cost
cost <- matrix(c(1, Inf, Inf, Inf, Inf, Inf, Inf, 2, 3), nrow = 3, byrow = TRUE)
result <- lap_solve(cost)
```

Error message: "No feasible assignment found" or total cost is Inf.

### Cause

A feasible assignment requires that every row can be assigned to at least one column with finite cost. When rows have all-Inf or all-NA entries, no valid assignment exists.

### Diagnosis

```{r}
# Check for infeasible rows
check_feasibility <- function(cost_matrix) {
  finite_per_row <- rowSums(is.finite(cost_matrix))
  infeasible_rows <- which(finite_per_row == 0)

  if (length(infeasible_rows) > 0) {
    cat("Infeasible rows (no finite costs):", infeasible_rows, "\n")
    return(FALSE)
  }

  finite_per_col <- colSums(is.finite(cost_matrix))
  infeasible_cols <- which(finite_per_col == 0)

  if (length(infeasible_cols) > 0) {
    cat("Infeasible columns (no finite costs):", infeasible_cols, "\n")
    return(FALSE)
  }

  cat("Problem appears feasible\n")
  return(TRUE)
}

# Check the problematic matrix
cost <- matrix(c(1, Inf, Inf, Inf, Inf, Inf, Inf, 2, 3), nrow = 3, byrow = TRUE)
check_feasibility(cost)
```

### Solutions

**1. Remove infeasible rows/columns:**

```{r}
# Remove rows with no valid assignments
cost <- matrix(c(1, Inf, Inf, Inf, Inf, Inf, Inf, 2, 3), nrow = 3, byrow = TRUE)
valid_rows <- rowSums(is.finite(cost)) > 0
cost_valid <- cost[valid_rows, , drop = FALSE]

if (nrow(cost_valid) > 0) {
  result <- lap_solve(cost_valid)
  cat("Matched", nrow(result), "of", nrow(cost), "rows\n")
}
```

**2. Add fallback costs:**

```{r}
# Replace Inf with high (but finite) penalty
cost_with_fallback <- cost
cost_with_fallback[!is.finite(cost_with_fallback)] <- 1e6  # Large penalty

result <- lap_solve(cost_with_fallback)
print(result)
```

**3. For matching: check covariate overlap:**

```{r, fig.width=7, fig.height=4, fig.alt="Density plot showing overlap between treatment and control groups on the age variable"}
# Simulate poor overlap scenario
set.seed(123)
left <- tibble(id = 1:50, age = rnorm(50, mean = 25, sd = 3))
right <- tibble(id = 1:50, age = rnorm(50, mean = 55, sd = 3))

# Visualize overlap
library(ggplot2)
combined <- bind_rows(
  left %>% mutate(group = "Left"),
  right %>% mutate(group = "Right")
)

ggplot(combined, aes(x = age, fill = group)) +
  geom_density(alpha = 0.5) +
  labs(title = "Poor Covariate Overlap",
       subtitle = "No overlap means no good matches possible") +
  theme_minimal() +
  theme(plot.background = element_rect(fill = "transparent", color = NA),
        panel.background = element_rect(fill = "transparent", color = NA))
```

---

## Poor Balance Despite Matching

### Symptom

After matching, `balance_diagnostics()` shows |std_diff| > 0.25 for some variables.

```{r}
# Example of poor balance
set.seed(456)
left <- tibble(
  id = 1:100,
  age = rnorm(100, 30, 5),
  income = rnorm(100, 80000, 20000)  # Very different from right
)
right <- tibble(
  id = 1:100,
  age = rnorm(100, 32, 5),
  income = rnorm(100, 40000, 10000)  # Very different income
)

result <- match_couples(left, right, vars = c("age", "income"), auto_scale = TRUE)
balance <- balance_diagnostics(result, left, right, vars = c("age", "income"))
print(balance)
```

### Causes

1. **Weak overlap**: Groups are too different on key variables

2. **Missing confounders**: Important variables not included in matching

3. **Caliper too loose**: Accepting poor matches

4. **Wrong scaling**: Variables not properly weighted

### Solutions

**1. Add more matching variables:**

```{r, eval=FALSE}
# Include additional relevant variables
result <- match_couples(
  left, right,
  vars = c("age", "income", "education", "region"),  # More variables
  auto_scale = TRUE
)
```

**2. Tighten caliper (fewer but better matches):**

