MXM: Discovering Multiple, Statistically-Equivalent Signatures
Version 0.9.9

Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.

Browse man pages Browse package API and functions Browse package files

AuthorIoannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Date of publication2017-03-26 16:11:42 UTC
MaintainerMichail Tsagris <mtsagris@csd.uoc.gr>
LicenseGPL-2
Version0.9.9
URL http://mensxmachina.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MXM")

Man pages

auc: ROC and area under the curve
beta.mod: Beta regression
beta.regs: Many simple beta regressions.
bic.fsreg: Variable selection in regression models with forward...
bic.glm.fsreg: Variable selection in generalised linear models with forward...
bs.reg: Variable selection in regression models with backward...
censIndCR: Conditional independence test for survival data
condi: Conditional independence test for continuous class variables...
cv.ses: Cross-Validation for SES and MMPC
dag2eg: Transforms a DAG into an essential graph
equivdags: Check Markov equivalence of two DAGs
findDescendants: Returns and plots, if asked, the descendants or ancestors of...
fs.reg: Variable selection in regression models with forward...
generatefolds: Generate random folds for cross-validation
glm.bsreg: Variable selection in generalised linear regression models...
glm.fsreg: Variable selection in generalised linear regression models...
gSquare: G-square conditional independence test for discrete data
iamb: IAMB variable selection
iamb.bs: IAMB backward selection phase
lm.fsreg: Variable selection in linear regression models with forward...
mammpc.output-class: Class '"mammpc.output"'
ma.ses: ma.ses: Feature selection algorithm for identifying multiple...
mases.output-class: Class '"mases.output"'
mb: Returns and plots, if asked, the Markov blanket of a node (or...
mmhc.skel: The skeleton of a Bayesian network as produced by MMHC
mmmb: Max-min Markov blanket algorithm
MMPCoutput-class: Class '"MMPCoutput"'
mmpc.path: MMPC solution paths for many combinations of hyper-parameters
MMPC.temporal.output-class: Class '"MMPC.temporal.output"'
MXMCondIndTests: MXM Conditional independence tests
MXM-internal: Internal MXM Functions
MXM-package: This is an R package that currently implements feature...
nei: Returns and plots, if asked, the node(s) and their...
partialcor: Partial correlation
pc.or: The orientations part of the PC algorithm.
pc.skel: The skeleton of a Bayesian network produced by the PC...
permcor: Permutation based p-value for the Pearson correlation...
plotnetwork: Interactive plot of an (un)directed graph
rdag: Simulation of data from DAG (directed acyclic graph)
reg.fit: Regression modelling
ridge.plot: Ridge regression
ridge.reg: Ridge regression
ridgereg.cv: Cross validation for the ridge regression
SES: SES: Feature selection algorithm for identifying multiple...
ses.model: Regression model(s) obtained from SES or MMPC
SESoutput-class: Class '"SESoutput"'
SES.temporal: SES.temporal: Feature selection algorithm for identifying...
SES.temporal.output-class: Class '"SES.temporal.output"'
tc.plot: Plot of longitudinal data
testIndBeta: Beta regression conditional independence test for...
testIndBinom: Binomial regression conditional independence test for success...
testIndClogit: Conditional independence test based on conditional logistic...
testIndFisher: Fisher and Spearman conditional independence test for...
testIndGLMM: Linear mixed models conditional independence test for...
testIndLogistic: Conditional independence test for binary, categorical or...
testIndPois: Regression conditional independence test for discrete...
testIndReg: Linear (and non-linear) regression conditional independence...
testIndSpeedglm: Conditional independence test for continuous, binary and...
transitiveClosure: Returns the transitive closure of an adjacency matrix
undir.path: Undirected path(s) between two nodes
univregs: Univariate regression based tests
zip.mod: Zero inflated Poisson regression
zip.regs: Many simple zero inflated Poisson regressions.

