rtables - Reporting Tables
Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.
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pharmaceuticalstables
14.52 score 253 stars 19 dependents 733 scripts 6.6k downloads
teal - Exploratory Web Apps for Analyzing Clinical Trials Data
A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.
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clinical-trialsnestshinywebapp
12.86 score 260 stars 6 dependents 316 scripts 1.2k downloads
tern - Create Common TLGs Used in Clinical Trials
Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.
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clinical-trialsgraphslistingsnestoutputstables
12.73 score 103 stars 11 dependents 606 scripts 1.6k downloads
cards - Analysis Results Data
Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.
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analysiscdiscdataset
12.41 score 58 stars 50 dependents 200 scripts 59k downloads
cardx - Extra Analysis Results Data Utilities
Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.
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11.63 score 23 stars 45 dependents 150 scripts 53k downloads
rlistings - Clinical Trial Style Data Readout Listings
Listings are often part of the submission of clinical trial data in regulatory settings. We provide a framework for the specific formatting features often used when displaying large datasets in that context.
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10.87 score 28 stars 13 dependents 114 scripts 2.0k downloads
formatters - ASCII Formatting for Values and Tables
We provide a framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.
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formatmatrixtable
10.71 score 19 stars 23 dependents 80 scripts 7.4k downloadsteal.modules.clinical - 'teal' Modules for Standard Clinical Outputs
Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.
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clinical-trialsmodulesnestoutputsshiny
10.67 score 42 stars 1 dependents 263 scripts 551 downloadsteal.modules.general - General Modules for 'teal' Applications
Prebuilt 'shiny' modules containing tools for viewing data, visualizing data, understanding missing and outlier values within your data and performing simple data analysis. This extends 'teal' framework that supports reproducible research and analysis.
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general-purposemodulesnestshiny
10.08 score 16 stars 196 scripts 434 downloadsteal.reporter - Reporting Tools for 'shiny' Modules
Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.
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nestreportingshiny
9.83 score 9 stars 7 dependents 30 scripts 1.7k downloadsteal.data - Data Model for 'teal' Applications
Provides a 'teal_data' class as a unified data model for 'teal' applications focusing on reproducibility and relational data.
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data-modelnest
9.78 score 11 stars 11 dependents 73 scripts 1.3k downloadsteal.widgets - 'shiny' Widgets for 'teal' Applications
Collection of 'shiny' widgets to support 'teal' applications. Enables the manipulation of application layout and plot or table settings.
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nestshinywidgets
9.62 score 6 stars 9 dependents 43 scripts 1.7k downloadsteal.slice - Filter Module for 'teal' Applications
Data filtering module for 'teal' applications. Allows for interactive filtering of data stored in 'data.frame' and 'MultiAssayExperiment' objects. Also displays filtered and unfiltered observation counts.
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modulesnestslice
9.47 score 12 stars 7 dependents 8 scripts 2.1k downloadsteal.code - Code Storage and Execution Class for 'teal' Applications
Introduction of 'qenv' S4 class, that facilitates code execution and reproducibility in 'teal' applications.
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nestshiny
9.19 score 12 stars 11 dependents 17 scripts 1.4k downloads
rbmi - Reference Based Multiple Imputation
Implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular, this package supports deterministic conditional mean imputation and jackknifing as described in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
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8.75 score 21 stars 4 dependents 101 scripts 548 downloadsnestcolor - Colors for NEST Graphs
Clinical reporting figures require to use consistent colors and configurations. As a part of the Roche open-source clinical reporting project, namely the NEST project, the 'nestcolor' package specifies the color code and default theme with specifying 'ggplot2' theme parameters. Users can easily customize color and theme settings before using the reset of NEST packages to ensure consistent settings in both static and interactive output at the downstream.
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8.44 score 5 stars 12 dependents 214 scripts 1.2k downloadsrandom.cdisc.data - Create Random ADaM Datasets
A set of functions to create random Analysis Data Model (ADaM) datasets and cached dataset. ADaM dataset specifications are described by the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model Team.
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cdiscdataset
8.27 score 45 stars 1 dependents 71 scripts 367 downloadsteal.transform - Functions for Extracting and Merging Data in the 'teal' Framework
A standardized user interface for column selection, that facilitates dataset merging in 'teal' framework.
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mergemodulesnesttransform
8.23 score 2 stars 5 dependents 20 scripts 526 downloads
rtables.officer - Exporting Tools for 'rtables'
Designed to create and display complex tables with R, the 'rtables' R package allows cells in an 'rtables' object to contain any high-dimensional data structure, which can then be displayed with cell-specific formatting instructions. Additionally, the 'rtables.officer' package supports export formats related to the Microsoft Office software suite, including Microsoft Word ('docx') and Microsoft PowerPoint ('pptx').
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pharmaceuticalstables
8.13 score 5 stars 9 dependents 10 scripts 1.7k downloadsteal.logger - Logging Setup for the 'teal' Family of Packages
Utilizing the 'logger' framework to record events within a package, specific to 'teal' family of packages. Supports logging namespaces, hierarchical logging, various log destinations, vectorization, and more.
