This page displays the data specifications for the various datasets used throughout the website.
# remove reference to home directory in libPaths
.libPaths(grep("home", .libPaths(), value=TRUE, invert=TRUE))
.libPaths(grep("usr", .libPaths(), value=TRUE, invert=TRUE))
# add localLib to libPaths for locally installed packages
.libPaths(c("localLib", .libPaths()))
# will load from first filepath first, then look in .libPaths for more packages not in first path
# version matches package in first filepath, in the case of multiple instances of a package
# library(rmarkdown)
library(gridExtra)
library(grid)
library(ggplot2)
library(dplyr)
library(RxODE)
library(caTools)
theme_set(theme_bw(base_size=12))htmltools::includeMarkdown("../Data/AE_xgx.md")Adverse Event (AE) data from multiple dose administration of a range of 20 mg to 60 mg doses.
| Column name | Description |
|---|---|
| SUBJID | Subject ID |
| DAY | Day of the AE |
| time | Day of the AE in (h) |
| Dose | Dose |
| AUC | Cumulative AUC at AE day |
| Cmax | Cmax at AE day |
| Cmin | Cmin at AE day |
| Cave | Caverage at AE day |
| AUCDAY1 | AUC at day 1 |
| AUCAVE | Average AUC up to the AE day |
| AETOXGRS | AE grades (Character) |
| AETOXGRDN | AE grades (numenric) |
| AE | Binary YES/NO AE |
htmltools::includeMarkdown("../Data/AUC_Safety.md")PK parameters derived from a popPK model for multiple dose administration of a range of 20 mg to 60 mg doses to use in safety plots.
| Column name | Description |
|---|---|
| SUBJID | Subject ID |
| time_hr | Simulation time in (h) |
| AUC_day | Time in Day |
| AUC_popPK | Cumulative AUC |
| Cmax_popPK | Cmax |
| Cmin_popPK | Cmin |
| Cave_popPK | Caverage |
htmltools::includeMarkdown("../Data/dzz_PKConc.md")An example dataset with the concentration data from a project. Collected following multiple dose administration over a range of doses.
| Column name | description |
|---|---|
| SUBJID | subject ID |
| ARM | arm of study in words |
| ARMCD | arm of study in abbreviation |
| VISIT | viisit description (e.g. CYCLE 1 DAY 1) |
| PCDTC | date and time of the sample |
| TMTPT | nominal time point relative to starting dose |
| RESN | drug concentration |
| RESU | drug concentration units |
htmltools::includeMarkdown("../Data/mt12345.md")PK and PD data involving multiple types of end points from continuous to ordinal response and count data. Collected following single and multiple dose administration ranging from 0.3 mg to 800 mg for SAD, and 10mg to 50mg for MAD.
| Column name | description |
|---|---|
| ID | Unique subject ID mapped to numerical values (numeric) |
| TIME | Time from first observation in hours (numeric) |
| TIM | Time from first dose administration in hours (numeric) |
| NTIM | Nominal time in hours (numeric) |
| TAD | Time since most recent dose in hours (numeric) |
| AMT | Dosing amount (for dosing events) in mg (numeric) |
| DOSE | Randomized dose in mg (numeric) |
| LIDV | Observation on a linear scale (Observation type determined by CMT), |
| units determined by UNIT column (numeric) | |
| LNDV | Observation on a natural log scale (numeric) |
| EVID | event ID (0 = observation, 1 = dosing event) (integer) |
| MDV | Flag for missing dependent variable (0 = not missing, 1 = missing) (integer) |
| CMT | Compartment number (determines observation type) (integer) |
| CMT 1 = Dosing event | |
| CMT 2 = PK concentration | |
| CMT 13 = Intensity score (composite score) | |
| UNIT | Unit for observation (string) |
| TRTTXT | Treatment group label (string) |
| RNDDOSE | randomized dose in mg (numeric) |
| NT | nominal time as from source data (numeric) |
| CENS | censored values (0 = not censored, 1 = censored) (integer) |
htmltools::includeMarkdown("../Data/Multiple_Ascending_Dose_Dataset2.md")Model generated PK and PD data to mimic an orally administered small molecule with various endpoints from continuous to ordinal response and count data. Simulated multiple dose administration ranging from 100 mg to 1600 mg, once per day.
