Software

R Packages on CRAN

Package	Status	Description	CRAN	GitHub	Docs	Publication	Commits	Merged PRs	Open PRs
serocalculator	Active	Estimate seroconversion rates and frequencies from antibody levels in cross-sectional samples	CRAN	GitHub	Docs		—	266	20
rwicc	Archived	Regression with interval-censored covariates	CRAN Archive	GitHub	Docs	DOI	—	18	1

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My Repositories

Repositories under my personal GitHub account, the UCD-SERG organization, and other organizations where I am an author or maintainer.

R Packages

Package	Description	GitHub	Commits	Merged PRs	Open PRs
rmb	Data sets from Regression Methods in Biostatistics (Vittinghoff et al.)	GitHub	—	8	0
snapr	Convenient snapshot testing functions for R packages	GitHub	—	12	1
pr.helpers	Generalization of pull-request helper functions from {usethis}	GitHub	—	3	0
binom.se	Sample size calculations for Bernoulli probability estimation	GitHub	—	0	0
CSICalc	Methods for estimating incidence from cross-sectional biomarker surveys	GitHub	—	0	0
ping	Graph ping data in R	GitHub	—	0	0
ucdavis/rSuStaIn	R implementation of the SuStaIn (Subtype and Stage Inference) algorithm	GitHub	—	3	0
ucdavis/serodynamics	Modeling longitudinal immune seroresponses to infections	GitHub	—	58	3
UCLA-PHP/FluView	Flu surveillance data visualization	GitHub	—	9	0

Quarto Extensions

Extension	Description	GitHub	Commits	Merged PRs	Open PRs
slidebreak	Insert slide breaks into Quarto revealjs presentations	GitHub	—	2	0
revealjs-html-links	Enable HTML-style links in revealjs presentations	GitHub	—	2	0
div-anchors	Anchors for theorem-variant divs in Quarto	GitHub	—	5	0
equation-anchors	Anchors for numbered equations in Quarto	GitHub	—	3	0
qet	Quarto extension template	GitHub	—	1	0
macros	Shared macro definitions for Quarto documents	GitHub	—	26	0

Quarto Books & Templates

Project	Description	GitHub	Commits	Merged PRs	Open PRs
rme	Regression Models for Epidemiology — an open Quarto textbook	GitHub	—	340	5
qwt	Template for building websites with Quarto	GitHub	—	35	3

Shiny Applications

App	Description	GitHub	Commits	Merged PRs	Open PRs
shiny.demos	Teaching demos for Shiny applications	GitHub	—	0	0
UCD-SERG/shiny_serocalculator	Shiny app for the serocalculator package	GitHub	—	3	0
UCD-SERG/shiny_decay_curve	Shiny app to display antibody decay curves	GitHub	—	1	1
UCLA-PHP/wastewater	Wastewater surveillance dashboard	GitHub	—	3	0

Analysis & Research Code

Repo	Description	GitHub	Commits	Merged PRs	Open PRs
UCD-IDDRC/fxtas	Analysis code for Fragile X-associated tremor/ataxia syndrome (FXTAS)	GitHub	—	114	5
ucdavis/win	UC Davis WIN (Workforce Inequity in Neuroscience) project	GitHub	—	38	1
ucdavis/ettbc	Analysis code for enteric disease burden estimation	GitHub	—	4	1
UCLA-PHP/school.epi.abm	Agent-based model of infection dynamics in K-6 schools during COVID-19	GitHub	—	4	1
ROBAS-UCLA/Brushing-Behavior	Longitudinal models of toothbrushing behavior	GitHub	—	3	0
vax.eff	Code from “Estimating Vaccine Effectiveness from Linking Population-Based Health Registries” (Brookmeyer & Morrison, AJE, 2022)	GitHub	—	0	0
LA.Vax.Data	Pre-processes LA County vaccination rates by community statistical area	GitHub	—	0	0
hybrid.charts.la	Adaptation of Wisconsin COVID-19 data visualizations for Los Angeles County	GitHub	—	0	0
UCD-SERG/SSudanTyphoidSeroIncidence	Analysis of seroincidence of enteric fever in Juba, South Sudan	GitHub	—	0	0
EM.examples	Examples of EM algorithms	GitHub	—	0	0

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External Contributions

Pull requests I have authored or been assigned to in repositories outside my own accounts, ordered by number of merged PRs.

Repository	Description	Commits	Merged PRs	Open PRs
hadley/mastering-shiny	Mastering Shiny book by Hadley Wickham	—	9	0
ajmichaelucd/mic.sim	Simulation of minimum inhibitory concentration (MIC) distributions	—	7	0
ucjug/workshop_julia_basics	UC Davis Julia Users Group introductory workshop materials	—	3	0
sun123zxy/quarto-callouty-theorem	Quarto extension for callout-style theorem environments	—	1	0
CHOP-CGTInformatics/REDCapTidieR	R package for tidying REDCap exports	—	2	0
Nowosad/colorblindcheck	R package for checking colorblind accessibility of color palettes	—	1	0
r-quantities/units	Measurement units for R vectors	—	1	0
r-lib/scales	Scale functions for ggplot2	—	1	0
easystats/parameters	Parameters and statistical summaries for model objects in R	—	1	0
glmmTMB/glmmTMB	Generalized linear mixed models via Template Model Builder	—	1	0
edwindj/ffbase	Base R functions for ff large-data objects	—	1	0