R package to create tables and plots for analysing adverse event data in clinical trials
How to install
You can install aeplots with:
# install.packages("devtools")
devtools::install_github("https://github.com/txx4986/aeplots.git")Please refer to the devtools documentation for instructions on how to set up a working development environment and install devtools depending on your platform.
Adverse Event Data
Functions available in the package:
-
aetable: Plots a table of AE summary by body system class -
aeseverity: Plots a table of AE summary by severity and body system class -
aedot: Plots a dot plot with proportions alongside treatment effect estimates with accompanying 95% confidence interval -
aestacked: Plots a stacked bar chart to present the proportions of participants with each event by arm and by maximum severity -
aebar: Plots a bar chart to present the number of events reported per participant -
aevolcano: Plots a volcano plot of treatment effect estimate against -log10(p-value) -
aemcf: Plots the mean cumulative function of AE with risk table
To see more detailed documentation of each function:
help(aetable)or
?aetableSample dataset
| id | arm | adverse_event | body_system_class | severity | date_rand | date_ae | last_visit | variable1 | variable2 |
|---|---|---|---|---|---|---|---|---|---|
| 2001 | Placebo | Cold | Respiratory | Moderate | 2015-10-28 | 2016-04-24 | 2016-08-31 | 2 | 910.785 |
| 2001 | Placebo | Anemia | Blood and lymphatic | Severe | 2015-10-28 | 2015-11-11 | 2016-08-31 | 2 | 910.785 |
| 2001 | Placebo | Anemia | Blood and lymphatic | Moderate | 2015-10-28 | 2016-05-10 | 2016-08-31 | 2 | 910.785 |
| 2001 | Placebo | Leukocytosis | Blood and lymphatic | Severe | 2015-10-28 | 2016-08-29 | 2016-08-31 | 2 | 910.785 |
| 2001 | Placebo | Nausea | Gastrointestinal | Severe | 2015-10-28 | 2016-02-23 | 2016-08-31 | 2 | 910.785 |
| 2002 | Intervention | Other | Blood and lymphatic | Moderate | 2015-08-18 | 2015-11-17 | 2016-07-29 | 2 | 736.752 |
| 2002 | Intervention | Toothache | Other | Moderate | 2015-08-18 | 2016-04-30 | 2016-07-29 | 2 | 736.752 |
| 2002 | Intervention | Accident | Other | Moderate | 2015-08-18 | 2016-03-02 | 2016-07-29 | 2 | 736.752 |
| 2004 | Placebo | Cystitis | Renal and urinary | Mild | 2015-04-26 | 2015-07-06 | 2016-08-11 | 1 | 307.814 |
| 2004 | Placebo | Vomiting | Gastrointestinal | Severe | 2015-04-26 | 2016-06-20 | 2016-08-11 | 1 | 307.814 |
| 2004 | Placebo | Vomiting | Gastrointestinal | Mild | 2015-04-26 | 2016-03-19 | 2016-08-11 | 1 | 307.814 |
| 2004 | Placebo | Vomiting | Gastrointestinal | Mild | 2015-04-26 | 2015-08-21 | 2016-08-11 | 1 | 307.814 |
| 2004 | Placebo | Anemia | Blood and lymphatic | Moderate | 2015-04-26 | 2016-07-26 | 2016-08-11 | 1 | 307.814 |
| 2004 | Placebo | Dry skin | Dermatological | Moderate | 2015-04-26 | 2016-03-26 | 2016-08-11 | 1 | 307.814 |
| 2008 | Intervention | Other | Blood and lymphatic | Moderate | 2015-12-04 | 2016-01-07 | 2016-04-28 | 4 | 380.890 |
| 2008 | Intervention | Anemia | Blood and lymphatic | Mild | 2015-12-04 | 2016-02-11 | 2016-04-28 | 4 | 380.890 |
| 2008 | Intervention | Anemia | Blood and lymphatic | Mild | 2015-12-04 | 2016-02-05 | 2016-04-28 | 4 | 380.890 |
| 2008 | Intervention | Nausea | Gastrointestinal | Moderate | 2015-12-04 | 2016-04-19 | 2016-04-28 | 4 | 380.890 |
| 2014 | Intervention | Headache | Neuruological | Mild | 2015-10-16 | 2016-01-18 | 2016-01-19 | 3 | 389.012 |
| 2014 | Intervention | Headache | Neuruological | Mild | 2015-10-16 | 2015-12-27 | 2016-01-19 | 3 | 389.012 |
Note that for each participant who did not experience any adverse events, a row should be included in the input dataset stating his/her id, arm, date_rand, last_visit and variables to be included in the model. adverse_event, body_system_class, severity and date_ae column should be specified as NA. For example:
