Practical Applications of qDEA

Joe Atwood

2026-04-07

Introduction

This vignette demonstrates practical applications of qDEA through real-world examples and workflows. We’ll cover:

Case Study 1: Hospital Efficiency Analysis

The Problem

A hospital administrator wants to evaluate the efficiency of 12 hospitals using:

The administrator suspects that 1-2 hospitals may have data quality issues or operate under exceptional circumstances.

Analysis

# Load hospital data
data(CST22)

# Examine the data
print(CST22)
#>    HOSPITAL DOCTORS NURSES OUT_PATIENTS IN_PATIENTS
#> 1         A      20    151          100          90
#> 2         B      19    131          150          50
#> 3         C      25    160          160          55
#> 4         D      27    168          180          72
#> 5         E      22    158           94          66
#> 6         F      55    255          230          90
#> 7         G      33    235          220          88
#> 8         H      31    206          152          80
#> 9         I      30    244          190         100
#> 10        J      50    268          250         100
#> 11        K      53    306          260         147
#> 12        L      38    284          250         120

# Prepare inputs and outputs
X <- as.matrix(CST22[, c("DOCTORS", "NURSES")])
Y <- as.matrix(CST22[, c("OUT_PATIENTS", "IN_PATIENTS")])

# Summary statistics
cat("Input summary:\n")
#> Input summary:
summary(X)
#>     DOCTORS          NURSES     
#>  Min.   :19.00   Min.   :131.0  
#>  1st Qu.:24.25   1st Qu.:159.5  
#>  Median :30.50   Median :220.5  
#>  Mean   :33.58   Mean   :213.8  
#>  3rd Qu.:41.00   3rd Qu.:258.2  
#>  Max.   :55.00   Max.   :306.0
cat("\nOutput summary:\n")
#> 
#> Output summary:
summary(Y)
#>   OUT_PATIENTS    IN_PATIENTS    
#>  Min.   : 94.0   Min.   : 50.00  
#>  1st Qu.:151.5   1st Qu.: 70.50  
#>  Median :185.0   Median : 89.00  
#>  Mean   :186.3   Mean   : 88.17  
#>  3rd Qu.:235.0   3rd Qu.:100.00  
#>  Max.   :260.0   Max.   :147.00

Step 1: Standard DEA Analysis

# Run standard DEA (no outliers allowed)
dea_result <- qDEA(X = X, Y = Y, 
                   orient = "in", 
                   RTS = "VRS", 
                   qout = 0,
                   getproject = TRUE)
#> [1] " on dmu 1 of 12"
#> [1] " on dmu 12 of 12"

# Create results table
results_dea <- data.frame(
  Hospital = CST22$HOSPITAL,
  Efficiency = round(dea_result$effvals, 3),
  Rank = rank(-dea_result$effvals, ties.method = "min")
)

print(results_dea)
#>    Hospital Efficiency Rank
#> 1         A      1.000    2
#> 2         B      1.000    2
#> 3         C      0.896   10
#> 4         D      1.000    1
#> 5         E      0.882   11
#> 6         F      0.939    9
#> 7         G      1.000    2
#> 8         H      0.799   12
#> 9         I      0.989    8
#> 10        J      1.000    2
#> 11        K      1.000    7
#> 12        L      1.000    6

cat("\nEfficient hospitals:", 
    sum(dea_result$effvals >= 0.99), "out of", nrow(X))
#> 
#> Efficient hospitals: 7 out of 12

Step 2: Robust qDEA Analysis

# Run qDEA allowing 10% outliers (≈1 hospital)
qdea_result <- qDEA(X = X, Y = Y,
                    orient = "in",
                    RTS = "VRS",
                    qout = 0.10,
                    getproject = TRUE)
#> [1] " on dmu 1 of 12"
#> [1] " on dmu 12 of 12"

