No packages match

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

pharmaceuticalstables

15.19 score 262 stars 23 dependents 900 scripts 8.5k downloads

tern - Create Common TLGs Used in Clinical Trials

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

Last updated

clinical-trialsgraphslistingsnestoutputstables

12.55 score 107 stars 12 dependents 697 scripts 2.6k downloads

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

clinical-trialsmodulesnestoutputsshiny

10.81 score 42 stars 1 dependents 297 scripts 731 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.

Last updated

clinical-trialsnestshinywebapp

10.35 score 265 stars 6 dependents 4 scripts 984 downloads

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

general-purposemodulesnestshiny

10.17 score 17 stars 175 scripts 577 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>.

Last updated

10.14 score 21 stars 4 dependents 137 scripts 827 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.

Last updated

formatmatrixtable

10.05 score 20 stars 24 dependents 84 scripts 11k 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.

Last updated

9.43 score 29 stars 13 dependents 113 scripts 1.3k downloads

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

nestreportingshiny

9.42 score 9 stars 8 dependents 30 scripts 1.1k downloads

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

nestshinywidgets

9.38 score 6 stars 10 dependents 42 scripts 1.1k downloads

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

modulesnestslice

9.14 score 13 stars 8 dependents 8 scripts 1.0k downloads

autoslider.core - Slide Automation for Tables, Listings and Figures

The normal process of creating clinical study slides is that a statistician manually type in the numbers from outputs and a separate statistician to double check the typed in numbers. This process is time consuming, resource intensive, and error prone. Automatic slide generation is a solution to address these issues. It reduces the amount of work and the required time when creating slides, and reduces the risk of errors from manually typing or copying numbers from the output to slides. It also helps users to avoid unnecessary stress when creating large amounts of slide decks in a short time window.

Last updated

8.75 score 9 stars 1 dependents 30 scripts 594 downloads

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

8.60 score 5 stars 13 dependents 238 scripts 1.4k downloads

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

data-modelnest

8.56 score 11 stars 13 dependents 74 scripts 1.1k downloads

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

cdiscdataset

8.25 score 45 stars 1 dependents 70 scripts 587 downloads

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

nestshiny

8.22 score 12 stars 15 dependents 18 scripts 1.2k downloads

teal.picks - Dataset and Variable Picker and Merge Module for 'teal' Applications

Allows users to interactively select datasets, variables, and values within 'teal' applications using a 'tidyselect'-style interface. Selected picks can be merged and transformed into analysis-ready data within 'teal' modules.

Last updated

8.00 score 4 stars 5 dependents 851 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.

Last updated

clinical-trialsgraphslistingsnestreportingtables

7.98 score 20 stars 17 scripts 883 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').

Last updated

pharmaceuticalstables

7.88 score 5 stars 11 dependents 10 scripts 1.0k 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.

Last updated

rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

7.81 score 12 stars 1 dependents 46 scripts 618 downloads

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.

Last updated

gtreproducible-researchsummary-statistics

7.36 score 15 stars 1 dependents 19 scripts 492 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.

Last updated

rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

7.33 score 12 stars 1 dependents 46 scripts

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

loggingnestutilities

7.16 score 7 stars 11 dependents 6 scripts 860 downloads

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

graphslistingsstatistical-engineeringtables

7.03 score 7 stars 2 dependents 9 scripts 659 downloads

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

6.94 score 8 stars 2 dependents 3 scripts 621 downloads

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

mergemodulesnesttransform

6.86 score 2 stars 5 dependents 623 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.

Last updated

multistate-modelssimulation-engine

6.53 score 14 stars 15 scripts 322 downloads

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

statistical-engineering

6.38 score 19 stars 30 scripts 1.7k downloads

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

modulesnest

6.13 score 3 stars 4 scripts

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

6.09 score 9 stars 17 scripts 913 downloads