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admiral - ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

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adamcdiscclinical-trialsopen-sourcepharmaverse

14.65 score 305 stars 4 dependents 996 scripts 3.3k downloads

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

mmrm - Mixed Models for Repeated Measures

Mixed models for repeated measures (MMRM) are a popular choice for analyzing longitudinal continuous outcomes in randomized clinical trials and beyond; see Cnaan, Laird and Slasor (1997) <doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E> for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso (2008) <doi:10.1177/009286150804200402> for a review. This package implements MMRM based on the marginal linear model without random effects using Template Model Builder ('TMB') which enables fast and robust model fitting. Users can specify a variety of covariance matrices, weight observations, fit models with restricted or standard maximum likelihood inference, perform hypothesis testing with Satterthwaite or Kenward-Roger adjustment, and extract least square means estimates by using 'emmeans'.

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cpp

13.45 score 158 stars 9 dependents 204 scripts 8.8k 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.

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clinical-trialsnestshinywebapp

13.16 score 257 stars 7 dependents 357 scripts 570 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

12.96 score 103 stars 11 dependents 606 scripts 1.5k downloads

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.

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analysiscdiscdataset

12.49 score 58 stars 50 dependents 238 scripts 59k downloads

ggsurvfit - Flexible Time-to-Event Figures

Ease the creation of time-to-event (i.e. survival) endpoint figures. The modular functions create figures ready for publication. Each of the functions that add to or modify the figure are written as proper 'ggplot2' geoms or stat methods, allowing the functions from this package to be combined with any function or customization from 'ggplot2' and other 'ggplot2' extension packages.

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11.98 score 106 stars 5 dependents 1.4k scripts 7.8k downloads

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.

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11.61 score 23 stars 45 dependents 143 scripts 53k downloads

r2rtf - Easily Create Production-Ready Rich Text Format (RTF) Tables and Figures

Create production-ready Rich Text Format (RTF) tables and figures with flexible format.

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11.15 score 84 stars 15 dependents 174 scripts 9.6k 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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10.96 score 28 stars 13 dependents 111 scripts 1.7k 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.

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clinical-trialsmodulesnestoutputsshiny

10.90 score 42 stars 1 dependents 263 scripts 484 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

10.86 score 19 stars 23 dependents 73 scripts 8.6k downloads

teal.reporter - Reporting Tools for 'shiny' Modules

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

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nestreportingshiny

10.36 score 9 stars 8 dependents 27 scripts 5.6k 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.

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general-purposemodulesnestshiny

10.30 score 16 stars 196 scripts 360 downloads

xportr - Utilities to Output CDISC SDTM/ADaM XPT Files

Tools to build CDISC compliant data sets and check for CDISC compliance.

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clinical-programmersxpt

10.09 score 52 stars 1 dependents 188 scripts 1.3k 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.

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data-modelnest

10.08 score 11 stars 11 dependents 67 scripts 2.0k 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.

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nestshinywidgets

9.95 score 6 stars 10 dependents 40 scripts 3.2k downloads

metacore - A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows

Create an immutable container holding metadata for the purpose of better enabling programming activities and functionality of other packages within the clinical programming workflow.

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9.80 score 47 stars 1 dependents 274 scripts 1.5k downloads

admiralonco - Oncology Extension Package for ADaM in 'R' Asset Library

Programming oncology specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam>). The package is an extension package of the 'admiral' package.

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9.66 score 43 stars 69 scripts 709 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.

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nestshiny

9.48 score 12 stars 12 dependents 16 scripts 1.7k downloads

tidytlg - Create TLGs using the 'tidyverse'

Generate tables, listings, and graphs (TLG) using 'tidyverse'. Tables can be created functionally, using a standard TLG process, or by specifying table and column metadata to create generic analysis summaries. The 'envsetup' package can also be leveraged to create environments for table creation.

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9.42 score 40 stars 2 dependents 62 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.

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modulesnestslice

9.20 score 12 stars 8 dependents 6 scripts 694 downloads

pharmaversesdtm - SDTM Test Data for the 'Pharmaverse' Family of Packages

A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.

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9.19 score 35 stars 1 dependents 380 scripts 1.3k downloads

crmPack - Object-Oriented Implementation of Dose Escalation Designs

Implements a wide range of dose escalation designs. The focus is on model-based designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy to setup a new design with custom JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules. Further details are presented in Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.

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jagscpp

9.11 score 22 stars 232 scripts 360 downloads

Tplyr - A Traceability Focused Grammar of Clinical Data Summary

A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.

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pharmatables

9.02 score 108 stars 162 scripts 1.2k 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>.