Functions

CondIndTests Man page
IdentifyEquivalence Man page Source code
IdentifyEquivalence.ma Man page Source code
IdentifyEquivalence.temporal Man page Source code
InternalMMPC Man page Source code
InternalMMPC.temporal Man page Source code
InternalSES Man page Source code
InternalSES.temporal Man page Source code
Internalmammpc Man page Source code
Internalmases Man page Source code
MMPC Man page Source code
MMPC.temporal Man page Source code
MMPC.temporal.output Man page
MMPC.temporal.output-class Man page
MMPCoutput Man page
MMPCoutput-class Man page
MXM-package Man page
R0 Man page Source code
R1 Man page Source code
R2 Man page Source code
R3 Man page Source code
SES Man page Source code
SES.temporal Man page Source code
SES.temporal.output Man page
SES.temporal.output-class Man page
SESoutput Man page
SESoutput-class Man page
acc.mxm Man page Source code
acc_multinom.mxm Man page Source code
apply_ideq Man page Source code
apply_ideq.ma Man page Source code
apply_ideq.temporal Man page Source code
auc Man page Source code
auc.mxm Man page Source code
beta.bsreg Man page Source code
beta.fsreg Man page Source code
beta.mod Man page Source code
beta.mxm Man page Source code
beta.reg Man page Source code
beta.regs Man page Source code
betamle.wei Man page Source code
bic.betafsreg Man page Source code
bic.fsreg Man page Source code
bic.glm.fsreg Man page Source code
bic.zipfsreg Man page Source code
binom.mxm Source code
binomdev.mxm Source code
bs.reg Man page Source code
cat.ci Man page Source code
censIndCR Man page Source code
censIndER Man page Source code
censIndWR Man page Source code
ci.mxm Man page Source code
ciwr.mxm Man page Source code
compare_p_values Man page Source code
condi Man page Source code
condi.perm Man page
coxph.mxm Man page Source code
cv.mmpc Man page Source code
cv.ses Man page Source code
cvmmpc.par Man page Source code
cvses.par Man page Source code
dag2eg Man page Source code
dag_to_eg Man page Source code
dist.condi Man page Source code
equivdags Man page Source code
exporeg.mxm Source code
findAncestors Man page Source code
findDescendants Man page Source code
fs.reg Man page Source code
gSquare Man page Source code
generatefolds Man page Source code
glm.bsreg Man page Source code
glm.fsreg Man page Source code
glm.fsreg_2 Man page Source code
glm.mxm Man page Source code
iamb Man page Source code
iamb.betabs Man page Source code
iamb.bs Man page Source code
iamb.glmbs Man page Source code
iamb.zipbs Man page Source code
identifyTheEquivalent Man page Source code
identifyTheEquivalent.ma Man page Source code
identifyTheEquivalent.temporal Man page Source code
internaliamb.betabs Source code
internaliamb.binombs Man page Source code
internaliamb.bs Source code
internaliamb.lmbs Man page Source code
internaliamb.poisbs Man page Source code
internaliamb.zipbs Source code
is.sepset Man page Man page Source code
lm.fsreg Man page Source code
lm.fsreg_2 Man page Source code
lm.fsreg_2.heavy Man page Source code
lm.fsreg_heavy Man page Source code
lm.mxm Man page Source code
lmrob.mxm Man page Source code
ma.mmpc Man page Source code