| id | arm | adverse_event | body_system_class | severity | date_rand | date_ae | last_visit | variable1 | variable2 |
|---|---|---|---|---|---|---|---|---|---|
| 2032 | Intervention | NA | NA | NA | 2015-05-22 | NA | 2016-04-22 | 2 | 1500 |
| 2033 | Placebo | NA | NA | NA | 2015-04-20 | NA | 2016-03-20 | 1 | 777 |
Variable description for sample dataset
| Variable name | Variable description | Variable type |
|---|---|---|
| id | Participant ID | Factor/Character/Numeric |
| arm | Treatment arm of participant (2, 3 or 4 arms) | Factor/Character/Numeric |
| adverse_event | Adverse event preferred term | Character |
| body_system_class | Body system class of adverse event | Factor |
| severity | Severity of adverse event (2, 3, 4 or 5 severity levels) | Factor |
| date_rand | Randomisation date | Date |
| date_ae | Date of adverse event | Date |
| last_visit | Date of last visit | Date |
| variable | Variables to be included in model for estimation of treatment effect estimates and 95% CIs | Factor/Character/Numeric |
Laboratory Data
Functions available in the package:
-
labtable: Plots a table that summarises laboratory values with continuous outcomes for baseline and each post-baseline timepoint by treatment arm
To see more detailed documentation of each function:
help(labtable)or
?labtableSample dataset
| id | arm | visit | lab_test | base | aval | lower | upper | region | strat | time |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Placebo | Week 0 | Lymphocytes (GI/L) | 2.57 | 2.57 | 0.85 | 4.1 | Europe | < 1 year | 0 |
| 1 | Placebo | Week 4 | Lymphocytes (GI/L) | 2.57 | 1.87 | 0.85 | 4.1 | Europe | < 1 year | 4 |
| 1 | Placebo | Week 8 | Lymphocytes (GI/L) | 2.57 | 3.14 | 0.85 | 4.1 | Europe | < 1 year | 8 |
| 1 | Placebo | Week 0 | Potassium (mmol/L) | 3.89 | 3.89 | 3.50 | 5.3 | Europe | < 1 year | 0 |
| 1 | Placebo | Week 4 | Potassium (mmol/L) | 3.89 | 3.90 | 3.50 | 5.3 | Europe | < 1 year | 4 |
| 1 | Placebo | Week 8 | Potassium (mmol/L) | 3.89 | 3.89 | 3.50 | 5.3 | Europe | < 1 year | 8 |
| 2 | Intervention | Week 0 | Lymphocytes (GI/L) | 2.31 | 2.31 | 0.85 | 4.1 | Other | >=1 year | 0 |
| 2 | Intervention | Week 4 | Lymphocytes (GI/L) | 2.31 | 2.54 | 0.85 | 4.1 | Other | >=1 year | 4 |
| 2 | Intervention | Week 8 | Lymphocytes (GI/L) | 2.31 | 1.07 | 0.85 | 4.1 | Other | >=1 year | 8 |
| 2 | Intervention | Week 0 | Potassium (mmol/L) | 4.08 | 4.08 | 3.50 | 5.3 | Other | >=1 year | 0 |
| 2 | Intervention | Week 4 | Potassium (mmol/L) | 4.08 | 3.97 | 3.50 | 5.3 | Other | >=1 year | 4 |
| 2 | Intervention | Week 8 | Potassium (mmol/L) | 4.08 | 3.92 | 3.50 | 5.3 | Other | >=1 year | 8 |
| 3 | Placebo | Week 0 | Lymphocytes (GI/L) | 2.50 | 2.50 | 0.85 | 4.1 | Other | >=1 year | 0 |
| 3 | Placebo | Week 4 | Lymphocytes (GI/L) | 2.50 | 3.25 | 0.85 | 4.1 | Other | >=1 year | 4 |
| 3 | Placebo | Week 8 | Lymphocytes (GI/L) | 2.50 | 3.17 | 0.85 | 4.1 | Other | >=1 year | 8 |
| 3 | Placebo | Week 0 | Potassium (mmol/L) | 4.08 | 4.08 | 3.50 | 5.3 | Other | >=1 year | 0 |
| 3 | Placebo | Week 4 | Potassium (mmol/L) | 4.08 | 4.12 | 3.50 | 5.3 | Other | >=1 year | 4 |
| 3 | Placebo | Week 8 | Potassium (mmol/L) | 4.08 | 4.38 | 3.50 | 5.3 | Other | >=1 year | 8 |
Variable description for sample dataset
| Variable name | Variable description | Variable type |
|---|---|---|
| id | Participant ID | Factor/Character/Numeric |
| arm | Treatment arm of participant (2, 3 or 4 arms) | Factor/Character/Numeric |
| visit | Timepoint of laboratory test taken | Ordered factor |
| lab_test | Laboratory test | Factor/Character |
| base | Baseline laboratory measurement value | Numeric |
| aval | Laboratory measurement value | Numeric |
| lower | Lower limit of normal range | Numeric |
| upper | Upper limit of normal range | Numeric |
| base / strat / region / time | Variables to be included in model for estimation of treatment effect estimates and 95% CIs | Factor/Character/Numeric |