# Compare DEA and qDEA results
results_comparison <- data.frame(
  Hospital = CST22$HOSPITAL,
  DEA_Eff = round(dea_result$effvals, 3),
  qDEA_Eff = round(qdea_result$effvalsq, 3),
  Change = round(qdea_result$effvalsq - dea_result$effvals, 3),
  DEA_Rank = rank(-dea_result$effvals, ties.method = "min"),
  qDEA_Rank = rank(-qdea_result$effvalsq, ties.method = "min")
)

print(results_comparison)
#>    Hospital DEA_Eff qDEA_Eff Change DEA_Rank qDEA_Rank
#> 1         A   1.000    1.423  0.423        2         1
#> 2         B   1.000    1.272  0.272        2         2
#> 3         C   0.896    1.000  0.104       10         7
#> 4         D   1.000    1.049  0.049        1         5
#> 5         E   0.882    0.956  0.074       11        10
#> 6         F   0.939    0.984  0.045        9         9
#> 7         G   1.000    1.001  0.001        2         6
#> 8         H   0.799    0.814  0.015       12        11
#> 9         I   0.989    1.000  0.011        8         8
#> 10        J   1.000    1.060  0.060        2         4
#> 11        K   1.000       NA     NA        7        12
#> 12        L   1.000    1.263  0.263        6         3

Step 3: Target Setting

# Calculate targets for inefficient hospitals
targets <- data.frame(
  Hospital = CST22$HOSPITAL,
  Current_Doctors = X[,1],
  Target_Doctors = round(qdea_result$PROJ_DATA$X0HATq[,1], 1),
  Doctor_Reduction = round(X[,1] - qdea_result$PROJ_DATA$X0HATq[,1], 1),
  Current_Nurses = X[,2],
  Target_Nurses = round(qdea_result$PROJ_DATA$X0HATq[,2], 1),
  Nurse_Reduction = round(X[,2] - qdea_result$PROJ_DATA$X0HATq[,2], 1),
  Efficiency = round(qdea_result$effvalsq, 3)
)

# Show only inefficient hospitals
inefficient <- targets[targets$Efficiency < 0.99, ]
print(inefficient)
#>    Hospital Current_Doctors Target_Doctors Doctor_Reduction Current_Nurses
#> 5         E              22           21.0              1.0            158
#> 6         F              55           54.1              0.9            255
#> 8         H              31           25.2              5.8            206
#> NA     <NA>              NA             NA               NA             NA
#>    Target_Nurses Nurse_Reduction Efficiency
#> 5          151.0             7.0      0.956
#> 6          250.9             4.1      0.984
#> 8          167.6            38.4      0.814
#> NA            NA              NA         NA

# Calculate total potential savings
cat("\nTotal potential reductions:\n")
#> 
#> Total potential reductions:
cat("Doctors:", sum(targets$Doctor_Reduction), "\n")
#> Doctors: NA
cat("Nurses:", sum(targets$Nurse_Reduction), "\n")
#> Nurses: NA

Step 4: Peer Benchmarks

# Identify peer hospitals for benchmarking
peers <- qdea_result$PEER_DATA$PEERSq

# Show peers for an inefficient hospital (e.g., Hospital D)
cat("Benchmark hospitals for Hospital D:\n")
#> Benchmark hospitals for Hospital D:
hospital_d_peers <- peers[peers$dmu0 == "D", ]
print(hospital_d_peers[order(-hospital_d_peers$z), ])
#> [1] dmu0 dmuz z   
#> <0 rows> (or 0-length row.names)