```{r}
result_strict <- match_couples(
  left, right,
  vars = c("age", "income"),
  max_distance = 0.3,  # Stricter caliper
  auto_scale = TRUE
)

cat("Original matches:", result$info$n_matched, "\n")
cat("With caliper:", result_strict$info$n_matched, "\n")

balance_strict <- balance_diagnostics(result_strict, left, right, vars = c("age", "income"))
print(balance_strict)
```

**3. Use blocking on problematic variable:**

```{r, eval=FALSE}
# Block on income tertiles to ensure exact balance
left$income_cat <- cut(left$income, breaks = 3, labels = c("low", "mid", "high"))
right$income_cat <- cut(right$income, breaks = 3, labels = c("low", "mid", "high"))

blocks <- matchmaker(left, right, block_type = "group", block_by = "income_cat")
result_blocked <- match_couples(
  blocks$left, blocks$right,
  vars = c("age"),  # Match on age within income blocks
  block_id = "block_id"
)
```

**4. Try different scaling:**

```{r}
# Compare scaling methods
for (scale_method in c("robust", "standardize", "range")) {
  res <- match_couples(left, right, vars = c("age", "income"),
                       auto_scale = TRUE, scale = scale_method)
  bal <- balance_diagnostics(res, left, right, vars = c("age", "income"))
  cat(scale_method, "- max |std_diff|:",
      round(bal$overall$max_abs_std_diff, 3), "\n")
}
```

---

## Performance Issues

### Symptom

`match_couples()` or `lap_solve()` takes too long or doesn't complete.

### Cause

Optimal matching has $O(n^3)$ complexity. For n = 5,000, this means ~125 billion operations.

### Diagnosis

```{r}
# Estimate runtime
estimate_runtime <- function(n, seconds_per_billion = 1) {
  ops <- n^3
  time_sec <- ops / 1e9 * seconds_per_billion

  if (time_sec < 60) {
    sprintf("%.1f seconds", time_sec)
  } else if (time_sec < 3600) {
    sprintf("%.1f minutes", time_sec / 60)
  } else {
    sprintf("%.1f hours", time_sec / 3600)
  }
}

cat("Estimated runtime for optimal matching:\n")
for (n in c(100, 500, 1000, 3000, 5000, 10000)) {
  cat(sprintf("  n = %5d: %s\n", n, estimate_runtime(n)))
}
```

### Solutions

**1. Use greedy matching for large problems:**

```{r}
set.seed(789)
n <- 500
large_left <- tibble(id = 1:n, x1 = rnorm(n), x2 = rnorm(n))
large_right <- tibble(id = 1:n, x1 = rnorm(n), x2 = rnorm(n))

# Greedy is much faster
time_greedy <- system.time({
  result_greedy <- greedy_couples(
    large_left, large_right,
    vars = c("x1", "x2"),
    strategy = "row_best"
  )
})

cat("Greedy matching (n=500):", round(time_greedy["elapsed"], 2), "seconds\n")
cat("Quality (mean distance):", round(mean(result_greedy$pairs$distance), 4), "\n")
```

**2. Use blocking to divide the problem:**

```{r, eval=FALSE}
# Create clusters to match within
blocks <- matchmaker(
  large_left, large_right,
  block_type = "cluster",
  block_vars = c("x1", "x2"),
  n_blocks = 10  # 10 blocks of ~200 each
)

# Match within blocks (10 x O(200^3) << O(2000^3))
result_blocked <- match_couples(
  blocks$left, blocks$right,
  vars = c("x1", "x2"),
  block_id = "block_id"
)
```

**3. Choose a faster algorithm:**

```{r, eval=FALSE}
# For n > 1000, auction algorithm often faster
result <- match_couples(
  large_left, large_right,
  vars = c("x1", "x2"),
  method = "auction"
)

# For sparse problems (many forbidden pairs)
result <- match_couples(
  left, right,
  vars = vars,
  max_distance = 0.5,  # Creates sparsity
  method = "sap"       # Sparse algorithm
)
```

**4. Pre-compute and cache distances:**

```{r}
# Compute once, reuse multiple times
dist_cache <- compute_distances(
  large_left, large_right,
  vars = c("x1", "x2"),
  scale = "robust"
)