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8.96 score 21 stars 4 dependents 101 scripts 479 downloads

pharmaverseadam - ADaM Test Data for the 'Pharmaverse' Family of Packages

A set of Analysis Data Model (ADaM) datasets constructed using the Study Data Tabulation Model (SDTM) datasets contained in the 'pharmaversesdtm' package and the template scripts from the 'admiral' family of packages. ADaM dataset specifications are described in the CDISC ADaM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.

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8.83 score 33 stars 2 dependents 216 scripts 1.5k 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

8.77 score 45 stars 1 dependents 75 scripts 425 downloads

tfrmt - Applies Display Metadata to Analysis Results Datasets

Creates a framework to store and apply display metadata to Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to define table format and styling without the data, and later apply the format to the data.

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8.65 score 89 stars 1 dependents 111 scripts 800 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

8.61 score 5 stars 10 dependents 9 scripts 4.5k 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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8.38 score 5 stars 12 dependents 214 scripts 1.0k 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.

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mergemodulesnesttransform

8.38 score 2 stars 5 dependents 20 scripts 510 downloads

admiralophtha - ADaM in R Asset Library - Ophthalmology

Aids the programming of Clinical Data Standards Interchange Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).

Last updated

8.30 score 21 stars 16 scripts 633 downloads

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.

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loggingnestutilities

8.29 score 7 stars 10 dependents 5 scripts 1.1k downloads

logrx - A Logging Utility Focus on Clinical Trial Programming Workflows

A utility to facilitate the logging and review of R programs in clinical trial programming workflows.

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8.03 score 48 stars 33 scripts 998 downloads

envsetup - Support the Setup of the R Environment for Clinical Trial Programming Workflows

The purpose of this package is to support the setup the R environment. The two main features are 'autos', to automatically source files and/or directories into your environment, and 'paths' to consistently set path objects across projects for input and output. Both are implemented using a configuration file to allow easy, custom configurations that can be used for multiple or all projects.

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7.85 score 12 stars 292 scripts 181 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.

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rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

7.80 score 12 stars 1 dependents 45 scripts

metatools - Enable the Use of 'metacore' to Help Create and Check Dataset

Uses the metadata information stored in 'metacore' objects to check and build metadata associated columns.

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7.54 score 22 stars 196 scripts 1.4k downloads

admiralvaccine - Vaccine Extension Package for ADaM in 'R' Asset Library

Programming vaccine specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. Flat model is followed as per Center for Biologics Evaluation and Research (CBER) guidelines for creating vaccine specific domains. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.

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cdisc

7.54 score 8 stars 18 scripts 392 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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7.36 score 8 stars 9 scripts 661 downloads

datacutr - SDTM Datacut

Supports the process of applying a cut to Standard Data Tabulation Model (SDTM), as part of the analysis of specific points in time of the data, normally as part of investigation into clinical trials. The functions support different approaches of cutting to the different domains of SDTM normally observed.

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7.36 score 17 stars 12 scripts 216 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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7.34 score 5 stars 1 dependents 56 scripts 186 downloads

pharmaRTF - Enhanced RTF Wrapper for Use with Existing Table Packages

Enhanced RTF wrapper written in R for use with existing R tables packages such as 'Huxtable' or 'GT'. This package fills a gap where tables in certain packages can be written out to RTF, but cannot add certain metadata or features to the document that are required/expected in a report for a regulatory submission, such as multiple levels of titles and footnotes, making the document landscape, and controlling properties such as margins.

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7.27 score 34 stars 136 scripts 601 downloads

tidyCDISC - Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets

Provides users a quick exploratory dive into common visualizations without writing a single line of code given the users data follows the Analysis Data Model (ADaM) standards put forth by the Clinical Data Interchange Standards Consortium (CDISC) <https://www.cdisc.org>. Prominent modules/ features of the application are the Table Generator, Population Explorer, and the Individual Explorer. The Table Generator allows users to drag and drop variables and desired statistics (frequencies, means, ANOVA, t-test, and other summary statistics) into bins that automagically create stunning tables with validated information. The Population Explorer offers various plots to visualize general trends in the population from various vantage points. Plot modules currently include scatter plot, spaghetti plot, box plot, histogram, means plot, and bar plot. Each plot type allows the user to plot uploaded variables against one another, and dissect the population by filtering out certain subjects. Last, the Individual Explorer establishes a cohesive patient narrative, allowing the user to interact with patient metrics (params) by visit or plotting important patient events on a timeline. All modules allow for concise filtering & downloading bulk outputs into html or pdf formats to save for later.

