Report the potential adverse events for drugs from contingency table

Usage

report_drug_AE_pairs(
  contin_table,
  contin_table_signal,
  along_rows = "AE",
  along_cols = "Drug"
)

Arguments

contin_table: A data matrix of an \(I\) x \(J\) contingency table with row (adverse event) and column (drug or vaccine) names. Please first check the input contingency table using the function check_and_fix_contin_table().
contin_table_signal: A data matrix with the same dimension and row and column names as contin_table, with entries either 1 (indicating signal) or 0 (indicating non-signal). This data matrix can be obtained via applying the function mddc_boxplot or mddc_mc.
along_rows: Specifies the content along the rows of the contin_table (e.g. AE or Drug).
along_cols: Specifies the content along the columns of the contin_table (e.g. AE or Drug).

Value

A data frame with five variables:

drug the drug name.
AE the potential adverse event for the drug or vaccine.
observed_num the observed count of the (drug or vaccine, AE) pair.
expected_num the expected count of the (drug or vaccine , AE) pair.
std_pearson_res the value of the standardized Pearson residual.

Examples

# load statin49 data
data(statin49)

# run mddc boxplot method
test1 <- mddc_boxplot(statin49)

# get the signals from step 2
contin_table_signal <- test1$boxplot_signal

# get the signals from step 5
contin_table_signal_corr <- test1$corr_signal_pval < 0.05

# identify the (drug, AE) signals for step 2
result_1 <- report_drug_AE_pairs(
  contin_table = statin49,
  contin_table_signal = contin_table_signal
)
result_1
#>            drug                                        AE observed_num
#> 1  Atorvastatin                            Rhabdomyolysis         2041
#> 2  Atorvastatin                                   Myalgia         5362
#> 3  Atorvastatin                                  Myopathy          849
#> 4  Atorvastatin                      Necrotising Myositis          279
#> 5  Atorvastatin    Blood Creatine Phosphokinase Increased         1175
#> 6   Fluvastatin                                   Myalgia          341
#> 7   Fluvastatin                                  Myopathy           64
#> 8   Fluvastatin    Blood Creatine Phosphokinase Increased          125
#> 9    Lovastatin                                  Myopathy           45
#> 10  Pravastatin                            Rhabdomyolysis          163
#> 11  Pravastatin                            Muscle Rupture           61
#> 12  Pravastatin                                   Myalgia          939
#> 13  Pravastatin                                  Myopathy          145
#> 14  Pravastatin    Blood Creatine Phosphokinase Increased          200
#> 15 Rosuvastatin                            Rhabdomyolysis          936
#> 16 Rosuvastatin                           Muscle Disorder          191
#> 17 Rosuvastatin                         Muscular Weakness          808
#> 18 Rosuvastatin                                   Myalgia         2757
#> 19 Rosuvastatin                                  Myopathy          377
#> 20 Rosuvastatin    Blood Creatine Phosphokinase Increased          562
#> 21 Rosuvastatin Blood Creatine Phosphokinase Mm Increased            9
#> 22  Simvastatin                            Rhabdomyolysis         1376
#> 23  Simvastatin                         Muscular Weakness          859
#> 24  Simvastatin                                   Myalgia         3216
#> 25  Simvastatin                                  Myopathy          544
#> 26  Simvastatin                      Necrotising Myositis           52
#> 27  Simvastatin    Blood Creatine Phosphokinase Increased          768
#> 28        Other                                  Other AE     61703817
#>     expected_num std_pearson_res
#> 1       112.0567        182.5555
#> 2        483.119        222.5852
#> 3        26.9011        158.7594
#> 4          1.916        200.4873
#> 5        82.2769        120.6793
#> 6        14.0537         87.3237
#> 7         0.7825         71.4713
#> 8         2.3934         79.2713
#> 9         0.4402         67.1676
#> 10       12.7651         42.0686
#> 11        1.2801          52.795
#> 12       55.0353        119.3226
#> 13        3.0645         81.0995
#> 14        9.3727         62.2901
#> 15       69.5139        104.0555
#> 16        15.174          45.183
#> 17      219.6389         39.7736
#> 18      299.7007        142.2533
#> 19        16.688         88.2922
#> 20       51.0401          71.604
#> 21        0.0478         40.9642
#> 22       48.5064        190.7859
#> 23      153.2629         57.0958
#> 24      209.1296        208.3192
#> 25       11.6448        156.1188
#> 26        0.8294         56.2256
#> 27       35.6155        122.8288
#> 28 61678483.2716        228.1052

# identify the (drug, AE) signals for step 5
result_2 <- report_drug_AE_pairs(
  contin_table = statin49,
  contin_table_signal = contin_table_signal_corr
)
result_2
#>            drug                                        AE observed_num
#> 1  Atorvastatin                      Necrotising Myositis          279
#> 2   Fluvastatin                            Muscle Rupture           25
#> 3   Fluvastatin                Musculoskeletal Discomfort           18
#> 4   Fluvastatin                             Myoglobinuria            4
#> 5    Lovastatin                Musculoskeletal Discomfort           15
#> 6   Pravastatin                            Muscle Rupture           61
#> 7  Rosuvastatin                           Muscle Disorder          191
#> 8  Rosuvastatin                         Muscular Weakness          808
#> 9  Rosuvastatin Blood Creatine Phosphokinase Mm Increased            9
#> 10  Simvastatin                         Muscular Weakness          859
#> 11  Simvastatin                      Necrotising Myositis           52
#>    expected_num std_pearson_res
#> 1         1.916        200.4873
#> 2        0.3269         43.1584
#> 3        1.8315         11.9498
#> 4        0.0302          22.827
#> 5        1.0302         13.7657
#> 6        1.2801          52.795
#> 7        15.174          45.183
#> 8      219.6389         39.7736
#> 9        0.0478         40.9642
#> 10     153.2629         57.0958
#> 11       0.8294         56.2256