# Fast: reuse cached distances
result1 <- match_couples(dist_cache, max_distance = 0.3)
result2 <- match_couples(dist_cache, max_distance = 0.5)
result3 <- match_couples(dist_cache, max_distance = 1.0)
```

---

## Memory Errors

### Symptom

R crashes or shows: "Error: cannot allocate vector of size X GB"

### Cause

A full distance matrix for nxn requires 8n² bytes:

```{r}
# Memory requirements
memory_needed <- function(n) {
  bytes <- 8 * n^2
  if (bytes < 1e6) {
    sprintf("%.1f KB", bytes / 1e3)
  } else if (bytes < 1e9) {
    sprintf("%.1f MB", bytes / 1e6)
  } else {
    sprintf("%.1f GB", bytes / 1e9)
  }
}

cat("Memory for full distance matrix:\n")
for (n in c(1000, 5000, 10000, 20000, 50000)) {
  cat(sprintf("  n = %5d: %s\n", n, memory_needed(n)))
}
```

### Solutions

**1. Use greedy matching (avoids full matrix):**

```{r, eval=FALSE}
# Greedy computes distances on-the-fly
result <- greedy_couples(
  left, right,
  vars = covariates,
  strategy = "row_best"  # Most memory-efficient
)
```

**2. Use blocking to create smaller subproblems:**

```{r, eval=FALSE}
# Each block is much smaller
blocks <- matchmaker(left, right, block_type = "cluster", n_blocks = 20)
result <- match_couples(blocks$left, blocks$right, vars = vars, block_id = "block_id")
```

**3. Use caliper to create sparse matrix:**

```{r, eval=FALSE}
# Caliper excludes distant pairs (sparse representation)
result <- match_couples(
  left, right,
  vars = covariates,
  max_distance = 0.5,
  method = "sap"  # Sparse-optimized algorithm
)
```

**4. Increase R's memory limit (Windows):**

```{r, eval=FALSE}
# Increase to 16 GB (if available)
memory.limit(size = 16000)
```

---

## Different Results with Different Methods

### Symptom

Different algorithms return different assignments:

```{r}
cost <- matrix(c(1, 2, 2, 2, 1, 2, 2, 2, 1), nrow = 3, byrow = TRUE)

result_jv <- lap_solve(cost, method = "jv")
result_hungarian <- lap_solve(cost, method = "hungarian")

cat("JV assignment:       ", result_jv$target, "\n")
cat("Hungarian assignment:", result_hungarian$target, "\n")
cat("JV total cost:       ", get_total_cost(result_jv), "\n")
cat("Hungarian total cost:", get_total_cost(result_hungarian), "\n")
```

### Cause

When multiple optimal solutions exist (tied costs), different algorithms may find different ones. **The total cost should be the same**; if not, report a bug.

### Diagnosis

```{r}
# Check for ties
check_ties <- function(cost_matrix) {
  n <- nrow(cost_matrix)
  # Check if diagonal dominates (trivial ties)
  diag_costs <- diag(cost_matrix)
  if (length(unique(diag_costs)) < n) {
    cat("Tied costs on diagonal - multiple optima likely\n")
  }

  # Check cost uniqueness
  unique_costs <- length(unique(as.vector(cost_matrix)))
  total_entries <- length(cost_matrix)
  if (unique_costs < total_entries * 0.5) {
    cat("Many repeated costs - ties possible\n")
  }
}

check_ties(cost)
```

### Solutions

**1. Verify total costs match:**

```{r}
# Total cost should be identical
stopifnot(get_total_cost(result_jv) == get_total_cost(result_hungarian))
cat("Both methods found optimal solutions (same total cost)\n")
```

**2. Use Hungarian for deterministic tie-breaking:**

```{r}
# Hungarian has consistent tie-breaking
result <- lap_solve(cost, method = "hungarian")
```

**3. Add small noise to break ties:**

```{r}
set.seed(42)
cost_perturbed <- cost + matrix(rnorm(9, 0, 1e-10), 3, 3)
result <- lap_solve(cost_perturbed)
```

---

## Missing Values in Data

### Symptom

Matching fails or produces unexpected results due to NA values.