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pharmarinpharma

7.06 score 122 stars 19 scripts 337 downloads

riskassessment - A web app designed to interface with the `riskmetric` package

A shiny application that allows users to define a list of R packages to assess metrics engineered by the `riskmetric` package. In general, those metrics evaluate package development best practices, code documentation, community engagement, and sustainability that culminate in a quantitative risk score. The app allows users to select and review one package at a time to consume interactive visuals, download reports for sharing, submit comments for group collaboration, and even tweak metric weights used to calculate the packages' risk scores. When deployed in the context of an organization, the app serves as a platform for package validation, offering an authentication wall where roles are assigned to various users and 'final decisions' can be made at the package level manually or through pre-defined automation rules.

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packagesshinyvalidation

6.90 score 111 stars 3 scripts

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

6.85 score 7 stars 2 dependents 9 scripts 435 downloads

sdtmchecks - Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

A series of checks to identify common issues in Study Data Tabulation Model (SDTM) datasets. These checks are intended to be generalizable, actionable, and meaningful for analysis.

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6.80 score 27 stars 13 scripts 258 downloads

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

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

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modulesrna-seq-analysisshiny

6.57 score 7 stars 33 scripts

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.

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multistate-modelssimulation-engine

6.47 score 14 stars 15 scripts 168 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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6.46 score 8 stars 2 dependents 3 scripts 359 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

6.42 score 19 stars 17 scripts 252 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.

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modulesnest

6.32 score 3 stars 3 scripts

visR - Clinical Graphs and Tables Adhering to Graphical Principles

To enable fit-for-purpose, reusable clinical and medical research focused visualizations and tables with sensible defaults and based on graphical principles as described in: "Vandemeulebroecke et al. (2018)" <doi:10.1002/pst.1912>, "Vandemeulebroecke et al. (2019)" <doi:10.1002/psp4.12455>, and "Morris et al. (2019)" <doi:10.1136/bmjopen-2019-030215>.

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6.22 score 188 stars 92 scripts 26 downloads

valtools - Automate Validated Package Creation

Automate the steps necessary to create a validation ready package to make the process of validation simple. This includes setting up the specifications, test cases, test code, and validation report. Also provides tools to be able to execute the validation report from a variety of situations to provide documentation for validation.

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6.11 score 56 stars 46 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.

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6.09 score 9 stars 17 scripts 878 downloads

covtracer - Contextualizing Tests

Dissects a package environment or 'covr' coverage object in order to cross reference tested code with the lines that are evaluated, as well as linking those evaluated lines to the documentation that they are described within. Connecting these three pieces of information provides a mechanism of linking tests to documented behaviors.

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6.01 score 23 stars 10 scripts 936 downloads

r.pkg.template - R Package Template

R package template with GitHub Actions workflows included.

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gitgithub-actionstemplate

5.65 score 43 stars 1 scripts

simaerep - Detect Clinical Trial Sites Over- or Under-Reporting Clinical Events

Monitoring reporting rates of subject-level clinical events (e.g. adverse events, protocol deviations) reported by clinical trial sites is an important aspect of risk-based quality monitoring strategy. Sites that are under-reporting or over-reporting events can be detected using bootstrap simulations during which patients are redistributed between sites. Site-specific distributions of event reporting rates are generated that are used to assign probabilities to the observed reporting rates. (Koneswarakantha 2024 <doi:10.1007/s43441-024-00631-8>).

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ae-reportingclinical-trials

5.39 score 27 stars 20 scripts 209 downloads

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.

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plotsummarization

5.35 score 5 stars 1 dependents

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

5.15 score 4 stars 5 scripts 12 downloads

teal.osprey - 'teal' Modules for TLG Functions in Osprey

Community efforts to collect 'teal' modules for TLGs defined in 'osprey' package. Enables 'teal' app developers to create 'shiny' applications with a use of 'osprey' analysis functions.

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modulesnest

4.93 score 5 stars 2 scripts

admiral.test - Test Data for the 'admiral' Package

A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) derivations inside the 'admiral' package.

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4.78 score 2 stars 332 scripts 385 downloads

osprey - R Package to Create TLGs

Community effort to collect TLG code and create a catalogue.

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cataloggraphslistingsnesttables

4.72 score 5 stars 1 dependents 1 scripts

scda - Package to Access Synthetic CDISC Archive Data

Access Synthetic CDISC Data from Archive Packages.

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cdiscnestsynthetic-data

4.67 score 13 stars 31 scripts

roxy.shinylive - A 'roxygen2' Extension for 'Shinylive'

An extension for 'roxygen2' to embed 'Shinylive' applications in the package documentation.

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documentationroxygen2shinyshinylivewebr

4.51 score 13 stars 1 scripts 443 downloads

respectables - Create Relationally-Specified Multi-Table Datasets

This package provides a general framework and utility functions for simulating or synthesizing database-like multiple-table datasets. This is done by defining and then applying data recipes, which support the simulation or derivation of multiple variables jointly and/or conditional on the value of other already existing or recipe-specified variables. It also supports the simulation or augmentation of data which encodes a 1-to-many relationship with a foreign-key in an existing table.