ma.ses Man page Source code
mammpc.output Man page
mammpc.output-class Man page
mases.output Man page
mases.output-class Man page
max_min_assoc Man page Source code
max_min_assoc.ma Man page Source code
max_min_assoc.temporal Man page Source code
mb Man page Source code
min_assoc Man page Source code
min_assoc.ma Man page Source code
min_assoc.temporal Man page Source code
mmhc.skel Man page Source code
mmmb Man page Source code
mmpc.model Man page Source code
mmpc.path Man page Source code
mse.mxm Man page Source code
multinom.mxm Man page Source code
nb.mxm Man page Source code
nbdev.mxm Man page Source code
nchoosek Man page Source code
nei Man page Source code
ord_mae.mxm Man page Source code
ordinal.mxm Man page Source code
partialcor Man page Source code
pc.con Man page Source code
pc.or Man page Source code
pc.skel Man page Source code
permFisher Man page Source code
permcor Man page Source code
permcorrels Man page Source code
plot,MMPC.temporal.output,ANY-method Man page
plot,MMPC.temporal.output-method Man page
plot,MMPCoutput,ANY-method Man page
plot,MMPCoutput-method Man page
plot,SES.temporal.output,ANY-method Man page
plot,SES.temporal.output-method Man page
plot,SESoutput,ANY-method Man page
plot,SESoutput-method Man page
plot,mammpc.output,ANY-method Man page
plot,mammpc.output-method Man page
plot,mases.output,ANY-method Man page
plot,mases.output-method Man page
plotnetwork Man page Source code
pois.mxm Man page Source code
poisdev.mxm Man page Source code
proc_time-class Man page
rdag Man page Source code
reg.fit Man page Source code
regbeta Man page Source code
regbetawei Man page Source code
regzip Man page Source code
regzipwei Man page Source code
ridge.plot Man page Source code
ridge.reg Man page Source code
ridgereg.cv Man page Source code
rq.mxm Man page Source code
ses.model Man page Source code
summary,MMPC.temporal.output-method Man page
summary,MMPCoutput-method Man page
summary,SES.temporal.output-method Man page
summary,SESoutput-method Man page
summary,mammpc.output-method Man page
summary,mases.output-method Man page
tc.plot Man page Source code
testIndBeta Man page Source code
testIndBinom Man page Source code
testIndClogit Man page Source code
testIndFisher Man page Source code
testIndGLMM Man page Source code
testIndIGreg Man page Source code
testIndLogistic Man page Source code
testIndMVreg Man page Source code
testIndNB Man page Source code
testIndPois Man page Source code
testIndRQ Man page Source code
testIndReg Man page Source code
testIndSpearman Man page Source code
testIndSpeedglm Man page Source code
testIndZIP Man page Source code
topological_sort Man page Source code
transitiveClosure Man page Source code
undir.path Man page Source code
univariateScore Man page Source code
univariateScore.ma Man page Source code
univariateScore.temporal Man page Source code
univregs Man page Source code
vara Man page Source code
weibreg.mxm Man page Source code
zip.bsreg Man page Source code
zip.fsreg Man page Source code
zip.mod Man page Source code
zip.reg Man page Source code
zip.regs Man page Source code
