MCMCvis

MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output - Published in JOSS (2018)

https://github.com/caseyyoungflesh/mcmcvis

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 6 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
3 of 6 committers (50.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Engineering Computer Science - 60% confidence

Last synced: 4 months ago · JSON representation

Repository

R package to visualize, manipulate, and summarize MCMC output

Basic Info

Host: GitHub
Owner: caseyyoungflesh
License: gpl-3.0
Language: HTML
Default Branch: master
Homepage:
Size: 38.1 MB

Statistics

Stars: 38
Watchers: 3
Forks: 4
Open Issues: 5
Releases: 8

Created almost 10 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License Codemeta

MCMCvis

MCMCvis is an R package used to visualize, manipulate, and summarize MCMC output. MCMC output may be derived from Bayesian models fit with Stan, NIMBLE, JAGS, and other software. This includes (but is not limited to) output from the rstan, cmdstanr, rstanarm, brms, rjags, nimble, R2jags, and jagsUI packages - object types are recognized automatically.

The package contains six functions:

MCMCsummary - summarize MCMC output for particular parameters of interest
MCMCpstr - summarize MCMC output for particular parameters of interest while preserving parameter structure
MCMCtrace - create trace and density plots of MCMC chains for particular parameters of interest
MCMCchains - easily extract posterior chains from MCMC output for particular parameters of interest
MCMCplot - create caterpillar plots from MCMC output for particular parameters of interest
MCMCdiag - create a .txt file and save specified objects that summarize model inputs, outputs, and diagnostics

MCMCvis was designed to perform key functions for MCMC analysis using minimal code, in order to free up time/brainpower for interpretation of analysis results. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output.

This package can be cited as:

Youngflesh, C. (2018) MCMCvis: Tools to visualize, manipulate, and summarize MCMC output. Journal of Open Source Software, 3(24), 640, https://doi.org/10.21105/joss.00640

Installation

You can install the released version on CRAN with: {r} install.packages('MCMCvis')

Or the latest, development version from Github with: {r} install.packages('remotes') remotes::install_github('caseyyoungflesh/MCMCvis', build_vignettes = TRUE)

Vignette

The vignette for this package can be run using: {r} vignette('MCMCvis')

Examples

Summarize

```{r} data(MCMCdata) MCMCsummary(MCMCdata, params = 'beta', round = 2)

> mean sd 2.5% 50% 97.5% Rhat n.eff

> beta[1] -4.62 6.54 -17.19 -4.62 8.38 1 10411

> beta[2] -14.17 6.63 -27.15 -14.08 -1.41 1 10500

> beta[3] -35.94 8.42 -52.60 -36.00 -19.26 1 10884

> beta[4] 6.17 10.72 -14.67 6.11 27.27 1 10500

> beta[5] 8.42 3.46 1.63 8.45 15.13 1 10500

> beta[6] -12.05 2.34 -16.66 -12.05 -7.54 1 10500

```

```{r} MCMCdiag(MCMCdata, filename = 'modelsummary.txt', objectname = 'model-fit.rds', save_object = TRUE, mkdir = 'results-YYYY-MM-DD', round = 3)

saves a text file summarizing model inputs, outputs, and diagnostics (and optionally saves model output and other objects of interest as '.rds' files into a new user-specified directory)

```

Evaluate

{r} PR <- rnorm(15000, 0, 32) MCMCvis::MCMCtrace(MCMC_data, params = 'beta[1]', ISB = FALSE, exact = TRUE, priors = PR, ind = TRUE, Rhat = TRUE, n.eff = TRUE, pdf = FALSE)

Manipulate

{r} just_betas_mcmc_obj <- MCMCchains(MCMC_data, params = 'beta', mcmc.list = TRUE)

Visualize

{r} MCMCplot(object = MCMC_data, object2 = MCMC_data2, params = 'beta', rank = TRUE, offset = 0.14, ref_ovl = TRUE)

Owner

Name: Casey Youngflesh
Login: caseyyoungflesh
Kind: user
Company: Michigan State University

Website: www.caseyyoungflesh.com
Twitter: caseyyoungflesh
Repositories: 2
Profile: https://github.com/caseyyoungflesh

Quantitative Ecology | Global Change | Population Biology | Biodiversity

JOSS Publication

MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output

Published

April 10, 2018

DOI

10.21105/joss.00640

Volume 3, Issue 24, Page 640

Authors

Casey Youngflesh

Stony Brook University

Editor

Arfon Smith

CodeMeta (codemeta.json)

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Papers & Mentions

Total mentions: 3

Tapping into non-English-language science for the conservation of global biodiversity

DOI: 10.1371/journal.pbio.3001296
OpenAlex ID: https://openalex.org/W3201666756
Published: October 2021

