Common Join Issues and Solutions

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Gilles Colling

2026-01-19

Overview

This vignette catalogs common join problems and shows how joinspy detects and resolves them. Each issue includes detection methods and recommended solutions.

Issue 1: Duplicate Keys

Problem: When one or both tables have duplicate keys, joins multiply rows unexpectedly.

orders <- data.frame(
  customer_id = c(1, 2, 2, 3),
  amount = c(100, 50, 75, 200)
)

addresses <- data.frame(
  customer_id = c(1, 2, 2, 3),
  address = c("NYC", "LA", "SF", "Chicago")
)

join_spy(orders, addresses, by = "customer_id")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: customer_id
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 4 Unique keys: 3 Duplicate keys: 1 NA keys: 0
#> Right table: Rows: 4 Unique keys: 3 Duplicate keys: 1 NA keys: 0
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 3
#> Keys only in left: 0
#> Keys only in right: 0
#> Match rate (left): "100%"
#> 
#> ── Issues Detected ──
#> 
#> ! Left table has 1 duplicate key(s) affecting 2 rows - may cause row multiplication
#> ! Right table has 1 duplicate key(s) affecting 2 rows - may cause row multiplication
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: 6
#> left_join: 6
#> right_join: 6
#> full_join: 6

Detection: join_spy() reports duplicate counts and expected row multiplication.

Solution: Aggregate or filter duplicates before joining.

key_duplicates(orders, by = "customer_id")
#>   customer_id amount .n_duplicates
#> 2           2     50             2
#> 3           2     75             2
key_duplicates(addresses, by = "customer_id")
#>   customer_id address .n_duplicates
#> 2           2      LA             2
#> 3           2      SF             2

Issue 2: Whitespace

Problem: Invisible leading/trailing spaces prevent matches.

sales <- data.frame(
  product = c("Widget", "Gadget ", " Gizmo"),
  units = c(10, 20, 30),
  stringsAsFactors = FALSE
)

inventory <- data.frame(
  product = c("Widget", "Gadget", "Gizmo"),
  stock = c(100, 200, 300),
  stringsAsFactors = FALSE
)

join_spy(sales, inventory, by = "product")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: product
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> Right table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 1
#> Keys only in left: 2
#> Keys only in right: 2
#> Match rate (left): "33.3%"
#> 
#> ── Issues Detected ──
#> 
#> ! Left column 'product' has 2 value(s) with leading/trailing whitespace
#> ℹ 2 near-match(es) found (e.g., 'Gadget ' ~ 'Gadget', ' Gizmo' ~ 'Gizmo') - possible typos?
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: 1
#> left_join: 3
#> right_join: 3
#> full_join: 5

Detection: join_spy() flags whitespace issues in the Issues section.

Solution: Use join_repair() or trimws().

sales_fixed <- join_repair(sales, by = "product")
#> ✔ Repaired 2 value(s)
key_check(sales_fixed, inventory, by = "product")
#> ✔ Key check passed: no issues detected

Issue 3: Case Mismatches

Problem: Keys differ only by case (“ABC” vs “abc”).

left <- data.frame(
  code = c("ABC", "def", "GHI"),
  value = 1:3,
  stringsAsFactors = FALSE
)

right <- data.frame(
  code = c("abc", "DEF", "ghi"),
  label = c("A", "D", "G"),
  stringsAsFactors = FALSE
)

join_spy(left, right, by = "code")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: code
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> Right table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 0
#> Keys only in left: 3
#> Keys only in right: 3
#> Match rate (left): "0%"
#> 
#> ── Issues Detected ──
#> 
#> ! 3 key(s) would match if case-insensitive (e.g., 'ABC' vs 'abc')
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: 0
#> left_join: 3
#> right_join: 3
#> full_join: 6

Detection: join_spy() detects case mismatches when keys would match if case-insensitive.

