TwoSampleMR - Two Sample MR Functions and Interface to MR Base Database

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU GWAS database <https://gwas.mrcieu.ac.uk/> to automatically obtain data, and a wide range of methods to run the analysis. You can use the MR-Base web app <https://www.mrbase.org/> to try out a limited range of the functionality in this package, but for any serious work we strongly recommend using this R package.

Last updated 4 months ago

11.15 score 453 stars 1 dependents 1.8k scripts

ieugwasr - Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Last updated 7 months ago

10.66 score 85 stars 6 dependents 366 scripts 3.4k downloads

TrialEmulation - Causal Analysis of Observational Time-to-Event Data

Implements target trial emulation methods to apply randomized clinical trial design and analysis in an observational setting. Using marginal structural models, it can estimate intention-to-treat and per-protocol effects in emulated trials using electronic health records. A description and application of the method can be found in Danaei et al (2013) <doi:10.1177/0962280211403603>.

Last updated 2 months ago

causal-inferencelongitudinal-datasurvival-analysiscpp

7.62 score 22 stars 25 scripts 348 downloads

colorout - Colorize R Output on Terminal Emulators

Colorize R output when it is running on a terminal emulator. The functions of this package only work if R is compiled for Unix systems and it is running interactively in a terminal emulator. The terminal must support Select Graphic Rendition (SGR, also known as ANSI escape codes or sequences). The package contains a C library with a function that replaces the default Rstd_WriteConsoleEx which, when enabled, is responsible for printing messages in the Console when R is running in interactive mode. It works with RStudio, but there is no support for Graphical User Interfaces that does not support ANSI colors, such as Windows RGui.

Last updated 3 months ago

7.37 score 292 stars 384 scripts 37 downloads

vscDebugger - Support for Visual Studio Code Debugger

Provides support for a visual studio code debugger

Last updated 1 months ago

debuggervscode

6.92 score 92 stars 15 scripts

OneSampleMR - One Sample Mendelian Randomization and Instrumental Variable Analyses

Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses. The package includes implementations of; the Sanderson and Windmeijer (2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic, the multiplicative structural mean model Hernán and Robins (2006) <doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor substitution and two-stage residual inclusion estimators explained by Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.

Last updated 12 days ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.66 score 19 stars 16 scripts 201 downloads

OneSampleMR - One Sample Mendelian Randomization and Instrumental Variable Analyses

Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses. The package includes implementations of; the Sanderson and Windmeijer (2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic, the multiplicative structural mean model Hernán and Robins (2006) <doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor substitution and two-stage residual inclusion estimators explained by Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.

Last updated 12 days ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.66 score 19 stars 16 scripts 201 downloads

Statamarkdown - 'Stata' Markdown

Settings and functions to extend the 'knitr' 'Stata' engine.

Last updated 1 years ago

6.16 score 59 stars 490 scripts 311 downloads

mrbayes - Bayesian Summary Data Models for Mendelian Randomization Studies

Bayesian estimation of inverse variance weighted (IVW), Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian randomization analyses.

Last updated 30 days ago

cpp

5.20 score 4 stars 2 scripts 270 downloads

mrbayes - Bayesian Summary Data Models for Mendelian Randomization Studies

Bayesian estimation of inverse variance weighted (IVW), Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian randomization analyses.

Last updated 30 days ago

cpp

5.20 score 4 stars 2 scripts 270 downloads

bpbounds - Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions

Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176, <doi:10.2307/2965583>). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).

Last updated 7 days ago

aceaverage-causal-effectboundsinstrumental-variableivmendelianmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomizationmrnonparametricnonparametric-boundspearlshiny

4.92 score 12 scripts 604 downloads

bpbounds - Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions

Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176, <doi:10.2307/2965583>). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).

Last updated 7 days ago

aceaverage-causal-effectboundsinstrumental-variableivmendelianmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomizationmrnonparametricnonparametric-boundspearlshiny

4.92 score 12 scripts 604 downloads

StepReg - Stepwise Regression Analysis

The stepwise regression analysis is a statistical technique used to identify a subset of predictor variables essential for constructing predictive models. This package performs stepwise regression analysis across various regression models such as linear, logistic, Cox proportional hazards, Poisson, and gamma regression. It incorporates diverse stepwise regression algorithms like forward selection, backward elimination, and bidirectional elimination alongside the best subset method. Additionally, it offers a wide range of selection criteria, including Akaike Information Criterion (AIC), corrected AIC (AICc), Sawa Bayesian Information Criterion (BIC), Schwarz Bayesian Information Criterion (SBC), Significant Levels (SL), among others. Moreover, it facilitates the concurrent selection of multiple methods and criteria for variable selection. For user-friendly exploration and analysis, StepReg provides an intuitive R Shiny app.

Last updated 10 months ago

3.97 score 34 scripts 1.4k downloads

knitexercise - Knit Exercise Questions and Solutions from the Same R Markdown Document

Provides a function to knit questions and solutions documents from the same R Markdown document.

Last updated 12 days ago

exercisesknitrrmarkdown

3.81 score 1 stars 1 scripts

tmsens - Sensitivity Analysis Using the Trimmed Means Estimator

Sensitivity analysis using the trimmed means estimator.

Last updated 5 months ago

missing-datasensitivity-analysistrimmed-means

2.70 score 1 stars 1 scripts 136 downloads

dd4d - Dummy Data for Dummies

Allows you to specify and sample from a Bayesian Network (a.k.a. a parametric Directed Acyclic Graph, or pDAG).

Last updated 1 months ago

2.30 score 2 stars 9 scripts

osutils - Useful Functions for OpenSAFELY

Contains functions that are often needed when using the OpenSAFELY platform <https://www.opensafely.org/>, such as redaction and low-memory processing.

Last updated 1 months ago

1.70 score 1 scripts