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.

Last updated 13 days ago

pharmaceuticalstables

223 stars 13.51 score 13 dependencies 14 dependents

tern - Create Common TLGs Used in Clinical Trials

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

Last updated 12 days ago

clinical-trialsgraphslistingsnestoutputstables

76 stars 12.41 score 73 dependencies 8 dependents

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.

Last updated 7 months ago

clinical-trialsnestshinywebapp

176 stars 12.05 score 109 dependencies 5 dependents

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.

Last updated 2 days ago

analysiscdiscdataset

30 stars 11.98 score 21 dependencies 93 dependents

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.

Last updated 23 days ago

formatmatrixtable

15 stars 10.24 score 11 dependencies 17 dependents

teal.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.

Last updated 5 months ago

data-modelnest

8 stars 9.94 score 7 dependencies 8 dependents

teal.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.

Last updated 5 months ago

clinical-trialsmodulesnestoutputsshiny

32 stars 9.73 score 189 dependencies

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.

Last updated 4 months ago

24 stars 9.58 score 19 dependencies 2 dependents

teal.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.

Last updated 5 months ago

modulesnestslice

11 stars 9.27 score 96 dependencies 6 dependents

teal.reporter - Reporting Tools for 'shiny' Modules

Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.

Last updated 7 months ago

nestreportingshiny

8 stars 9.12 score 61 dependencies 6 dependents

teal.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.

Last updated 7 months ago

general-purposemodulesnestshiny

9 stars 9.03 score 148 dependencies

teal.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.

Last updated 10 months ago

nestshinywidgets

4 stars 9.01 score 67 dependencies 8 dependents

teal.code - Code Storage and Execution Class for 'teal' Applications

Introduction of 'qenv' S4 class, that facilitates code execution and reproducibility in 'teal' applications.

Last updated 9 months ago

nestshiny

11 stars 8.77 score 6 dependencies 9 dependents

teal.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.

Last updated 8 months ago

mergemodulesnesttransform

3 stars 8.15 score 79 dependencies 4 dependents

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.

Last updated 3 months ago

rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

10 stars 8.07 score 124 dependencies 1 dependents

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.

Last updated 5 months ago

clinical-trialsgraphslistingsnestreportingtables

10 stars 7.91 score 79 dependencies

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.

Last updated 3 months ago

rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

10 stars 7.89 score 124 dependencies 1 dependents

teal.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.

Last updated 7 months ago

loggingnestutilities

4 stars 7.79 score 31 dependencies 8 dependents

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.

Last updated 1 months ago

12 stars 7.64 score 22 dependencies

tern.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.

Last updated 13 days ago

graphslistingsstatistical-engineeringtables

6 stars 7.46 score 94 dependencies 1 dependents

dunlin - Preprocessing Tools for Clinical Trial Data

A collection of functions to preprocess data and organize them in a format amenable to use by chevron.

Last updated 10 months ago

3 stars 7.22 score 22 dependencies 1 dependents

tern.gee - Tables and Graphs for Generalized Estimating Equations (GEE) Model Fits

Generalized estimating equations (GEE) are a popular choice for analyzing longitudinal binary outcomes. This package provides an interface for fitting GEE, currently for logistic regression, within the 'tern' <https://cran.r-project.org/package=tern> framework (Zhu, Sabanés Bové et al., 2023) and tabulate results easily using 'rtables' <https://cran.r-project.org/package=rtables> (Becker, Waddell et al., 2023). It builds on 'geepack' <doi:10.18637/jss.v015.i02> (Højsgaard, Halekoh and Yan, 2006) for the actual GEE model fitting.

Last updated 1 months ago

8 stars 7.20 score 106 dependencies 1 dependents

random.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.

Last updated 6 months ago

cdiscdataset

30 stars 7.18 score 26 dependencies

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.

Last updated 10 months ago

multistate-modelssimulation-engine

11 stars 7.07 score 23 dependencies

nestcolor - 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.

Last updated 1 years ago

5 stars 6.98 score 30 dependencies 1 dependents

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>.

Last updated 1 years ago

16 stars 6.94 score 73 dependencies 1 dependents

teal.modules.hermes - RNA-Seq Analysis Modules to Add to a Teal Application

RNA-seq analysis teal modules based on the `hermes` package.

Last updated 8 months ago

modulesrna-seq-analysisshiny

7 stars 6.49 score 209 dependencies

goshawk - 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.

Last updated 2 months ago

plotsummarization

5 stars 6.49 score 41 dependencies 1 dependents

ggplot2.utils - Selected Utilities Extending 'ggplot2'

Selected utilities, in particular 'geoms' and 'stats' functions, extending the 'ggplot2' package. This package imports functions from 'EnvStats' <doi:10.1007/978-1-4614-8456-1> by Millard (2013), 'ggpp' <https://CRAN.R-project.org/package=ggpp> by Aphalo et al. (2023) and 'ggstats' <doi:10.5281/zenodo.10183964> by Larmarange (2023), and then exports them. This package also contains modified code from 'ggquickeda' <https://CRAN.R-project.org/package=ggquickeda> by Mouksassi et al. (2023) for Kaplan-Meier lines and ticks additions to plots. All functions are tested to make sure that they work reliably.

Last updated 3 months ago

6 stars 6.49 score 51 dependencies

teal.goshawk - Longitudinal Visualization `teal` Modules

Modules that produce web interfaces through which longitudinal visualizations can be dynamically modified and displayed. These included box plot, correlation plot, density distribution plot, line plot, scatter plot and spaghetti plot with accompanying summary. 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.

Last updated 2 months ago

modulesnest

3 stars 6.47 score 121 dependencies

sasr - '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.

Last updated 1 years ago

statistical-engineering

14 stars 5.85 score 14 dependencies

verdepcheck - 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.

Last updated 20 days ago

checkdevtoolstestingutils

6 stars 5.29 score 35 dependencies

tern.rbmi - Create interface for rbmi and tern

`RBMI` tabulation with `rtables` and `tern` packages.

Last updated 6 months ago

graphslistingstables

3 stars 5.07 score 107 dependencies

osprey - R Package to Create TLGs

Community effort to collect TLG code and create a catalogue.

Last updated 1 years ago

cataloggraphslistingsnesttables

4 stars 4.32 score 68 dependencies 1 dependents

teal.osprey - R Package of Teal Module for TLG Functions in Osprey

Community efforts to collect teal modules for TLGs defined in the osprey package. The teal modules add an encoding panel to interactively change the encoding within teal.

Last updated 1 years ago

modulesnest

5 stars 3.80 score 159 dependencies

roxy.shinylive - A Roxygen2 Extension for Shinylive

An extension for roxygen2 that allows to auto-create links to shinylive from examples in the documentation.

Last updated 3 days ago

documentationroxygen2shinyshinylivewebr

2.60 score 31 dependencies