Solution: Standardize case with join_repair().

repaired <- join_repair(left, right, by = "code", standardize_case = "upper")
#> ✔ Repaired 3 value(s)
key_check(repaired$x, repaired$y, by = "code")
#> ✔ Key check passed: no issues detected

Issue 4: NA Keys

Problem: NA values in key columns never match (by design in R).

orders <- data.frame(
  customer_id = c(1, NA, 3, NA),
  amount = c(100, 200, 300, 400)
)

customers <- data.frame(
  customer_id = c(1, 2, 3, NA),
  name = c("Alice", "Bob", "Carol", "Unknown")
)

join_spy(orders, customers, by = "customer_id")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: customer_id
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 4 Unique keys: 2 Duplicate keys: 0 NA keys: 2
#> Right table: Rows: 4 Unique keys: 3 Duplicate keys: 0 NA keys: 1
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 2
#> Keys only in left: 0
#> Keys only in right: 1
#> Match rate (left): "100%"
#> 
#> ── Issues Detected ──
#> 
#> ! Left table has 2 NA key(s) - these will not match
#> ! Right table has 1 NA key(s) - these will not match
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: 2
#> left_join: 4
#> right_join: 4
#> full_join: 6

Detection: join_spy() reports NA counts in the Table Summary.

Solution: Handle NA values explicitly—remove them or replace with a placeholder.

# Option 1: Remove rows with NA keys
orders_clean <- orders[!is.na(orders$customer_id), ]

# Option 2: Replace NA with placeholder
orders$customer_id[is.na(orders$customer_id)] <- -999

Issue 5: No Matches

Problem: Inner join returns zero rows when you expected matches.

system_a <- data.frame(
  user_id = c("USR001", "USR002", "USR003"),
  score = c(85, 90, 78),
  stringsAsFactors = FALSE
)

system_b <- data.frame(
  user_id = c("1", "2", "3"),
  department = c("Sales", "Marketing", "Engineering"),
  stringsAsFactors = FALSE
)

report <- join_spy(system_a, system_b, by = "user_id")

Detection: Match analysis shows 0% match rate.

Solution: Create a mapping table or transform keys to a common format.

# Extract numeric part
system_a$user_num <- gsub("USR0*", "", system_a$user_id)
key_check(system_a, system_b, by = c("user_num" = "user_id"))
#> ✔ Key check passed: no issues detected

Issue 6: Many-to-Many Explosion

Problem: Both tables have duplicate keys, causing exponential row growth.

order_items <- data.frame(
  order_id = c(1, 1, 2, 2, 2),
  item = c("A", "B", "C", "D", "E")
)

order_payments <- data.frame(
  order_id = c(1, 1, 2, 2),
  payment = c("CC1", "CC2", "Cash", "Check")
)

report <- join_spy(order_items, order_payments, by = "order_id")

Detection: Expected row counts show multiplication (inner join = 10 rows from 9 source rows).

Solution: Aggregate one table first, or use check_cartesian().

check_cartesian(order_items, order_payments, by = "order_id")
#> ✔ No Cartesian product risk (expansion factor: 2x)

# Enforce cardinality to catch this
join_strict(order_items, order_payments, by = "order_id", expect = "1:m")
#> Error:
#> ! Cardinality violation: expected 1:m but found m:m
#>   Left duplicates: 2, Right duplicates: 2

Issue 7: Type Mismatches

Problem: Keys have different types (numeric vs character).

orders <- data.frame(
  product_id = c(1, 2, 3),
  quantity = c(10, 20, 30)
)

products <- data.frame(
  product_id = c("1", "2", "3"),
  name = c("Widget", "Gadget", "Gizmo"),
  stringsAsFactors = FALSE
)

join_spy(orders, products, by = "product_id")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: product_id
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> Right table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 3
#> Keys only in left: 0
#> Keys only in right: 0
#> Match rate (left): "100%"
#> 
#> ── Issues Detected ──
#> 
#> ! Type mismatch: 'product_id' is numeric, 'product_id' is character - may cause unexpected results
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: 3
#> left_join: 3
#> right_join: 3
#> full_join: 3

Detection: join_spy() flags type coercion warnings.

