R (>= 2.10), GOSim, SubpathwayMiner, dynamicTreeCut,
moduleColor, RBGL, graph, Rgraphviz
This package implements multiple similarity measures for
DO terms and gene products. It is aiming at disease analyis for
gene sets. Modules of a gene set could be detected and further
multilayer annoated on DO, GO and KEGG. We also provides users
to conduct DO enrichment analysis and basic information
fetching for DO.DOSim: An R package for similarity between
diseases based on Disease
Ontology(http://www.biomedcentral.com/1471-2105/12/266)

R (>= 2.10), GOSim, dynamicTreeCut, moduleColor, RBGL, graph,
Rgraphviz

Renders DOT diagram markup language in R and also provides the possibility to
export the graphs in PostScript and SVG (Scalable Vector Graphics) formats.
In addition, it supports literate programming packages such as 'knitr' and
'rmarkdown'.

c(person("Danyu", "Lin", role = "aut"),
person("Donglin", "Zeng", role = "aut"),
person("Shannon", "Holloway", role = c("aut", "cre"),
email = "sthollow@ncsu.edu"))
Implements a nonparametric maximum likelihood method for evaluating the durability of vaccine efficacy in a randomized, placebo-controlled clinical trial with staggered enrollment of participants and potential crossover of placebo recipients. Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021) <doi:10.1101/2021.01.13.21249779>.
'vcFit.R' 'vaccine.R' 'dove.R' 'doveData.R' 'plot.doveObj.R'
'print.doveObj.R'
Danyu Lin [aut],
Donglin Zeng [aut],
Shannon Holloway [aut, cre]

c(person("Danyu", "Lin", role = "aut"),
person("Yu", "Gu", role = "aut"),
person("Donglin", "Zeng", role = "aut"),
person("Shannon", "Holloway", role = c("aut", "cre"),
email = "sthollow@ncsu.edu"))
Implements maximum likelihood methods for
evaluating the durability of vaccine efficacy in a randomized,
placebo-controlled clinical trial with staggered enrollment of participants
and potential crossover of placebo recipients before the end of the trial.
Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab226>
and
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
'VEplot_type2.R' 'VEcal.R' 'postProcess.R' 'CoxReg.R'
'RcppExports.R' 'VEplot_type1.R' 'postInterval.R' 'postBeta.R'
'infBeta.R' 'postProcessDove.R' 'scores.R' 'loc.R' 'vcFit.R'
'verifyInputs.R' 'dove.R' 'dove2.R' 'doveData.R' 'iterations.R'
'plot.DOVE.R' 'postVE.R' 'print.DOVE.R' 'vaccine.R'
Danyu Lin [aut],
Yu Gu [aut],
Donglin Zeng [aut],
Shannon Holloway [aut, cre]