```{r, error=TRUE}
left <- tibble(id = 1:5, age = c(25, 30, NA, 35, 40))
right <- tibble(id = 1:5, age = c(28, 32, 33, 36, 42))

# This may fail or give unexpected results
result <- match_couples(left, right, vars = "age")
```

### Cause

couplr requires complete cases for distance computation. NA values in matching variables cause issues.

### Solutions

**1. Remove rows with NA (before matching):**

```{r}
left_clean <- left %>% filter(!is.na(age))
right_clean <- right %>% filter(!is.na(age))

result <- match_couples(left_clean, right_clean, vars = "age")
cat("Matched", result$info$n_matched, "pairs (excluded 1 left unit with NA)\n")
```

**2. Impute missing values:**

```{r}
# Simple mean imputation
left_imputed <- left %>%
  mutate(age = if_else(is.na(age), mean(age, na.rm = TRUE), age))

result <- match_couples(left_imputed, right, vars = "age")
cat("Matched", result$info$n_matched, "pairs (imputed 1 NA with mean)\n")
```

**3. Use preprocessing to diagnose:**

```{r}
health <- preprocess_matching_vars(
  left, right,
  vars = "age"
)
print(health)
```

---

## Installation Issues

### C++ Compilation Errors

#### Symptom

```
Error in .Call("_couplr_assignment_impl"): object not found
```

or

```
Error: package 'couplr' was built under R version X.X
```

#### Cause

C++ code not compiled properly, or object files are stale.

#### Solutions

**1. Clean and reinstall:**

```{r, eval=FALSE}
# In R:
remove.packages("couplr")
install.packages("couplr")

# Or from GitHub:
devtools::install_github("gcol33/couplr", force = TRUE)
```

**2. Clean compiled files (development):**

```powershell
# PowerShell
Remove-Item src\*.o, src\*.dll -Force
```

```bash
# Bash
rm src/*.o src/*.so
```

Then rebuild:

```{r, eval=FALSE}
devtools::clean_dll()
devtools::load_all()
```

**3. Check Rtools/compiler (Windows):**

```{r}
# Check if Rtools is properly configured
Sys.which("make")
Sys.which("g++")
```

Make sure Rtools is installed and PATH is configured correctly.

---

## Common Error Messages

### "method_used attribute is NULL"

**Cause**: Result object wasn't created properly.

**Solution**: Use `lap_solve()` instead of `assignment()` for the tidy interface.

### "Cost matrix contains non-finite values"

**Cause**: NA or NaN values in cost matrix (not Inf).

**Solution**: Replace NA with Inf for forbidden assignments, or remove rows/cols.

```{r}
cost <- matrix(c(1, NA, 3, 4), 2, 2)
cost[is.na(cost)] <- Inf  # Mark as forbidden
result <- lap_solve(cost)
```

### "All rows assigned to Inf columns"

**Cause**: Caliper is too strict; all potential matches exceed threshold.

**Solution**: Increase `max_distance` or check for overlap issues.

### "subscript out of bounds"

**Cause**: Empty left or right data frame, or ID mismatch.

**Solution**: Check data dimensions and ID column consistency.

```{r}
# Always verify data before matching
stopifnot(nrow(left) > 0, nrow(right) > 0)
```

---

## Getting Help

If you encounter an issue not covered here:

1. **Check function documentation**: `?match_couples`, `?lap_solve`

2. **Search GitHub issues**: [github.com/gcol33/couplr/issues](https://github.com/gcol33/couplr/issues)

3. **Create a minimal reproducible example**:

```{r, eval=FALSE}
# Minimal example template
library(couplr)

# Minimal data that reproduces the issue
set.seed(123)
left <- tibble(id = 1:10, x = rnorm(10))
right <- tibble(id = 1:10, x = rnorm(10))

# Code that causes the error
result <- match_couples(left, right, vars = "x")

# Expected vs actual behavior
# Expected: ...
# Actual: [error message]

# Session info
sessionInfo()
```

4. **Open an issue** with your example at [github.com/gcol33/couplr/issues/new](https://github.com/gcol33/couplr/issues/new)

---

## See Also

- `vignette("getting-started")` - Basic usage

- `vignette("matching-workflows")` - Production matching pipelines

- `vignette("algorithms")` - Algorithm selection guide

- `vignette("comparison")` - Comparison with other packages