Solution: Convert to matching types before joining.

orders$product_id <- as.character(orders$product_id)
key_check(orders, products, by = "product_id")
#> ✔ Key check passed: no issues detected

Issue 8: Empty Strings vs NA

Problem: Empty strings ("") and NA behave differently in joins.

left <- data.frame(
  id = c("A", "", "C"),
  value = 1:3,
  stringsAsFactors = FALSE
)

right <- data.frame(
  id = c("A", "B", ""),
  label = c("Alpha", "Beta", "Empty"),
  stringsAsFactors = FALSE
)

join_spy(left, right, by = "id")
#> 
#> ── Join Diagnostic Report ──────────────────────────────────────────────────────
#> Join columns: id
#> 
#> ── Table Summary ──
#> 
#> Left table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> Right table: Rows: 3 Unique keys: 3 Duplicate keys: 0 NA keys: 0
#> 
#> ── Match Analysis ──
#> 
#> Keys in both: 2
#> Keys only in left: 1
#> Keys only in right: 1
#> Match rate (left): "66.7%"
#> 
#> ── Issues Detected ──
#> 
#> ℹ Left column 'id' has 1 empty string(s) - these match other empty strings but not NA
#> ℹ Right column 'id' has 1 empty string(s) - these match other empty strings but not NA
#> 
#> ── Expected Row Counts ──
#> 
#> inner_join: NA
#> left_join: NA
#> right_join: NA
#> full_join: NA

Detection: join_spy() warns about empty strings in keys.

Solution: Convert empty strings to NA with join_repair().

left_fixed <- join_repair(left, by = "id", empty_to_na = TRUE)
#> ✔ Repaired 1 value(s)
left_fixed$id
#> [1] "A" NA  "C"

Using join_strict() for Safety

When you know the expected cardinality, use join_strict() to fail fast:

products <- data.frame(id = 1:3, name = c("A", "B", "C"))
prices <- data.frame(id = c(1, 2, 2, 3), price = c(10, 20, 25, 30))

join_strict(products, prices, by = "id", expect = "1:1")
#> Error:
#> ! Cardinality violation: expected 1:1 but found 1:m
#>   Left duplicates: 0, Right duplicates: 1

Automatic Detection with detect_cardinality()

Let joinspy determine the actual relationship:

orders <- data.frame(id = c(1, 1, 2, 3), item = c("A", "B", "C", "D"))
customers <- data.frame(id = 1:3, name = c("Alice", "Bob", "Carol"))

detect_cardinality(orders, customers, by = "id")
#> ℹ Detected cardinality: "m:1"
#> Left duplicates: 1 key(s)

Quick Reference

Issue	Detection	Solution
Duplicates	`join_spy()`, `key_duplicates()`	Aggregate or filter
Whitespace	`join_spy()`, `key_check()`	`join_repair()`, `trimws()`
Case mismatch	`join_spy()`	`join_repair(standardize_case=)`
NA keys	`join_spy()` Table Summary	Remove or replace
No matches	`join_spy()` Match Analysis	Check key format/mapping
M:M explosion	`join_spy()`, `check_cartesian()`	Aggregate first
Type mismatch	`join_spy()`	Convert types
Empty strings	`join_spy()`	`join_repair(empty_to_na=TRUE)`

Troubleshooting Workflow

Run join_spy(x, y, by) to get a comprehensive diagnostic
Check the Issues section for detected problems
Use key_duplicates() to locate specific duplicate rows
Apply join_repair() to fix whitespace/case/encoding issues
Use join_strict() to enforce expected cardinality
After joining, use join_explain() to understand row count changes

Session Info

sessionInfo()
#> R version 4.5.2 (2025-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: Europe/Luxembourg
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] joinspy_0.7.3
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.39   R6_2.6.1        fastmap_1.2.0   xfun_0.55      
#>  [5] glue_1.8.0      cachem_1.1.0    knitr_1.51      htmltools_0.5.9
#>  [9] rmarkdown_2.30  lifecycle_1.0.5 cli_3.6.5       vctrs_0.7.0    
#> [13] sass_0.4.10     jquerylib_0.1.4 compiler_4.5.2  tools_4.5.2    
#> [17] pillar_1.11.1   evaluate_1.0.5  bslib_0.9.0     yaml_2.3.12    
#> [21] otel_0.2.0      rlang_1.1.7     jsonlite_2.0.0

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They may not be fully stable and should be used with caution. We make no claims about them.
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Common Join Issues and Solutions

Gilles Colling

2026-01-19

Overview

Issue 1: Duplicate Keys

Issue 2: Whitespace

Issue 3: Case Mismatches

Issue 4: NA Keys

Issue 5: No Matches

Issue 6: Many-to-Many Explosion

Issue 7: Type Mismatches

Issue 8: Empty Strings vs NA

Using join_strict() for Safety

Automatic Detection with detect_cardinality()

Quick Reference

Troubleshooting Workflow

See Also

Session Info