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loggingnestutilities
7.98 score 7 stars 10 dependents 5 scripts 673 downloads
chevron - Standard TLGs for Clinical Trials Reporting
Provide standard tables, listings, and graphs (TLGs) libraries used in clinical trials. This package implements a structure to reformat the data with 'dunlin', create reporting tables using 'rtables' and 'tern' with standardized input arguments to enable quick generation of standard outputs. In addition, it also provides comprehensive data checks and script generation functionality.
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clinical-trialsgraphslistingsnestreportingtables
7.82 score 19 stars 17 scripts 272 downloads
hermes - Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
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rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
7.80 score 12 stars 1 dependents 45 scripts 456 downloadsdunlin - Preprocessing Tools for Clinical Trial Data
A collection of functions to preprocess data and organize them in a format amenable to use by chevron.
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7.34 score 5 stars 1 dependents 56 scripts 186 downloads
hermes - Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
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rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
7.32 score 12 stars 1 dependents 45 scripts
crane - Supplements the 'gtsummary' Package for Pharmaceutical Reporting
Tables summarizing clinical trial results are often complex and require detailed tailoring prior to submission to a health authority. The 'crane' package supplements the functionality of the 'gtsummary' package for creating these often highly bespoke tables in the pharmaceutical industry.
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gtreproducible-researchsummary-statistics
6.73 score 14 stars 16 scripts 647 downloadssasr - 'SAS' Interface
Provides a 'SAS' interface, through 'SASPy'(<https://sassoftware.github.io/saspy/>) and 'reticulate'(<https://rstudio.github.io/reticulate/>). This package helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS' servers, retrieve execution results and log, and exchange datasets between 'SAS' and 'R'. It also helps you to install 'SASPy' and create a configuration file for the connection. Please review the 'SASPy' license file as instructed so that you comply with its separate and independent license.
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statistical-engineering
6.69 score 19 stars 30 scripts 3.4k downloadstern.mmrm - Tables and Graphs for Mixed Models for Repeated Measures (MMRM)
Mixed models for repeated measures (MMRM) are a popular choice for analyzing longitudinal continuous outcomes in randomized clinical trials and beyond; see for example Cnaan, Laird and Slasor (1997) <doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>. This package provides an interface for fitting MMRM within the 'tern' <https://cran.r-project.org/package=tern> framework by Zhu et al. (2023) and tabulate results easily using 'rtables' <https://cran.r-project.org/package=rtables> by Becker et al. (2023). It builds on 'mmrm' <https://cran.r-project.org/package=mmrm> by Sabanés Bové et al. (2023) for the actual MMRM computations.
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graphslistingsstatistical-engineeringtables
6.55 score 7 stars 2 dependents 9 scripts 493 downloads
simIDM - Simulating Oncology Trials using an Illness-Death Model
Based on the illness-death model a large number of clinical trials with oncology endpoints progression-free survival (PFS) and overall survival (OS) can be simulated, see Meller, Beyersmann and Rufibach (2019) <doi:10.1002/sim.8295>. The simulation set-up allows for random and event-driven censoring, an arbitrary number of treatment arms, staggered study entry and drop-out. Exponentially, Weibull and piecewise exponentially distributed survival times can be generated. The correlation between PFS and OS can be calculated.
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multistate-modelssimulation-engine
6.33 score 14 stars 11 scripts 200 downloads
teal.modules.hermes - RNA-Seq Analysis Modules to Add to a Teal Application
RNA-seq analysis teal modules based on the `hermes` package.
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modulesrna-seq-analysisshiny
5.57 score 7 stars 33 scriptsgoshawk - Longitudinal Visualization Functions
Functions that plot and summarize biomarkers/labs of interest. Visualizations include: box plot, correlation plot, density distribution, line plot and spaghetti plot. Data are expected in ADaM structure. Requires analysis subject level (ADSL) and analysis laboratory (ADLB) data sets. Beyond core variables, Limit of Quantification flag variable (LOQFL) is expected with levels 'Y', 'N' or NA.
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plotsummarization
5.35 score 5 stars 1 dependentsosprey - R Package to Create TLGs
Community effort to collect TLG code and create a catalogue.
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cataloggraphslistingsnesttables
4.72 score 5 stars 1 dependents 1 scriptsroxy.shinylive - A 'roxygen2' Extension for 'Shinylive'
An extension for 'roxygen2' to embed 'Shinylive' applications in the package documentation.
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documentationroxygen2shinyshinylivewebr
4.51 score 13 stars 1 scripts 434 downloadstern.rbmi - Create Interface for 'RBMI' and 'tern'
'RBMI' implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). This package provides an interface for 'RBMI' uses the 'tern' <https://cran.r-project.org/package=tern> framework by Zhu et al. (2023) and tabulate results easily using 'rtables' <https://cran.r-project.org/package=rtables> by Becker et al. (2023).
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graphslistingstables
4.45 score 4 stars 5 scripts 13 downloadsverdepcheck - Check Package using Various Versions of Dependencies
Derive package dependencies from DESCRIPTION file using various strategies and run "R CMD CHECK" to validate package compatibility.
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checkdevtoolstestingutils
4.30 score 8 stars 1 scripts