Management Report

# Create executive summary
cat("=" , rep("=", 50), "\n", sep="")
#> ===================================================
cat("HOSPITAL EFFICIENCY ANALYSIS - EXECUTIVE SUMMARY\n")
#> HOSPITAL EFFICIENCY ANALYSIS - EXECUTIVE SUMMARY
cat("=" , rep("=", 50), "\n", sep="")
#> ===================================================

cat("\nDATA: 12 hospitals\n")
#> 
#> DATA: 12 hospitals
cat("INPUTS: Doctors, Nurses\n")
#> INPUTS: Doctors, Nurses
cat("OUTPUTS: Outpatients, Inpatients\n")
#> OUTPUTS: Outpatients, Inpatients
cat("METHOD: qDEA with VRS, 10% outlier allowance\n")
#> METHOD: qDEA with VRS, 10% outlier allowance

cat("\n--- EFFICIENCY RESULTS ---\n")
#> 
#> --- EFFICIENCY RESULTS ---
cat("Mean efficiency:", round(mean(qdea_result$effvalsq), 3), "\n")
#> Mean efficiency: NA
cat("Median efficiency:", round(median(qdea_result$effvalsq), 3), "\n")
#> Median efficiency: NA
cat("Efficient hospitals:", sum(qdea_result$effvalsq >= 0.99), "\n")
#> Efficient hospitals: NA
cat("Inefficient hospitals:", sum(qdea_result$effvalsq < 0.99), "\n")
#> Inefficient hospitals: NA

cat("\n--- IMPROVEMENT POTENTIAL ---\n")
#> 
#> --- IMPROVEMENT POTENTIAL ---
cat("If all hospitals achieve target efficiency:\n")
#> If all hospitals achieve target efficiency:
cat("  Doctor reduction:", sum(targets$Doctor_Reduction), 
    "(", round(100*sum(targets$Doctor_Reduction)/sum(X[,1]), 1), "%)\n")
#>   Doctor reduction: NA ( NA %)
cat("  Nurse reduction:", sum(targets$Nurse_Reduction),
    "(", round(100*sum(targets$Nurse_Reduction)/sum(X[,2]), 1), "%)\n")
#>   Nurse reduction: NA ( NA %)

cat("\n--- TOP PERFORMERS ---\n")
#> 
#> --- TOP PERFORMERS ---
top3 <- head(results_comparison[order(-results_comparison$qDEA_Eff), ], 3)
print(top3[, c("Hospital", "qDEA_Eff")])
#>    Hospital qDEA_Eff
#> 1         A    1.423
#> 2         B    1.272
#> 12        L    1.263

cat("\n--- NEEDS IMPROVEMENT ---\n")
#> 
#> --- NEEDS IMPROVEMENT ---
bottom3 <- head(results_comparison[order(results_comparison$qDEA_Eff), ], 3)
print(bottom3[, c("Hospital", "qDEA_Eff")])
#>   Hospital qDEA_Eff
#> 8        H    0.814
#> 5        E    0.956
#> 6        F    0.984

Case Study 2: Retail Store Performance

The Problem

A retail chain wants to evaluate store performance with potential outliers due to: - Special events or temporary factors - Data entry errors - Unique local market conditions

# Load retail data
data(CST21)
print(CST21)
#>   STORE EMPLOYEES FLOOR_AREA SALES
#> 1     A       4.0        3.0     1
#> 2     B       7.0        3.0     1
#> 3     C       8.0        1.0     1
#> 4     D       4.0        2.0     1
#> 5     E       2.0        4.0     1
#> 6     F       5.0        2.0     1
#> 7     G       6.0        4.0     1
#> 8     H       5.5        2.5     1
#> 9     I       6.0        2.5     1

# Prepare data
X <- as.matrix(CST21[, c("EMPLOYEES", "FLOOR_AREA")])
Y <- as.matrix(CST21$SALES)

Sensitivity Analysis: How Many Outliers?