| Column name | description |
|---|---|
| ID | Unique subject id (numeric) |
| TIME | Time relative to first drug administration |
| NOMTIME | Nominal time |
| TIMEUNIT | unit of TIME |
| AMT | Dosing amount (for dosing events) in mg (numeric) |
| LIDV | Observation on a linear scale (Observation type determined by CMT), |
| units determined by EVENTU column (numeric) | |
| CMT | Compartment number (determines observation type) (integer) |
| CMT 1 = Dosing event | |
| CMT 2 = PK concentration | |
| CMT 3 = Continuous response data | |
| CMT 4 = Count response data | |
| CMT 5 = Ordinal response data | |
| CMT 6 = Binary response data | |
| NAME | description of event |
| EVENTU | unit for observation |
| CENS | censored values (0 = not censored, 1 = censored) (integer) |
| EVID | event ID (0 = observation, 1 = dosing event) (integer) |
| WEIGHTB | baseline bodyweight (kg) |
| SEX | sex |
| TRTACT | Treatment group label (string) |
| DOSE | randomized dose in mg (numeric) |
| PROFDAY | Day of profile |
| PROFTIME | Time within PROFDAY |
| CYCLE | count of drug administrations received |
htmltools::includeMarkdown("../Data/PPtmp_NCA.md")Example noncompartmental (NCA) parameters calculated from PK data over a range of doses.
| Column name | description |
|---|---|
| SUBJID | subject identifcation |
| ARM | arm of the study, i.e. which dose group the subject was in |
| WNLPARM | NCA parameter name |
| PPORRESN | NCA parameter value |
| PPORRESU | NCA parameter unit |
htmltools::includeMarkdown("../Data/Single_Ascending_Dose_Dataset2.md")Model generated PK data to mimic an orally administered small molecule. Simulated single dose administration ranging from 100 mg to 1600 mg.
| Column name | description |
|---|---|
| ID | Unique subject id (numeric) |
| TIME | Time relative to first drug administration |
| NOMTIME | Nominal time |
| TIMEUNIT | unit of TIME |
| AMT | Dosing amount (for dosing events) in mg (numeric) |
| LIDV | Observation on a linear scale (Observation type determined by CMT), |
| units determined by EVENTU column (numeric) | |
| CMT | Compartment number (determines observation type) (integer) |
| CMT 1 = Dosing event | |
| CMT 2 = PK concentration | |
| NAME | description of event |
| EVENTU | unit for observation |
| CENS | censored values (0 = not censored, 1 = censored) (integer) |
| EVID | event ID (0 = observation, 1 = dosing event) (integer) |
| WEIGHTB | baseline bodyweight (kg) |
| SEX | sex |
| TRTACT | Treatment group label (string) |
| DOSE | randomized dose in mg (numeric) |
htmltools::includeMarkdown("../Data/Oncology_Efficacy_Data.md")Oncology efficacy data from merged RECIST (Response Evaluation Criteria in Solid Tumor) data with modeling and dosing history datasets.
| Column name | Description |
|---|---|
| IDSHORT | Subject ID |
| BOR | Best Overall Response |
| BPCHG | Best Percent Change from Baseline |
| OR | Overall Response |
| BORNUM | Best Overall Response Value |
| psld | Percent Change in Sum of Longest Diameters |
| DOSE_ABC | Dose of Agent 1 (numeric) |
| DOSE_DEF | Dose of Agent 2 (numeric) |
| DOSE_combo | ARM of the study (character) |
| binary_BOR | Binary Best Overall Response |
| PR_rate | Partial Response rate |
| n | The number of total subjects in each dose group |
| count_cr_pr | Count the number of CR or PR subjects in each dose group |
| TIME | Evaluation time |
| COMB | Combo status |
| TIME_OR | Overall Response evaluation time |
| auc0_24 | AUC0-24 |
htmltools::includeMarkdown("../Data/Oncology_Efficacy_Dose.md")Oncology efficacy dose data, specifying patients dosing history including duration of the dose, dose amount, and dose interruptions information.
| Column name | Description |
|---|---|
| IDSHORT | Subject ID |
| DOSE | Dose amount |
| TIME | Dosing time |
| COMB | Single agent or combo |