gtsummary - Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

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easy-to-usegthtml5regression-modelsreproducibilityreproducible-researchstatisticssummary-statisticssummary-tablestable1tableone

17.91 score 1.2k stars 44 dependents 13k scripts 70k 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

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

12.41 score 58 stars 50 dependents 200 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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12.07 score 104 stars 5 dependents 1.5k scripts 8.8k 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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12.07 score 104 stars 5 dependents 1.5k scripts 8.8k downloads

broom.helpers - Helpers for Model Coefficients Tibbles

Provides suite of functions to work with regression model 'broom::tidy()' tibbles. The suite includes functions to group regression model terms by variable, insert reference and header rows for categorical variables, add variable labels, and more.

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11.96 score 25 stars 6 dependents 402 scripts 25k downloads

admiraldev - Utility Functions and Development Tools for the Admiral Package Family

Utility functions to check data, variables and conditions for functions used in 'admiral' and 'admiral' extension packages. Additional utility helper functions to assist developers with maintaining documentation, testing and general upkeep of 'admiral' and 'admiral' extension packages.

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11.81 score 22 stars 7 dependents 242 scripts 4.5k 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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11.63 score 23 stars 45 dependents 150 scripts 53k 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

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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9.52 score 33 stars 1 dependents 358 scripts 2.7k 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 875 downloads

tidycmprsk - Competing Risks Estimation

Provides an intuitive interface for working with the competing risk endpoints. The package wraps the 'cmprsk' package, and exports functions for univariate cumulative incidence estimates and competing risk regression. Methods follow those introduced in Fine and Gray (1999) <doi:10.1002/sim.7501>.

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competing-risks

8.06 score 25 stars 2 dependents 402 scripts 6.3k downloads

dcurves - Decision Curve Analysis for Model Evaluation

Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>, Vickers (2008) <doi:10.1186/1472-6947-8-53>, and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.

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decision-curve-analysis

7.87 score 44 stars 1 dependents 167 scripts 3.4k downloads

tidycmprsk - Competing Risks Estimation

Provides an intuitive interface for working with the competing risk endpoints. The package wraps the 'cmprsk' package, and exports functions for univariate cumulative incidence estimates and competing risk regression. Methods follow those introduced in Fine and Gray (1999) <doi:10.1002/sim.7501>.

Last updated

competing-risks

7.79 score 25 stars 1 dependents 400 scripts 6.9k downloads

starter - Starter Kit for New Projects

Get started with new projects by dropping a skeleton of a new project into a new or existing directory, initialise git repositories, and create reproducible environments with the 'renv' package. The package allows for dynamically named files, folders, file content, as well as the functionality to drop individual template files into existing projects.

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template

5.91 score 27 stars 30 scripts 328 downloads

rstudio.prefs - Set 'RStudio' Preferences

As of 'RStudio' v1.3, the preferences in the Global Options dialog (and a number of other preferences that aren’t) are now saved in simple, plain-text JSON files. This package provides an interface for working with these 'RStudio' JSON preference files to easily make modifications without using the point-and-click option menus. This is particularly helpful when working on teams to ensure a unified experience across machines and utilizing settings for best practices.

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rstudio

4.94 score 29 stars 2 dependents 10 scripts 452 downloads

updater - Utilities for Updating R

When updating major or minor R versions all packages should be re-installed. The utilities in this package assist in getting a user up-and-running again by installing all previously installed R packages. The package uses 'renv' to install; immediately replenishing your 'renv' package cache.

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4.75 score 9 stars 126 scripts 456 downloads

affirm - Secular affirmations against data

What the package does (one paragraph).

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4.15 score 7 stars 6 scripts

crc - Competing Risks Combined

Use two independently estimated risks of death from other causes and death from disease to get a corrected estimate of risk of death from disease. For example, given a patient's risk of death from cancer based on their oncologic burden and their risk of death from other causes based on their comorbidities, we calculate an adjusted risk of death from cancer. To illustrate the importance of this correction, image two patients with identical disease burden, and therefore, identical predicted risk of death from disease. Now imagine, that one of these patients also has sever heart disease and it likely we pass away from hear disease before they would succumb to the cancer. Our correction makes the appropriate update to the risk of death from disease incorporating the risk of death from other causes.

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2.70 score 3 scripts