bayesbio: Miscellaneous Functions for Bioinformatics and Bayesian Statistics

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A hodgepodge of hopefully helpful functions. Two of these perform shrinkage estimation: one using a simple weighted method where the user can specify the degree of shrinkage required, and one using James-Stein shrinkage estimation for the case of unequal variances.

Author
Andrew McKenzie [aut, cre]
Date of publication
2016-05-24 16:32:42
Maintainer
Andrew McKenzie <amckenz@gmail.com>
License
GPL-3
Version
1.0.0

View on CRAN

Man pages

a_hat_mle
Likelihood function of the James-Stein shrinkage factor.
allDups
Identify all duplicates values in a vector.
bayesbio
bayesbio: Miscellaneous functions useful in bioinformatics...
cbindFill
cbind while converting missing entries to NA.
createStrings
Creates random, unique character strings.
ggHorizBar
Create a color-labeled horizontal bar plot in ggplot2.
jaccardSets
Jaccard index of two character vectors.
mgsub
Multiple pattern gsub.
nearestTime
Merge data frames based on the nearest datetime differences.
nearestTimeandID
Merge data frames based on the nearest datetime differences...
p.adjust.nlp
Adjust p-values where n is less than p.
pubmedQuery
Perform PubMed queries on 2x2 combinations of term vectors.
subsupDiag
Add values to the super- and sub-diagonals of a matrix.
unequalVarShrink
Perform James-Stein shrinkage estimation using unequal...
weightedShrink
Weighted shrinkage estimation.

Files in this package

bayesbio
bayesbio/tests
bayesbio/tests/testthat.R
bayesbio/tests/testthat
bayesbio/tests/testthat/test_dates.R
bayesbio/tests/testthat/test_misc.R
bayesbio/NAMESPACE
bayesbio/NEWS.md
bayesbio/R
bayesbio/R/pubmedQuery.R
bayesbio/R/ggHorizBar.R
bayesbio/R/p.adjust.nlp.R
bayesbio/R/mergeTime.R
bayesbio/R/cbindFill.R
bayesbio/R/supsubDiag.R
bayesbio/R/weightedShrinkage.R
bayesbio/R/bayesbio_package.R
bayesbio/R/unequalVarShink.R
bayesbio/R/allDups.R
bayesbio/R/mgsub.R
bayesbio/R/jaccardSets.R
bayesbio/R/createStrings.R
bayesbio/MD5
bayesbio/DESCRIPTION
bayesbio/man
bayesbio/man/a_hat_mle.Rd
bayesbio/man/pubmedQuery.Rd
bayesbio/man/nearestTimeandID.Rd
bayesbio/man/nearestTime.Rd
bayesbio/man/createStrings.Rd
bayesbio/man/p.adjust.nlp.Rd
bayesbio/man/weightedShrink.Rd
bayesbio/man/unequalVarShrink.Rd
bayesbio/man/cbindFill.Rd
bayesbio/man/mgsub.Rd
bayesbio/man/subsupDiag.Rd
bayesbio/man/jaccardSets.Rd
bayesbio/man/allDups.Rd
bayesbio/man/ggHorizBar.Rd
bayesbio/man/bayesbio.Rd