Last synced: 2 months ago

Cognitive Mapping Without Vision: Comparing Wayfinding Performance After Learning From Digital Touchscreen-Based Multimodal Maps vs. Embossed Tactile Overlays

DOI: 10.3389/fnhum.2020.00087
OpenAlex ID: https://openalex.org/W3010660260
Published: March 2020

Last synced: 2 months ago

Large‐scale assessment of intra‐ and inter‐annual breeding success using a remote camera network

DOI: 10.1002/rse2.171
OpenAlex ID: https://openalex.org/W3081781080
Published: August 2020

Last synced: 2 months ago

GitHub Events

Total

Issues event: 4
Watch event: 1
Issue comment event: 2
Push event: 1

Last Year

Issues event: 4
Watch event: 1
Issue comment event: 2
Push event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 712
Total Committers: 6
Avg Commits per committer: 118.667
Development Distribution Score (DDS): 0.36

Past Year

Commits: 2
Committers: 1
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Casey Youngflesh	c**h@g**m	456
Casey Youngflesh	c**h@s**u	224
CCheCastaldo	c**b@i**m	19
Christian Che-Castaldo	c**o@i**m	10
Tyler Hardy	t**y@e**u	2
Caseyyoungflesh	C**h@s**u	1

Committer Domains (Top 20 + Academic)

stonybrook.edu: 2 eagles.usm.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 72
Total pull requests: 5
Average time to close issues: 7 months
Average time to close pull requests: about 22 hours
Total issue authors: 12
Total pull request authors: 2
Average comments per issue: 1.42
Average comments per pull request: 1.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: about 1 hour
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Issue Authors

caseyyoungflesh (58)
HAB1990 (3)
jcavieresg (2)
rebeccaltaylor (1)
emmatalis (1)
johnnymdoubleu (1)
jkarreth (1)
kalebentley (1)
dslramsey (1)
ceciliaOLearySBU (1)
tlyons253 (1)
CCheCastaldo (1)

Pull Request Authors

caseyyoungflesh (4)
tylerthardy (1)

Top Labels

Issue Labels

enhancement (29) bug (15) Priority (11)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 1,822 last-month
Total docker downloads: 22,502

Total dependent packages: 2
Total dependent repositories: 6
Total versions: 26
Total maintainers: 1

cran.r-project.org: MCMCvis

Tools to Visualize, Manipulate, and Summarize MCMC Output

Homepage: https://github.com/caseyyoungflesh/MCMCvis
Documentation: http://cran.r-project.org/web/packages/MCMCvis/MCMCvis.pdf
License: GPL-3
Latest release: 0.16.3
published about 2 years ago

Versions: 26
Dependent Packages: 2
Dependent Repositories: 6
Downloads: 1,822 Last month
Docker Downloads: 22,502

Rankings

Docker downloads count: 0.6%

Stargazers count: 9.0%

Average: 10.0%

Downloads: 10.5%

Dependent repos count: 12.0%

Dependent packages count: 13.7%

Forks count: 14.2%

Maintainers (1)

caseyyoungflesh@gmail.com

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
coda * imports
colorspace * imports
methods * imports
overlapping * imports
rstan * imports
knitr * suggests
rmarkdown * suggests
testthat * suggests

MCMCvis

Science Score: 95.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

MCMCvis

Installation

Vignette

Examples

Summarize

> mean sd 2.5% 50% 97.5% Rhat n.eff

> beta[1] -4.62 6.54 -17.19 -4.62 8.38 1 10411

> beta[2] -14.17 6.63 -27.15 -14.08 -1.41 1 10500

> beta[3] -35.94 8.42 -52.60 -36.00 -19.26 1 10884

> beta[4] 6.17 10.72 -14.67 6.11 27.27 1 10500

> beta[5] 8.42 3.46 1.63 8.45 15.13 1 10500

> beta[6] -12.05 2.34 -16.66 -12.05 -7.54 1 10500

saves a text file summarizing model inputs, outputs, and diagnostics (and optionally saves model output and other objects of interest as '.rds' files into a new user-specified directory)

Evaluate

Manipulate

Visualize

Owner

JOSS Publication

MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output

Authors

Editor

Tags

CodeMeta (codemeta.json)

Papers & Mentions

Tapping into non-English-language science for the conservation of global biodiversity

Cognitive Mapping Without Vision: Comparing Wayfinding Performance After Learning From Digital Touchscreen-Based Multimodal Maps vs. Embossed Tactile Overlays

Large‐scale assessment of intra‐ and inter‐annual breeding success using a remote camera network

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: MCMCvis

Rankings

Maintainers (1)

Dependencies