# Test different outlier proportions
qout_values <- c(0, 0.05, 0.10, 0.15, 0.20)

sensitivity_results <- data.frame(
  Store = CST21$STORE
)

for (q in qout_values) {
  result <- qDEA(X = X, Y = Y, orient = "out", RTS = "CRS", qout = q)
  col_name <- paste0("qout_", sprintf("%.2f", q))
  sensitivity_results[[col_name]] <- round(result$effvalsq, 3)
}
#> [1] " on dmu 1 of 9"
#> [1] " on dmu 9 of 9"
#> [1] " on dmu 1 of 9"
#> [1] " on dmu 9 of 9"
#> [1] " on dmu 1 of 9"
#> [1] " on dmu 9 of 9"
#> [1] " on dmu 1 of 9"
#> [1] " on dmu 9 of 9"
#> [1] " on dmu 1 of 9"
#> [1] " on dmu 9 of 9"

print(sensitivity_results)
#>   Store qout_0.00 qout_0.05 qout_0.10 qout_0.15 qout_0.20
#> 1     A        NA     1.167     1.167     1.062     1.062
#> 2     B        NA     1.583     1.583     1.438     1.438
#> 3     C        NA     1.000     1.000     0.500     0.500
#> 4     D        NA     1.000     1.000     0.875     0.875
#> 5     E        NA     1.000     1.000     0.500     0.500
#> 6     F        NA     1.083     1.083     1.000     1.000
#> 7     G        NA     1.667     1.667     1.500     1.500
#> 8     H        NA     1.292     1.292     1.156     1.156
#> 9     I        NA     1.333     1.333     1.219     1.219

# Calculate how efficiency changes with qout
sensitivity_results$Range <- apply(
  sensitivity_results[, -1], 1, 
  function(x) max(x) - min(x)
)

cat("\nStores most sensitive to outlier allowance:\n")
#> 
#> Stores most sensitive to outlier allowance:
print(sensitivity_results[order(-sensitivity_results$Range), 
                          c("Store", "Range")])
#>   Store Range
#> 1     A    NA
#> 2     B    NA
#> 3     C    NA
#> 4     D    NA
#> 5     E    NA
#> 6     F    NA
#> 7     G    NA
#> 8     H    NA
#> 9     I    NA

Case Study 3: Dealing with Outliers

Identifying Outliers

data(CST11)
X <- as.matrix(CST11$EMPLOYEES)
Y <- as.matrix(CST11$SALES_EJOR)

# Run with very restrictive outlier allowance
strict <- qDEA(X = X, Y = Y, orient = "out", RTS = "CRS", qout = 0.01)
#> [1] " on dmu 1 of 8"
#> [1] " on dmu 8 of 8"

# Run with moderate outlier allowance  
moderate <- qDEA(X = X, Y = Y, orient = "out", RTS = "CRS", qout = 0.15)
#> [1] " on dmu 1 of 8"
#> [1] " on dmu 8 of 8"

# Stores with big efficiency changes are likely outliers
outlier_check <- data.frame(
  Store = CST11$STORE,
  Strict = round(strict$effvalsq, 3),
  Moderate = round(moderate$effvalsq, 3),
  Change = round(moderate$effvalsq - strict$effvalsq, 3)
)

print(outlier_check)
#>   Store Strict Moderate Change
#> 1     A  2.667    1.600 -1.067
#> 2     B  1.000    0.600 -0.400
#> 3     C  2.000    1.200 -0.800
#> 4     D  1.778    1.067 -0.711
#> 5     E  1.667    1.000 -0.667
#> 6     F  3.333    2.000 -1.333
#> 7     G  2.667    1.600 -1.067
#> 8     H  2.133    1.280 -0.853

# Flag potential outliers (large efficiency changes)
outlier_check$Potential_Outlier <- outlier_check$Change > 0.10

cat("\nPotential outliers identified:\n")
#> 
#> Potential outliers identified:
print(outlier_check[outlier_check$Potential_Outlier, ])
#> [1] Store             Strict            Moderate          Change           
#> [5] Potential_Outlier
#> <0 rows> (or 0-length row.names)

