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 1 months ago

pharmaceuticalstables

13.71 score 230 stars 18 dependents 238 scripts 2.2k downloads

tern - Create Common TLGs Used in Clinical Trials

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

Last updated 1 months ago

clinical-trialsgraphslistingsnestoutputstables

12.62 score 79 stars 9 dependents 186 scripts 1.9k 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 1 months ago

10.34 score 27 stars 9 dependents 44 scripts 922 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 1 months ago

formatmatrixtable

10.25 score 16 stars 21 dependents 22 scripts 3.1k 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 10 months ago

clinical-trialsmodulesnestoutputsshiny

9.63 score 34 stars 136 scripts 617 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 4 months ago

cdiscdataset

8.64 score 33 stars 52 scripts 462 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 28 days ago

8.50 score 5 stars 4 dependents 109 scripts 562 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 5 months ago

graphslistingsstatistical-engineeringtables

7.36 score 6 stars 1 dependents 8 scripts 336 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 months ago

7.07 score 8 stars 1 dependents 3 scripts 332 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 22 hours ago

pharmaceuticalstables

6.80 score 1 stars 7 dependents 3 scripts 849 downloads

tern.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).

Last updated 3 months ago

graphslistingstables

6.40 score 3 stars 3 scripts 221 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 1 months ago

5.91 score 3 stars 3 scripts 374 downloads

DEploid - Deconvolute Mixed Genomes with Unknown Proportions

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

Last updated 29 days ago

deconvoluting-mixed-genomeshmmmalariamcmcparasitesphasingunknown-proportionszlibcpp

4.99 score 1 stars 39 scripts 373 downloads

DEploid.utils - 'DEploid' Data Analysis and Results Interpretation

'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>) is designed for deconvoluting mixed genomes with unknown proportions. Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. This package provides R functions to support data analysis and results interpretation.

Last updated 2 months ago

zlibcpp

2.18 score 1 dependents 241 downloads

filters - A "Snake_case" Filter System for R

Enables filtering datasets by a prior specified identifiers which correspond to saved filter expressions.

Last updated 10 months ago

1.88 score 15 scripts 470 downloads