`r params$title`
In clinDataReview: Clinical Data Review Tool

Introduction

library(knitr)
opts_chunk$set(
    echo = FALSE, 
    warning = FALSE, error = FALSE, message = FALSE, 
    results = "asis",
    cache = FALSE,
    fig.width = 8, fig.height = 7,
    fig.path = "./figures/",
    fig.align = 'center'
)

# print warnings where they occur (warn = 0 by default)
options(warn = 1)

library(clinDataReview)

Current data transfer: r params$currentDataTransfer

Previous data transfer (used for comparisons): r params$previousDataTransfer

This report works best with Mozilla Firefox and Google Chrome. Please do not use Internet Explorer or Edge as they do not contain all functionalities.

Please send questions, requests, suggestions and issues about these reports to r toString(params$contactPerson).

The table of contents in the side panel on the left and "<" and ">" buttons on the left and right side of the main panel can be used to navigate the report. An empty page (with a header) indicates that the data is split in subsections and you should navigate further to the subsection of interest.

For instructions on how to use the visualizations and tables please go to the next section by either clicking the ">" button on the right, or by selecting "Tutorial: Subject-level visualizations and tables" in the table of contents on the left.

# Current metadata associated with this report
metadataFile <- list.files(
    path = params$pathDataFolder, 
    pattern = "metadata.yml", 
    full.names = TRUE
)
namesInfo <- c(
    "pathSDTMs" = "Original data (SDTM) path:",
    "dateTimeSDTMcreation" = "Data creation date:"
)
if(length(metadataFile) > 0) {
  cat("The **metadata associated with this report** are:\n\n")
  getMetadata(metadataFile, namesInfo = namesInfo)
}
cat("\n\n")

# Old metadata associated with comparison data
metadataFileOldData <- list.files(
    path = params$pathDataFolderOld, 
    pattern = "metadata.yml", 
    full.names = TRUE
)
namesInfo <- c(
    "pathSDTMs" = "Original data (SDTM) path:",
    "dateTimeSDTMcreation" = "Report creation date:"
)
if(length(metadataFileOldData) > 0) {
  cat("The **metadata associated with the comparison data** are:\n\n")
  getMetadata(metadataFileOldData, namesInfo = namesInfo)
}

Tutorial: Subject-level visualizations and tables {#tutorialSubjectLevel}

Subject-level analyses (e.g. spaghetti plots, shift plots, eDISH,...) are represented with interactive visualizations and tables. Patient profiles can be opened from the visualizations as well as the tables. More detailed instructions can be found in the screenshots below.

Scatter plots and spaghetti plots

In the scatter and spaghetti plots of the reports, points are selectable and associated patient profiles (if available) are downloaded by pressing the 'P' key on your keyboard.

Records selected on the visualizations are filtered on the interactive table available at the bottom of the visualization.

Linked tables

Patients profiles are downloaded when clicking on the subject identifier hyperlink in the table (if available).

Tutorial: Summarized visualizations and tables

Summary data (e.g. counts per category) are displayed in interactive summary visualizations and tables. They follow the same principles as highlighted in the previous section.
Functionalities specific of these visualizations and tables are mentioned in the sections below.