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.

Last updated 2 months ago

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

16.61 score 1.1k stars 16 packages 7.6k scripts 49k 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.

Last updated 3 months ago

11.66 score 21 stars 10 packages 148 scripts 20k 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.

Last updated 2 months ago

analysiscdiscdataset

11.18 score 33 stars 20 packages 87 scripts 45k 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.

Last updated 17 days ago

10.98 score 17 stars 7 packages 195 scripts 1.3k 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.

Last updated 6 months ago

10.39 score 72 stars 2 packages 616 scripts 6.2k downloads

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>.

Last updated 8 months ago

8.46 score 179 stars 100 scripts 119 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.

Last updated 3 months ago

7.73 score 14 stars 33 scripts 7.8k 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/>.

Last updated 30 days ago

7.45 score 14 stars 184 scripts 822 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 3 months ago

competing-risks

7.09 score 22 stars 1 packages 141 scripts 4.4k 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.

Last updated 1 months ago

template

6.94 score 26 stars 2 packages 28 scripts 669 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 4 months ago

competing-risks

6.79 score 22 stars 1 packages 141 scripts 4.4k 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>.

Last updated 4 months ago

decision-curve-analysis

6.61 score 37 stars 87 scripts 1.3k 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.

Last updated 2 years ago

rstudio

4.94 score 29 stars 2 packages 9 scripts 419 downloads

bstfun - Functions for the MSK Biostatistics Department

A miscellaneous collection of functions to used by members of the Biostatistics Department at MSKCC.

Last updated 2 years ago

4.87 score 34 stars 31 scripts

affirm - Secular affirmations against data

What the package does (one paragraph).

Last updated 10 days ago

4.78 score 6 stars 4 scripts

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.

Last updated 1 years ago

4.69 score 9 stars 109 scripts 696 downloads

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.

Last updated 2 years ago

2.70 score 3 scripts

hotfun - Collection of Functions Used in the Health Outcomes Team at MSKCC

A mixed-bag of utility functions to ease analyses and reporting results.

Last updated 3 years ago

2.48 score 6 stars 1 scripts

gt.doc.images - Save Help File Images

Exports tools for creating help file documents that contain images of 'gtsummary', 'gt', and 'flextable' images.

Last updated 2 years ago

1.70 score

ghe.utils - Utilities for Working with GitHub Enterprise

Set the location of your company's GitHub Enterprise address, and seamlessly interact with a GitHub Enterprise Instance from the R console.

Last updated 3 years ago

1.70 score

sjofun - Misc package for Daniel Sjoberg

Misc package for Daniel Sjoberg.

Last updated 3 years ago

1.70 score 1 stars