From f6c5a5757b592e2761da45172fa96ba6b9896546 Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Thu, 17 Mar 2022 14:31:14 -0700 Subject: [PATCH 1/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 48afff11..0339c112 100644 --- a/README.md +++ b/README.md @@ -4,4 +4,4 @@ A Flexible Quasi-Copula Distribution for Statistical Modeling | **Documentation** | **Build Status** | **Code Coverage** | |-------------------|------------------|--------------------| -| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/latest) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions) [![CI (Julia nightly)](https://github.com/openmendel/QuasiCopula.jl/workflows/JuliaNightly/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | +| [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/dev) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | From 234f7a792f35339a420fea650b24cce7c320dc0a Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Thu, 17 Mar 2022 14:31:55 -0700 Subject: [PATCH 2/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0339c112..8bd07ea8 100644 --- a/README.md +++ b/README.md @@ -4,4 +4,4 @@ A Flexible Quasi-Copula Distribution for Statistical Modeling | **Documentation** | **Build Status** | **Code Coverage** | |-------------------|------------------|--------------------| -| [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/dev) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | +| [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/dev) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | From fa82dbc513040bc47755a6369388f6b6197ced9d Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Thu, 17 Mar 2022 16:26:34 -0700 Subject: [PATCH 3/6] Update Project.toml --- Project.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Project.toml b/Project.toml index dbdd9231..3e5881e4 100644 --- a/Project.toml +++ b/Project.toml @@ -20,6 +20,7 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" ToeplitzMatrices = "c751599d-da0a-543b-9d20-d0a503d91d24" [compat] +BenchmarkTools = "1" Convex = "0.14" DataFrames = "1" Distributions = "0.25" @@ -28,6 +29,7 @@ GLM = "1" Ipopt = "0.8" LoopVectorization = "0.12" MathProgBase = "0.7" +RDatasets = "0.7" Reexport = "1.2" SpecialFunctions = "2.1" StatsFuns = "0.9" From 5172258d32f58449e2c8a6b49e44368419075e3a Mon Sep 17 00:00:00 2001 From: Sarah Date: Wed, 4 May 2022 18:50:45 -0700 Subject: [PATCH 4/6] Update README.md --- README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8bd07ea8..6fcdb45d 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,21 @@ # QuasiCopula.jl A Flexible Quasi-Copula Distribution for Statistical Modeling - | **Documentation** | **Build Status** | **Code Coverage** | |-------------------|------------------|--------------------| -| [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/dev) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | +| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/latest) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions) [![CI (Julia nightly)](https://github.com/openmendel/QuasiCopula.jl/workflows/JuliaNightly/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | + +QuasiCopula.jl is a Julia package for the analysis of correlated data with specified margins. Currently the package supports multivariate simulation and analysis utilities for the Poisson, Negative Binomial, Bernoulli, Gaussian, Bivariate Poisson/Bernoulli Mixed distributions. QuasiCopula.jl supports covariance matrices structured under the variance component model (VCM) framework, autoregressive AR(1) covariance structure, and the compound symmetric (CS) covariance structure. QuasiCopula.jl supports Julia v1.6 or later. See the [documentation](https://openmendel.github.io/QuasiCopula.jl/dev/) for usage under the different models. + +QuasiCopula.jl is a registered package, and it will require running the following code to install. + +```{julia} +using Pkg +pkg"add QuasiCopula" +``` + +## Citation + +If you use [OpenMendel](https://openmendel.github.io) analysis packages in your research, please cite the following reference in the resulting publications: + +*OPENMENDEL: a cooperative programming project for statistical genetics. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. Hum Genet. 139, 61–71 (2020). [doi:10.1007/s00439-019-02001-z](10.1007/s00439-019-02001-z). PMID: 30915546* From 05ea43a1d3b072040bd70c46933a9d19e8ab15a6 Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Wed, 4 May 2022 20:57:03 -0700 Subject: [PATCH 5/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6fcdb45d..ff99c6e1 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ A Flexible Quasi-Copula Distribution for Statistical Modeling | **Documentation** | **Build Status** | **Code Coverage** | |-------------------|------------------|--------------------| -| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/latest) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions) [![CI (Julia nightly)](https://github.com/openmendel/QuasiCopula.jl/workflows/JuliaNightly/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | +| [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/dev) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/QuasiCopula.jl/stable) | [![build Actions Status](https://github.com/OpenMendel/QuasiCopula.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions) [![CI (Julia nightly)](https://github.com/openmendel/QuasiCopula.jl/workflows/JuliaNightly/badge.svg)](https://github.com/OpenMendel/QuasiCopula.jl/actions/workflows/JuliaNightly.yml)| [![codecov](https://codecov.io/gh/OpenMendel/QuasiCopula.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/QuasiCopula.jl) | QuasiCopula.jl is a Julia package for the analysis of correlated data with specified margins. Currently the package supports multivariate simulation and analysis utilities for the Poisson, Negative Binomial, Bernoulli, Gaussian, Bivariate Poisson/Bernoulli Mixed distributions. QuasiCopula.jl supports covariance matrices structured under the variance component model (VCM) framework, autoregressive AR(1) covariance structure, and the compound symmetric (CS) covariance structure. QuasiCopula.jl supports Julia v1.6 or later. See the [documentation](https://openmendel.github.io/QuasiCopula.jl/dev/) for usage under the different models. From f84fc5030fb71003b55dbf1a024d1b756260a15e Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Wed, 4 May 2022 21:02:05 -0700 Subject: [PATCH 6/6] Update Project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 3e5881e4..8d32363e 100644 --- a/Project.toml +++ b/Project.toml @@ -2,7 +2,7 @@ name = "QuasiCopula" uuid = "c47b6ae2-b804-4668-9957-eb588c99ffbc" keywords = ["Quasi Copula", "GLMM", "autoregressive model", "compound symmetric model", "variance components model"] authors = ["Sarah Ji ", "OpenMendel Team"] -version = "0.1.0" +version = "0.1.1" [deps] Convex = "f65535da-76fb-5f13-bab9-19810c17039a"