pk_summarize {apmx}

Produce summary tables for a PK(PD) dataset

Description

Summarize BLQ distributions, categorical covariates, and continuous covariates in three tables. Outputs are default .csv files, but can also be .docx and/or .pptx Tables are default stratified by study, but can be stratified by any variable requested by the user.

Usage

pk_summarize(
  df,
  dir = NA,
  strat.by = "NSTUDYC",
  ignore.c = TRUE,
  na = -999,
  docx = FALSE,
  pptx = FALSE,
  docx.font = "Times New Roman",
  docx.size = 9,
  docx.template = NULL,
  pptx.template = NULL,
  pptx.font = "Times New Roman",
  pptx.size = 12,
  docx.orientation = "portrait",
  ignore.request = c()
)

Arguments

df

dataset produced by pk_build().

dir

filepath for output directory.

strat.by

vector of variables names to stratify the summary tables.

ignore.c

ignores records flagged in the C column when TRUE.

na

numeric value to be interpreted as NA or missing.

docx

creates summary tables as a Word document when TRUE.

pptx

creates summary tables as a PowerPoint document when TRUE.

docx.font

font for the summary tables in the Word document.

docx.size

font size for the summary tables in the Word document.

docx.template

filepath for template .docx file. When NULL, the summary tables print to a blank document.

pptx.template

filepath for template .pptx file. When NULL, the summary tables print to a blank slide.

pptx.font

font for the summary tables in the PowerPoint document.

pptx.size

font size for the summary tables in the PowerPoint document.

docx.orientation

orientation of .docx files.

ignore.request

vector of additional logical expressions to filter the datase prior to summary.

Value

summary tables as .csv, .docx, and .pptx files

Examples

## Simple ex domain with 1 subject and 1 dose
ex <- data.frame(STUDYID = "ABC101",
                 USUBJID = "ABC101-001",
                 EXSTDTC = "2000-01-01 10:00:00",
                 EXSTDY = 1,
                 EXTPTNUM = 0,
                 EXDOSE = 100,
                 CMT = 1,
                 EXTRT = "ABC",
                 EXDOSU = "mg",
                 VISIT = "Day 1",
                 EXTPT = "Dose",
                 EXDOSFRQ = "Once",
                 EXROUTE = "Oral")

## Simple pc domain with 1 subject and 3 observations
pc <- data.frame(USUBJID = "ABC101-001",
                 PCDTC = c("2000-01-01 09:40:00",
                           "2000-01-01 10:29:00",
                           "2000-01-01 12:05:00"),
                 PCDY = 1,
                 PCTPTNUM = c(0, ##Units of hours
                              0.021,
                              0.083),
                 PCSTRESN = c(NA,
                              469,
                              870),
                 PCLLOQ = 25,
                 CMT = 2,
                 VISIT = "Day 1",
                 PCTPT = c("Pre-dose",
                           "30-min post-dose",
                           "2-hr post-dose"),
                 PCTEST = "ABC",
                 PCSTRESU = "ug/mL")

## Create with pk_build()
df <- pk_build(ex, pc)


## Generate summary statistics with pk_summarize()
pk_summarize(df)