zipmle.wei Man page Source code
zipwei Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/article.pdf
inst/doc/article.ltx
NAMESPACE
R
R/beta.reg.R
R/SES.R
R/zip.reg.R
R/testIndLogistic.R
R/rdag.R
R/permcor.R
R/lm.fsreg.R
R/bic.zipfsreg.R
R/testIndClogit.R
R/zip.regs.R
R/censIndCR.R
R/ma.mmpc.R
R/univregs.R
R/transitiveClosure.R
R/cvses.par.R
R/bic.glm.fsreg.R
R/SES.temporal.R
R/lm.fsreg_2.heavy.R
R/pc.or.R
R/glm.fsreg.R
R/mmpc.path.R
R/permFisher.R
R/topological_sort.R
R/bic.fsreg.R
R/iamb.R
R/testIndIGreg.R
R/testIndGLMM.R
R/iamb.glmbs.R
R/testIndSpearman.R
R/beta.mod.R
R/testIndReg.R
R/testIndZIP.R
R/cv.mmpc.R
R/cvmmpc.par.R
R/testIndRQ.R
R/MMPC.R
R/findDescendants.R
R/censIndWR.R
R/dist.condi.R
R/bs.reg.R
R/lm.fsreg_2.R
R/zip.mod.R
R/ridge.reg.R
R/gSquare.R
R/generatefolds.R
R/dag2eg.R
R/iamb.zipbs.R
R/ma.ses.R
R/testIndFisher.R
R/MMPC.temporal.R
R/zip.fsreg.R
R/permcorrels.R
R/mammpc.output_script.R
R/glm.bsreg.R
R/bic.betafsreg.R
R/condi.R
R/lm.fsreg_heavy.R
R/testIndMVreg.R
R/mmpc.model.R
R/SES.temporal.opoutput_script.R
R/equivdags.R
R/findAncestors.R
R/testIndPois.R
R/iamb.betabs.R
R/ses.model.R
R/testIndNB.R
R/undir.path.R
R/MMPCoutput_script.R
R/MMPC.temporal.output_script.R
R/dag_to_eg.R
R/testIndSpeedglm.R
R/mases.output_script.R
R/pc.con.R
R/ridge.plot.R
R/vara.R
R/zip.bsreg.R
R/testIndBinom.R
R/ridgereg.cv.R
R/censIndER.R
R/pc.skel.R
R/partialcor.R
R/glm.fsreg_2.R
R/mb.R
R/plotnetwork.R
R/iamb.bs.R
R/beta.regs.R
R/nei.R
R/reg.fit.R
R/tc.plot.R
R/cat.ci.R
R/beta.fsreg.R
R/testIndBeta.R
R/cv.ses.R
R/auc.R
R/fs.reg.R
R/SESoutput_script.R
R/beta.bsreg.R
R/mmhc.skel.R
R/mmmb.R
vignettes
vignettes/claim2_boxplot_ses_coefvar.eps
vignettes/claim2_boxplot_ses_coefvar-eps-converted-to.pdf
vignettes/athineou.bib
vignettes/boxplot_perf_ses_lasso-eps-converted-to.pdf
vignettes/JSS.bib
vignettes/article.ltx
vignettes/jsslogo.jpg
vignettes/boxplot_perf_ses_lasso.eps
MD5
build
build/vignette.rds
DESCRIPTION
man
man/univregs.Rd
man/dag2eg.Rd
man/SES.temporal.output-class.Rd
man/gSquare.Rd
man/censIndCR.Rd
man/testIndGLMM.Rd
man/testIndBinom.Rd
man/mammpc.output-class.Rd
man/beta.regs.Rd
man/rdag.Rd
man/findDescendants.Rd
man/zip.mod.Rd
man/MXMCondIndTests.Rd
man/testIndBeta.Rd
man/glm.fsreg.Rd
man/bic.fsreg.Rd
man/ses.model.Rd
man/equivdags.Rd
man/iamb.bs.Rd
man/testIndClogit.Rd
man/testIndPois.Rd
man/generatefolds.Rd
man/partialcor.Rd
man/zip.regs.Rd
man/MMPCoutput-class.Rd
man/MXM-package.Rd
man/tc.plot.Rd
man/auc.Rd
man/testIndSpeedglm.Rd
man/MMPC.temporal.output-class.Rd
man/testIndLogistic.Rd
man/bs.reg.Rd
man/transitiveClosure.Rd
man/bic.glm.fsreg.Rd
man/condi.Rd
man/reg.fit.Rd
man/lm.fsreg.Rd
man/testIndReg.Rd
man/ridge.plot.Rd
man/ridgereg.cv.Rd
man/ridge.reg.Rd
man/cv.ses.Rd
man/fs.reg.Rd
man/SES.Rd
man/mmmb.Rd
man/pc.or.Rd
man/undir.path.Rd
man/SESoutput-class.Rd
man/permcor.Rd
man/nei.Rd
man/mmpc.path.Rd
man/beta.mod.Rd
man/SES.temporal.Rd
man/MXM-internal.Rd
man/mmhc.skel.Rd
man/plotnetwork.Rd
man/ma.ses.Rd
man/iamb.Rd
man/mb.Rd
man/glm.bsreg.Rd
man/testIndFisher.Rd
man/mases.output-class.Rd
man/pc.skel.Rd
MXM documentation built on May 19, 2017, 7:37 p.m.