Impact of Outlier Removal

# Compare DEA vs qDEA to see impact of outlier allowance
impact <- data.frame(
  Store = CST11$STORE,
  DEA = round(strict$effvals, 3),
  qDEA = round(moderate$effvalsq, 3),
  Difference = round(moderate$effvalsq - strict$effvals, 3)
)

print(impact)
#>   Store   DEA  qDEA Difference
#> 1     A 2.667 1.600     -1.067
#> 2     B 1.000 0.600     -0.400
#> 3     C 2.000 1.200     -0.800
#> 4     D 1.778 1.067     -0.711
#> 5     E 1.667 1.000     -0.667
#> 6     F 3.333 2.000     -1.333
#> 7     G 2.667 1.600     -1.067
#> 8     H 2.133 1.280     -0.853

cat("\nMean efficiency:\n")
#> 
#> Mean efficiency:
cat("DEA (no outliers):", round(mean(strict$effvals), 3), "\n")
#> DEA (no outliers): 2.156
cat("qDEA (15% outliers):", round(mean(moderate$effvalsq), 3), "\n")
#> qDEA (15% outliers): 1.293

Workflow: Complete Analysis Template

Here’s a complete workflow you can adapt:

# ==========================================
# COMPLETE qDEA ANALYSIS WORKFLOW
# ==========================================

# 1. Load and examine data
data(CST22)  # Replace with your data
X <- as.matrix(CST22[, c("DOCTORS", "NURSES")])
Y <- as.matrix(CST22[, c("OUT_PATIENTS", "IN_PATIENTS")])

# Check data quality
summary(X)
summary(Y)
# Look for: missing values, extreme values, data entry errors

# 2. Run standard DEA baseline
baseline <- qDEA(X = X, Y = Y, 
                 orient = "in",    # Choose: in, out, inout
                 RTS = "VRS",      # Choose: CRS, VRS, DRS, IRS
                 qout = 0)

# 3. Run robust qDEA
robust <- qDEA(X = X, Y = Y,
               orient = "in",
               RTS = "VRS",
               qout = 0.10,       # Adjust based on expected outliers
               nqiter = 3,        # Iterative refinement
               getproject = TRUE) # Get targets

# 4. Compare results
comparison <- data.frame(
  Unit = rownames(X),
  DEA = round(baseline$effvals, 3),
  qDEA = round(robust$effvalsq, 3),
  Change = round(robust$effvalsq - baseline$effvals, 3)
)

# 5. Identify outliers
potential_outliers <- comparison$Unit[abs(comparison$Change) > 0.10]

# 6. Calculate targets
targets <- data.frame(
  Unit = rownames(X),
  Efficiency = round(robust$effvalsq, 3),
  Current_Input1 = X[,1],
  Target_Input1 = round(robust$PROJ_DATA$X0HATq[,1], 2),
  Current_Input2 = X[,2],
  Target_Input2 = round(robust$PROJ_DATA$X0HATq[,2], 2)
)

# 7. Generate report
# Export to CSV
write.csv(comparison, "efficiency_comparison.csv", row.names = FALSE)
write.csv(targets, "efficiency_targets.csv", row.names = FALSE)

# 8. Optional: Bootstrap for confidence intervals
boot_result <- qDEA(X = X, Y = Y,
                    orient = "in",
                    RTS = "VRS",
                    qout = 0.10,
                    nboot = 1000,
                    seedval = 12345)

boot_ci <- data.frame(
  Unit = rownames(X),
  Efficiency = round(boot_result$effvalsq, 3),
  BC_Efficiency = round(boot_result$BOOT_DATA$effvalsq.bc, 3),
  Bias = round(boot_result$effvalsq - boot_result$BOOT_DATA$effvalsq.bc, 3)
)

Best Practices Summary

1. Data Preparation

✓ Check for missing values
✓ Verify all values are positive
✓ Look for extreme outliers or data entry errors
✓ Ensure comparable units (scale if necessary)
✓ Document data sources and definitions

2. Model Selection

✓ Choose orientation based on managerial control
✓ Use VRS unless scale efficiency is of interest
✓ Start with qout = 0.10 (10% outliers)
✓ Test sensitivity to qout selection

