## 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 2 months ago

11.14 score 432 stars 1 packages 1.7k 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 4 months ago

10.51 score 72 stars 5 packages 348 scripts 3.6k 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-analysis

7.49 score 19 stars 24 scripts 259 downloads## Statamarkdown - 'Stata' Markdown

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

Last updated 11 months ago

6.75 score 59 stars 478 scripts 392 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 2 months ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.69 score 18 stars 16 scripts 259 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 2 months ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.69 score 18 stars 16 scripts 259 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 2 months ago

5.08 score 4 stars 2 scripts 330 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 2 months ago

5.08 score 4 stars 2 scripts 330 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 2 months ago

5.08 score 4 stars 2 scripts 317 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 2 months ago

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

4.95 score 12 scripts 600 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 2 months ago

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

4.95 score 12 scripts 600 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 2 months ago

exercisesknitrrmarkdown

3.78 score 1 stars 1 scripts## tmsens - Sensitivity Analysis Using the Trimmed Means Estimator

Sensitivity analysis using the trimmed means estimator.

Last updated 2 months ago

missing-datasensitivity-analysistrimmed-means

2.70 score 1 stars 1 scripts 171 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 years ago

2.00 score 2 stars 8 scripts