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4.38 score 8 stars 8 scripts

flexsurvPlus - Provides Functions to Perform Survival Analysis for Economic models

A group of functions designed to perform survival analyses.

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cost-effectivenesscost-effectiveness-analysishealth-economic-evaluationhealth-economicshtasurvival-analysis

4.32 score 3 stars 8 scripts

psborrow - Bayesian Dynamic Borrowing with Propensity Score

A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.

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jagscpp

4.08 score 4 scripts 570 downloads

scda.2022 - Synthetic CDISC Data Archive 2022

An archive of synthetic CDISC data for 2022.

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cdiscnestsynthetic-data

3.95 score 10 stars 4 scripts

MAIC - Package to Perform Matched-adjusted Indirect Comparisons

A group of functions designed to perform matched-adjusted indirect comparisons as per NICE TSD 18 and summarise the results for survival data (using hazard ratios) and binary data (using odds ratios.)

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evidence-synthesishealth-economic-evaluationhta

3.86 score 8 stars 45 scripts

staged.dependencies - Install R packages from Particular Git Branches

When developing multiple dependent packages, it is often useful to introduce development stages (devel, pre-release, release) that synchronize these packages. This package provides an implementation of development stages via branch naming rules. It defines RStudio addins that allow to install the matching upstream and downstream dependencies.

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3.68 score 12 stars 5 scripts

scda.2021 - Synthetic CDISC Data Archive 2021

An archive of synthetic CDISC data for 2021.

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cdiscnestsynthetic-data

3.53 score 4 stars

mtdesign - Mander and Thompson Designs

Implements Mander & Thompson's (2010) <doi:10.1016/j.cct.2010.07.008> methods for two-stage designs optimal under the alternative hypothesis for phase II [cancer] trials. Also provides an implementation of Simon's (1989) <doi:10.1016/0197-2456(89)90015-9> original methodology and allows exploration of the operating characteristics of sub-optimal designs.

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cpp

3.48 score 3 stars 4 scripts 568 downloads

gemtcPlus - Provides a suite of extension functions for NMA using the `gemtc` package

Functions for generating outputs: tables and plots for NMA reports.

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evidence-synthesishealth-economic-evaluationhealth-economicshtajagscpp

3.03 score 6 stars 12 scripts

CTP - Closed Testing Procedure (CTP)

This is a package for constructing hypothesis trees for treatment comparisons based on the closure principle and analysing the corresponding Closed Testing Procedures (CTP) using adjusted p-values. For reference, see Marcus, R., Peritz, E, and Gabriel, K.R. (1976) <doi:10.2307/2335748> and Bauer, P (1991) <doi:10.1002/sim.4780100609>.

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3.00 score 1 stars 3 scripts 23 downloads

nesttemplate - `pkgdown` Template for NEST Packages

This is a private template for use by core NEST packages. Please don't use for your own code.

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nestpkgdown-templatetemplate

2.70 score 2 stars

RDO - Reproducible Data Objects

A Reproducible Data Object (RDO) encapsulates both data and R code needed to reproduce those data. Each RDO can have other RDOs as dependencies. RDOs can be composed into complex tree hierarchies. Interacting with an RDO tree is similar to interacting with a single RDO. You can (re)run the code and refresh the cache, check status, validate if the code still gives the same cached data, clear data cache, access code and data cache of any of the dependencies. RDOs can be cloned and code of cloned dependencies can be modified.

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2.70 score 10 stars 8 scripts

facetsr - facets R wrapper

The goal of facetsr is to create an R wrapper for facets. So use facets to explore your dataset.

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2.30 score 4 stars 4 scripts

descem - Discrete Event Simulation for Cost-Effectiveness Modelling

A package designed to perform discrete event simulation for cost-effectiveness modelling.

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health-economic-evaluationhealth-economicshtasurvival-analysis

2.00 score 2 stars 6 scripts

rpsftmPlus - Extensions To Rpsftm Package

A collection of extenstions to the rpsftm package to enable descriptive analysis of trials affected by treatment switching and enable additional analysis of rpsft models.

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health-economic-evaluationhealth-economicshtasurvival-analysis

2.00 score 2 stars 1 scripts

syntrial - synthesize data from real clinical trial

Syntrial takes as input the data of a clinical trial in SDTM format (https://www.cdisc.org/standards/foundational/sdtm). For each synthesized patient a number of source patients is selected. From the source patients' data randomly weighted numeric values or, for categorical variables, one value is selected in a modification of classical bootstrap.

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1.70 score 1 stars 1 scripts