3. Interpretation

✓ Efficiency scores are relative, not absolute
✓ Compare units within same analysis only
✓ Consider context (outliers may be legitimate)
✓ Verify targets are achievable
✓ Use peers for benchmarking

4. Reporting

✓ Document methodology clearly
✓ Report both DEA and qDEA results
✓ Explain outlier allowance rationale
✓ Provide actionable recommendations
✓ Include sensitivity analysis

5. Common Mistakes to Avoid

✗ Comparing efficiency across different analyses
✗ Using CRS when scale varies significantly
✗ Setting qout too high (> 0.25)
✗ Ignoring data quality issues
✗ Over-interpreting small efficiency differences

Exporting Results

To CSV

# Prepare comprehensive results
results_export <- data.frame(
  Unit = CST22$HOSPITAL,
  Input1 = X[,1],
  Input2 = X[,2],
  Output1 = Y[,1],
  Output2 = Y[,2],
  DEA_Efficiency = round(baseline$effvals, 4),
  qDEA_Efficiency = round(robust$effvalsq, 4),
  Target_Input1 = round(robust$PROJ_DATA$X0HATq[,1], 2),
  Target_Input2 = round(robust$PROJ_DATA$X0HATq[,2], 2)
)

# Export
write.csv(results_export, "qDEA_results.csv", row.names = FALSE)

To Excel (requires openxlsx package)

library(openxlsx)

# Create workbook
wb <- createWorkbook()

# Add worksheets
addWorksheet(wb, "Efficiency Scores")
addWorksheet(wb, "Targets")
addWorksheet(wb, "Peers")

# Write data
writeData(wb, "Efficiency Scores", comparison)
writeData(wb, "Targets", targets)
writeData(wb, "Peers", robust$PEER_DATA$PEERSq)

# Save
saveWorkbook(wb, "qDEA_analysis.xlsx", overwrite = TRUE)

Visualization Examples

Efficiency Distribution

data(CST22)
X <- as.matrix(CST22[, c("DOCTORS", "NURSES")])
Y <- as.matrix(CST22[, c("OUT_PATIENTS", "IN_PATIENTS")])

result <- qDEA(X = X, Y = Y, orient = "in", RTS = "VRS", qout = 0.10)
#> [1] " on dmu 1 of 12"
#> [1] " on dmu 12 of 12"

# Histogram
hist(result$effvalsq, 
     breaks = 10,
     col = "lightblue",
     border = "white",
     main = "Distribution of Efficiency Scores",
     xlab = "Efficiency",
     ylab = "Frequency")
abline(v = mean(result$effvalsq), col = "red", lwd = 2, lty = 2)
legend("topleft", 
       legend = paste("Mean =", round(mean(result$effvalsq), 3)),
       col = "red", lty = 2, lwd = 2)

Efficiency Comparison

# Compare DEA and qDEA
dea <- qDEA(X = X, Y = Y, orient = "in", RTS = "VRS", qout = 0)
#> [1] " on dmu 1 of 12"
#> [1] " on dmu 12 of 12"
qdea <- qDEA(X = X, Y = Y, orient = "in", RTS = "VRS", qout = 0.10)
#> [1] " on dmu 1 of 12"
#> [1] " on dmu 12 of 12"

# Scatter plot
plot(dea$effvals, qdea$effvalsq,
     xlim = c(0.4, 1.2), ylim = c(0.4, 1.2),
     xlab = "DEA Efficiency",
     ylab = "qDEA Efficiency",
     main = "DEA vs qDEA Efficiency Scores",
     pch = 19, col = "blue")
abline(0, 1, col = "red", lty = 2)  # 45-degree line
text(dea$effvals, qdea$effvalsq, 
     labels = CST22$HOSPITAL, 
     pos = 3, cex = 0.8)
grid()

Conclusion

This vignette has demonstrated practical applications of qDEA including:

For more details on the underlying methodology, see the main package vignette.

Further Reading

Contact: