simstudy

simstudy: Illuminating research methods through data generation - Published in JOSS (2020)

https://github.com/kgoldfeld/simstudy

Keywords

data-generation data-simulation r simulation statistical-models

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simstudy: Illuminating research methods through data generation

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Host: GitHub
Owner: kgoldfeld
License: gpl-3.0
Language: R
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Homepage: https://kgoldfeld.github.io/simstudy/
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data-generation data-simulation r simulation statistical-models

Created over 9 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Support Codemeta

README.Rmd

---
title: "simstudy"
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```



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The `simstudy` package is a collection of functions that allow users to generate simulated data sets in order to explore modeling techniques or better understand data generating processes. The user defines the distributions of individual variables, specifies relationships between covariates and outcomes, and generates data based on these specifications. The final data sets can represent randomized control trials, repeated measure designs, cluster randomized trials, or naturally observed data processes. Other complexities that can be added include survival data, correlated data, factorial study designs, step wedge designs, and missing data processes.

Simulation using `simstudy` has two fundamental steps. The user (1) **defines** the data elements of a data set and (2) **generates** the data based on these definitions. Additional functionality exists to simulate observed or randomized **treatment assignment/exposures**, to create **longitudinal/panel** data, to create **multi-level/hierarchical** data, to create datasets with **correlated variables** based on a specified covariance structure, to **merge** datasets, to create data sets with **missing** data, and to create non-linear relationships with underlying **spline** curves.

The overarching philosophy of `simstudy` is to create data generating processes that mimic the typical models used to fit those types of data. So, the parameterization of some of the data generating processes may not follow the standard parameterizations for the specific distributions. For example, in `simstudy` *gamma*-distributed data are generated based on the specification of a mean μ (or log(μ)) and a dispersion $d$, rather than shape α and rate β parameters that more typically characterize the *gamma* distribution. When we estimate the parameters, we are modeling μ (or some function of μ), so we should explicitly recover the `simstudy` parameters used to generate the model, thus illuminating the relationship between the underlying data generating processes and the models. For more details on the
package, use cases, examples, and function reference see the [documentation page](https://kgoldfeld.github.io/simstudy/articles/simstudy.html).


## Installation

You can install the released version of simstudy from [CRAN](https://CRAN.R-project.org){target="_blank"} with:

``` r
install.packages("simstudy")
```

And the development version from [GitHub](https://github.com/){target="_blank"} with:

``` r
# install.packages("devtools")
devtools::install_github("kgoldfeld/simstudy")
```
## Example

Here is some simple sample code, much more in the vignettes:

```{r, echo = TRUE}
library(simstudy)
set.seed(1965)

def <- defData(varname="x", formula = 10, variance = 2, dist = "normal")
def <- defData(def, varname="y", formula = "3 + 0.5 * x", variance = 1, dist = "normal")
dd <- genData(250, def)

dd <- trtAssign(dd, nTrt = 4, grpName = "grp", balanced = TRUE)

dd
```

## Contributing & Support

If you find a bug or need help, please file an issue with a [reprex](https://www.tidyverse.org/help/){target="_blank"} on [Github](https://github.com/kgoldfeld/simstudy/issues){target="_blank"}. We are happy to accept contributions to simstudy. More information on how to propose changes or fix bugs can be found [here](https://kgoldfeld.github.io/simstudy/CONTRIBUTING.html){target="_blank"}.

## Code of Conduct

Please note that the simstudy project is released with a [Contributor Code of Conduct](https://kgoldfeld.github.io/simstudy/CODE_OF_CONDUCT.html){target="_blank"}. By contributing to this project, you agree to abide by its terms.

Owner

Login: kgoldfeld
Kind: user

Repositories: 2
Profile: https://github.com/kgoldfeld

JOSS Publication

simstudy: Illuminating research methods through data generation

Published

October 27, 2020

DOI

10.21105/joss.02763

Volume 5, Issue 54, Page 2763

Authors

Keith Goldfeld

NYU Grossman School of Medicine.

Jacob Wujciak-Jens

Independent Researcher

Editor

Mikkel Meyer Andersen

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "simstudy" in publications use:'
type: software
license: GPL-3.0-only
title: 'simstudy: Simulation of Study Data'
version: 0.8.1.9000
doi: 10.21105/joss.02763
identifiers:
- type: doi
  value: 10.32614/CRAN.package.simstudy
- type: url
  value: https://kgoldfeld.github.io/simstudy/dev/
abstract: Simulates data sets in order to explore modeling techniques or better understand
  data generating processes. The user specifies a set of relationships between covariates,
  and generates data based on these specifications. The final data sets can represent
  data from randomized control trials, repeated measure (longitudinal) designs, and
  cluster randomized trials. Missingness can be generated using various mechanisms
  (MCAR, MAR, NMAR).
authors:
- family-names: Goldfeld
  given-names: Keith
  email: keith.goldfeld@nyulangone.org
  orcid: https://orcid.org/0000-0002-0292-8780
- family-names: Wujciak-Jens
  given-names: Jacob
  email: jacob@wujciak.de
  orcid: https://orcid.org/0000-0002-7281-3989
preferred-citation:
  type: article
  title: 'simstudy: Illuminating research methods through data generation'
  authors:
  - family-names: Goldfeld
    given-names: Keith
    email: keith.goldfeld@nyulangone.org
    orcid: https://orcid.org/0000-0002-0292-8780
  - family-names: Wujciak-Jens
    given-names: Jacob
    email: jacob@wujciak.de
    orcid: https://orcid.org/0000-0002-7281-3989
  publisher:
    name: The Open Journal
  journal: Journal of Open Source Software
  year: '2020'
  volume: '5'
  issue: '54'
  url: https://doi.org/10.21105/joss.02763
  doi: 10.21105/joss.02763
  start: '2763'
repository: https://CRAN.R-project.org/package=simstudy
repository-code: https://github.com/kgoldfeld/simstudy
url: https://kgoldfeld.github.io/simstudy/
date-released: '2024-07-29'
contact:
- family-names: Goldfeld
  given-names: Keith
  email: keith.goldfeld@nyulangone.org
  orcid: https://orcid.org/0000-0002-0292-8780
keywords:
- data-generation
- data-simulation
- r
- simulation
- statistical-models
references:
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  notes: Depends
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  notes: Imports
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  title: backports
  abstract: 'backports: Reimplementations of Functions Introduced Since R-3.0.0'
  notes: Imports
  url: https://github.com/r-lib/backports
  repository: https://CRAN.R-project.org/package=backports
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  - name: R Core Team
  year: '2025'
  doi: 10.32614/CRAN.package.backports
- type: software
  title: fastglm
  abstract: 'fastglm: Fast and Stable Fitting of Generalized Linear Models using ''RcppEigen'''
  notes: Imports
  url: https://github.com/jaredhuling/fastglm
  repository: https://CRAN.R-project.org/package=fastglm
  authors:
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    given-names: Jared
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  year: '2025'
  doi: 10.32614/CRAN.package.fastglm
- type: software
  title: pbv
  abstract: 'pbv: Probabilities for Bivariate Normal Distribution'
  notes: Imports
  url: https://sites.google.com/view/alexander-robitzsch/software
  repository: https://CRAN.R-project.org/package=pbv
  authors:
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    given-names: Alexander
    orcid: https://orcid.org/0000-0002-8226-3132
  year: '2025'
  doi: 10.32614/CRAN.package.pbv
  version: '>= 0.5.47'
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.covr
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Suggests
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
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    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: formatR
  abstract: 'formatR: Format R Code Automatically'
  notes: Suggests
  url: https://github.com/yihui/formatR
  repository: https://CRAN.R-project.org/package=formatR
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    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.formatR
- type: software
  title: gee
  abstract: 'gee: Generalized Estimation Equation Solver'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=gee
  authors:
  - family-names: Carey
    given-names: Vincent J
  year: '2025'
  doi: 10.32614/CRAN.package.gee
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Suggests
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
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    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
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    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
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    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
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    orcid: https://orcid.org/0000-0002-7470-9261
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  year: '2025'
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- type: software
  title: grid
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Suggests
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
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  notes: Suggests
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- type: software
  title: hedgehog
  abstract: 'hedgehog: Property-Based Testing'
  notes: Suggests
  url: https://hedgehog.qa
  repository: https://CRAN.R-project.org/package=hedgehog
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  doi: 10.32614/CRAN.package.hedgehog
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=knitr
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    given-names: Yihui
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  doi: 10.32614/CRAN.package.knitr
- type: software
  title: magrittr
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  notes: Suggests
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
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  title: Matrix
  abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
  notes: Suggests
  url: https://Matrix.R-forge.R-project.org
  repository: https://CRAN.R-project.org/package=Matrix
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- type: software
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  abstract: 'mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=mgcv
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    given-names: Simon
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  notes: Suggests
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=rmarkdown
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  year: '2025'
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- type: software
  title: scales
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  notes: Suggests
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
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    given-names: Hadley
    email: hadley@posit.co
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    orcid: https://orcid.org/0000-0002-5147-4711
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  year: '2025'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: splines
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Suggests
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: survival
  abstract: 'survival: Survival Analysis'
  notes: Suggests
  url: https://github.com/therneau/survival
  repository: https://CRAN.R-project.org/package=survival
  authors:
  - family-names: Therneau
    given-names: Terry M
    email: therneau.terry@mayo.edu
  year: '2025'
  doi: 10.32614/CRAN.package.survival
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
- type: software
  title: gtsummary
  abstract: 'gtsummary: Presentation-Ready Data Summary and Analytic Result Tables'
  notes: Suggests
  url: https://www.danieldsjoberg.com/gtsummary/
  repository: https://CRAN.R-project.org/package=gtsummary
  authors:
  - family-names: Sjoberg
    given-names: Daniel D.
    email: danield.sjoberg@gmail.com
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Papers & Mentions

Total mentions: 1

Estimands in epigenome-wide association studies

DOI: 10.1186/s13148-021-01083-9
OpenAlex ID: https://openalex.org/W3158164318
Published: April 2021

Last synced: 2 months ago

GitHub Events

Total

Issues event: 3
Watch event: 4
Delete event: 1
Issue comment event: 8
Push event: 49
Pull request review event: 5
Pull request review comment event: 7
Pull request event: 4
Create event: 2

Last Year

Issues event: 3
Watch event: 4
Delete event: 1
Issue comment event: 8
Push event: 49
Pull request review event: 5
Pull request review comment event: 7
Pull request event: 4
Create event: 2

Committers

Last synced: 5 months ago

All Time

Total Commits: 758
Total Committers: 14
Avg Commits per committer: 54.143
Development Distribution Score (DDS): 0.728

Past Year

Commits: 10
Committers: 1
Avg Commits per committer: 10.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Keith Goldfeld	k**d@g**m	206
assignUser	g**b@k**e	194
Keith Goldfeld	k**d@n**g	190
elinsooon	m**n@g**m	54
Keith Goldfeld	g**1@G**l	30
Keith Goldfeld	g**1@g**g	27
GitHub Actions	a**s@g**m	22
Keith Goldfeld	K**G@1**g	10
James Joseph Balamuta	b**2@i**u	6
GertjanV	g****n	6
Keith Goldfeld	g**1@1**l	5
Keith Goldfeld	k**g@K**l	5
Michael Bradley, Jr	m**r@g**m	2
Keith Goldfeld	K**G@K**d	1

Committer Domains (Top 20 + Academic)

ksg-macbook-pro.local.tld: 1 illinois.edu: 1 180madphmlt162.wireless.nyumc.org: 1 github.com: 1 goldfk01-mbp13t.wireless.nyumc.org: 1 nyumc.org: 1 krushak.me: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 74
Total pull requests: 70
Average time to close issues: 5 months
Average time to close pull requests: 2 days
Total issue authors: 16
Total pull request authors: 3
Average comments per issue: 3.18
Average comments per pull request: 3.6
Merged pull requests: 61
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 2
Average time to close issues: 10 months
Average time to close pull requests: 4 days
Issue authors: 2
Pull request authors: 1
Average comments per issue: 1.5
Average comments per pull request: 3.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

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kgoldfeld (44)
assignUser (9)
elinsooon (7)
gabgilling (2)
simonelgato (1)
NielsKrarup (1)
zackarno (1)
Alik-V (1)
moosterwegel (1)
momozinho (1)
ddsjoberg (1)
ecohen13 (1)
DAVIDCRUZ0202 (1)
lorenzoFabbri (1)
hebaalhosainyTU (1)

Pull Request Authors

kgoldfeld (51)
assignUser (12)
elinsooon (7)

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Packages

Total packages: 1
Total downloads:
- cran 949 last-month

Total dependent packages: 3
Total dependent repositories: 6
Total versions: 27
Total maintainers: 1

cran.r-project.org: simstudy

Simulation of Study Data

Homepage: https://github.com/kgoldfeld/simstudy
Documentation: http://cran.r-project.org/web/packages/simstudy/simstudy.pdf
License: GPL-3
Latest release: 0.8.1
published over 1 year ago

Versions: 27
Dependent Packages: 3
Dependent Repositories: 6
Downloads: 949 Last month

Rankings

Stargazers count: 5.2%

Forks count: 7.9%

Average: 9.4%

Dependent packages count: 10.9%

Downloads: 11.2%

Dependent repos count: 11.9%

Maintainers (1)

keith.goldfeld@nyulangone.org

Last synced: 4 months ago

simstudy

Science Score: 100.0%

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README.Rmd

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JOSS Publication

simstudy: Illuminating research methods through data generation

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Papers & Mentions

Estimands in epigenome-wide association studies

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