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
14.53 score 252 stars 20 dependents 717 scripts 5.6k 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
13.35 score 103 stars 11 dependents 563 scripts 6.0k 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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10.90 score 28 stars 13 dependents 111 scripts 1.9k 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 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
8.73 score 5 stars 10 dependents 9 scripts 5.9k 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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8.31 score 5 stars 12 dependents 191 scripts 897 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 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
7.88 score 19 stars 14 scripts 273 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 downloadstern.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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6.90 score 8 stars 2 dependents 3 scripts 2.8k 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
6.73 score 14 stars 16 scripts 647 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 396 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 4 scripts 6 downloadsDEploid - 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
4.29 score 1 stars 39 scripts 163 downloadsfilters - 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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2.77 score 118 scripts 301 downloads