SimReg: Similarity Regression
Version 3.0

Functions for performing Bayesian similarity regression, and evaluating the probability of association between sets of ontological terms and binary response vector. A random model is compared with one in which the log odds of a true response is linked to the semantic similarity between terms and a latent characteristic ontological profile.

AuthorDaniel Greene
Date of publication2016-10-15 18:51:56
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version3.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SimReg")

Getting started

Package overview
Prior phenotypic information
Similarity Regression - Introduction

Popular man pages

log_BF: Calculate log Bayes factor for similarity the model,...
plot.sim_reg_summary: Plot summary of 'sim_reg_output' object
plot_term_marginals: Create ontological plot of marginal probabilities of terms
print.sim_reg_summary: Print 'sim_reg_summary' object
sum_log_probs: Calculate sum of log probabilities on log scale without...
summary.sim_reg_output: Get summary of 'sim_reg_output' object
term_marginals: Calculate marginal probability of terms inclusion in 'phi'
See all...

All man pages Function index File listing

Man pages

get_term_marginals: Calculate marginal probability of terms inclusion in 'phi'...
get_terms: Get full set of terms to use in inference procedure based on...
log_BF: Calculate log Bayes factor for similarity the model,...
plot.sim_reg_summary: Plot summary of 'sim_reg_output' object
plot_term_marginals: Create ontological plot of marginal probabilities of terms
print.sim_reg_output: Print 'sim_reg_output' object
print.sim_reg_summary: Print 'sim_reg_summary' object
prob_association: Calculate probability of association between 'y' and 'x'
sim_reg: Similarity regression
SimReg-package: Similarity Regression Functions
sum_log_probs: Calculate sum of log probabilities on log scale without...
summary.sim_reg_output: Get summary of 'sim_reg_output' object
term_marginals: Calculate marginal probability of terms inclusion in 'phi'

Functions

ML Source code
SimReg3 Man page
SimReg3-package Man page
bg Source code
bg_ML Source code
bg_rate Source code
cumsumgrid Source code
demotions Source code
dendroterms Source code
dendroterms_list Source code
discrete_gamma Source code
f Source code
f_ML Source code
f_step Source code
fg Source code
fg_step Source code
geom_phi_log_prob Source code
get_phi_roots Source code
get_term_marginals Man page Source code
get_terms Man page Source code
log_BF Man page Source code
log_BF.default Man page Source code
log_BF.sim_reg_output Man page Source code
min_req_signif Source code
plot.sim_reg_output Man page Source code
plot.sim_reg_summary Man page Source code
plot_term_marginals Man page Source code
print.sim_reg_output Man page Source code
print.sim_reg_summary Man page Source code
prob_association Man page Source code
promotions Source code
sim_reg Man page Source code
stack_dendro Source code
sum_log_probs Man page Source code
summary.sim_reg_output Man page Source code
term_marginals Man page Source code
term_set_names Source code
unique_term_sets Source code

Files

inst
inst/doc
inst/doc/SimReg-Introduction.R
inst/doc/SimReg-Priors.html
inst/doc/SimReg-Priors.Rmd
inst/doc/SimReg-Introduction.html
inst/doc/SimReg-Introduction.Rmd
inst/doc/SimReg-Priors.R
src
src/fml.cpp
src/bgml.cpp
src/ml.cpp
src/utils.h
src/RcppExports.cpp
NAMESPACE
R
R/generic.R
R/plot.R
R/phi-priors.R
R/ml.R
R/inference.R
R/RcppExports.R
R/pick.R
vignettes
vignettes/SimReg-Priors.Rmd
vignettes/SimReg-Introduction.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/print.sim_reg_summary.Rd
man/get_term_marginals.Rd
man/log_BF.Rd
man/SimReg-package.Rd
man/term_marginals.Rd
man/prob_association.Rd
man/plot.sim_reg_summary.Rd
man/print.sim_reg_output.Rd
man/sim_reg.Rd
man/get_terms.Rd
man/sum_log_probs.Rd
man/plot_term_marginals.Rd
man/summary.sim_reg_output.Rd
SimReg documentation built on May 19, 2017, 1:31 p.m.

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