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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

13.94 score 260 stars 20 dependents 654 scripts 7.3k 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

12.55 score 107 stars 12 dependents 697 scripts 2.6k 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

9.89 score 20 stars 23 dependents 86 scripts 7.1k 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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9.71 score 29 stars 12 dependents 117 scripts 1.2k 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.

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8.41 score 5 stars 12 dependents 230 scripts 1.0k 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.

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cdiscdataset

8.27 score 45 stars 1 dependents 73 scripts 515 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

7.78 score 5 stars 9 dependents 10 scripts 904 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

7.78 score 20 stars 14 scripts 1.1k 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.

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7.69 score 9 stars 1 dependents 30 scripts 728 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.

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gtreproducible-researchsummary-statistics

7.31 score 15 stars 1 dependents 17 scripts 599 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.

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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.

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6.94 score 8 stars 2 dependents 3 scripts 621 downloads

cardinalfda - FDA Safety Tables and Figures

Provides implementations of safety tables and figures recommended by the FDA (U.S. Food and Drug Administration) for clinical trial reporting. Functions generate standard outputs for adverse events, laboratory abnormalities, vital signs, exposure, and other safety domains following the FDA's Safety Reporting guidelines. Outputs are built on the 'gtsummary', 'cards', and 'cardx' frameworks, enabling reproducible and submission-ready clinical trial safety summaries.

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6.87 score 60 stars 5 scripts 337 downloads

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.

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6.29 score 5 stars 1 dependents 521 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).

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graphslistingstables

4.45 score 4 stars 5 scripts 11 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.

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deconvoluting-mixed-genomeshmmmalariamcmcparasitesphasingunknown-proportionszlibcpp

4.32 score 1 stars 42 scripts 365 downloads

filters.trade - A Filter System for Selecting Trading Instruments

Enables filtering datasets of tradable instruments by prior specified identifiers which correspond to saved filter expressions. A filter is a named expression bound to a target dataset, stored once in a package level registry, and later applied to select trading codes such as tickers or symbols out of a universe, price or signal dataset. The design follows the `filters` package, replacing the clinical study dataset convention with a trading instrument convention.

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3.18 score 228 downloads

autoslider.trade - Slide Automation for Trading Tables, Listings and Figures

A downstream package of 'autoslider.core' that produces tables, listings and figures for finance trading, in the same style as 'autoslider'. Where 'autoslider.core' automates clinical study outputs, this package automates trading outputs from price and trade data: performance tables, equity curves and trade listings.

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3.18 score 39 downloads

filters - A "Snake_case" Filter System for R

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

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3.00 score 200 scripts 449 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.

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zlibcpp

2.18 score 1 dependents 281 downloads