duckdb - DBI Package for the DuckDB Database Management System

The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.

Last updated 19 days ago

databaseduckdbolapcpp

13.79 score 159 stars 46 dependents 1.7k scripts 30k downloads

TwoSampleMR - Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU OpenGWAS database <https://gwas.mrcieu.ac.uk/> to automatically obtain data, and a wide range of methods to run the analysis.

Last updated 5 days ago

11.28 score 476 stars 1 dependents 1.8k scripts

ieugwasr - Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Last updated 19 days ago

9.97 score 89 stars 6 dependents 366 scripts 3.0k 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 16 days ago

causal-inferencelongitudinal-datasurvival-analysiscpp

7.74 score 25 stars 29 scripts 534 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 6 months ago

7.20 score 294 stars 384 scripts 74 downloads

vscDebugger - Support for Visual Studio Code Debugger

Provides support for a visual studio code debugger

Last updated 18 days ago

debuggervscode

7.00 score 95 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 2 days ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.69 score 19 stars 16 scripts 251 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 days ago

instrumental-variableinstrumental-variablesmendelian-randomisationmendelian-randomizationmendelianrandomisationmendelianrandomization

6.69 score 19 stars 16 scripts 251 downloads

Statamarkdown - 'Stata' Markdown

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

Last updated 1 years ago

6.16 score 59 stars 488 scripts 366 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 days ago

cpp

5.60 score 4 stars 2 scripts 300 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 days ago

cpp

5.60 score 4 stars 2 scripts 300 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 days ago

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

4.95 score 12 scripts 547 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 days ago

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

4.95 score 12 scripts 547 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 10 days ago

exercisesknitrrmarkdown

3.85 score 1 stars 1 scripts

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 12 months ago

3.52 score 33 scripts 935 downloads

tmsens - Sensitivity Analysis Using the Trimmed Means Estimator

Sensitivity analysis using the trimmed means estimator.

Last updated 7 months ago

missing-datasensitivity-analysistrimmed-means

2.70 score 1 stars 1 scripts 157 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 4 months ago

2.30 score 2 stars 9 scripts

quickdag - Make Beautiful Directed Acyclic Graphs

This package allows the user the save directed acyclic graphs (DAGs) generated in DiagrammeR and export them to pdf, png, or svg format. Users may optionally choose to view the DAG without saving or to embed it in an RMarkdown document. In addition, quickDAG allows the user easily to reformat DAGs as single-world intervention graph (SWIG) templates.

Last updated 2 years ago

causal-inferencediagramsdirected-acyclic-graphsepidemiology

2.30 score 4 stars

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 4 months ago

1.70 score 1 scripts