Graphical modelling by log-linear models (an interface from R to CoCo)

Documentation for package ‘CoCo’ version 0.1.7.6

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-- --

-- B --

backward	Stepwise model selection by backward elimination and forward selection of edges or interaction terms
Byssinosis38	Byssinosis

-- C --

call.coco	Call CoCo
call.coco.chars	Call Coco with only code, subcode, and one argument
call.coco.longs	Call Coco with only code, subcode, and one argument
call.coco.message	Call CoCo
call.coco.reals	Call Coco with only code, subcode, and one argument
call.coco.simple	Call Coco with only code and subcode
cleanData	Remove cases from cells set to zero by structurally
clearCoCoObjects	Clear CoCo object
CoCo	The CoCo package
coco.enter.all	Call CoCo with all arguemnts
coco.enter.string	Call Coco with only code, subcode, and one argument
coco.init	Init a CoCo object.
coco.load	Load CoCo
coco.replace.all	Call CoCo with all arguemnts
coco.resume	Enter a CoCo object
coco.simple.command	Call Coco with only code and subcode
coco.simple.double	Call CoCo with setting of models
coco.simple.model	Call CoCo with setting of models
coco.start	Enter a CoCo object
coco.string.double	Call CoCo with setting of models
coco.string.model	Call CoCo with setting of models
CoCoClass-class	CoCoClass Class
CoCoIdClass-class	CoCoIdClass Class
CoCoModelClass-class	CoCoModelClass Class
currentCoCo	Make CoCo object to default CoCo object

-- D --

Dawid79	Dawid and Skene (1979)
dG	The CoCo package
disposeOfEh	Dispose of the model classes of the EH procedure
disposeOfModel	Dispose of models
disposeOfQtable	Dispose of Q-tables and Q-lists (structurally zero cells)

-- E --

editModel	Edit model
eh	The Edwards and Havranek model search procedure
ehExtract	Extract models from the EH-procedure
ehFindDual	Find duals in the EH procedure
ehFit	Fit and classify models in the EH procedure
ehForceAccept	Force models into the classes of the EH procedure
ehForceAddDualToClass	Force a dual into a class of models of the EH procedure
ehForceFix	Fix edges or terms of the models in the EH procedure
ehForceReject	Force models into the classes of the EH procedure
ehSetBase	The base model of the EH procedure
ehSetMainEffects	Set the main effects of the models in the EH procedure
emOn	Handling of latent variables and missing values by the EM algorithm
endCoCo	End a CoCo object
enterDataFrame	Enter a data.frame into a CoCo object
enterList	Enter a list of cases into a CoCo object
enterModel	Enter a model
enterNames	Enter a specification of variables into the CoCo object
enterQlist	Enter initial values for the IPS algorithm and declare cells to be zero by structure
enterQtable	Enter initial values for the IPS algorithm and declare cells to be zero by structure
enterTable	Enter a table of counts of the tables formed by cross classifying discrete variables
enterTwoLists	Enter a list of cases into a CoCo object
excludeMissing	Handling of missing values by excluding cases
exportCoCo	Write and read the CoCo data and the models to a binary file
extractData	Extract the data from a CoCo Object

-- F --

Fever	Risk of rheumatic fever recurrence after streptococcal infections
forward	Stepwise model selection by backward elimination and forward selection of edges or interaction terms
Fuchs82	Fuchs, C. (1982)

-- H --

Highway safety

-- I --

importCoCo	Write and read the CoCo data and the models to a binary file
is.gc	Generating classes
is.number	Test for a number
isSubmodel	Is the CURRENT model a sub model of the BASE model ?

-- M --

make.coco	Make a CoCo object
make.cococg	Make a CoCo object
make.model	Make a CoCo model object
makeBase	Move the pointer named CURRENT (BASE) in the CoCo object
makeCoCo	Make a CoCo object
makeCurrent	Move the pointer named CURRENT (BASE) in the CoCo object
makeCurrentCoCo	Make CoCo object to default CoCo object
makeModel	Make a CoCo model object
my.assign	Assign a value to a name
my.not.a.number	The invalid number for CoCo objects

-- N --

The number of variables in the CoCo object

-- O --

ok.coco	Test if the call to CoCo succeeded
ok.coco.start	Test if the call to CoCo succeeded
optionsCoCo	Options settings for CoCo objects

-- P --

partialAssociations	Show partial associations
propertyModel	Ask a query for a model
propertySet	Ask a query for a set of variables

-- Q --

End a CoCo object

-- R --

randomTableReplacement	Replace the table of counts with a random table with margins unchanged
recover.coco.model	Recover a CoCo model object
Reinis	Reinis: Coronary heart disease
returnDeviance	Return likelihoods, deviance, dimensions, etc.
returnEdges	Return the indices of vertices of edges
returnExpression	Return the expression of the estimates of parameters
returnFix	Return the edges fixed in model selection
returnJunctionTree	Return the junction tree
returnModel	Return the model
returnModelNumber	Return the number of the CURRENT, BASE, or the LAST model
returnModelVariates	Return the variates of the model
returnNcells	Return the number of cells in a table
returnSets	Return a specific subset of the variables
returnTable	Return the counts and fitted values of a marginal table
returnTest	Return the Pearson Chi-square, the power divergence, etc.
returnVariableDescription	Return the specification of the data in the CoCo object
returnVertexOrder	Return vertex order

-- S --

Scrotal94	Scrotal Swelling Data
setOrdinal	Declare some of the discrete variables to be ordinal
setUseVariables	Declare which variables to enter
showDeviance	Show the difference between likelihoods, dimension, etc.
showFormula	Show the model formula
showModel	Show the model
showOptions	Show the options of the CoCo object
showTable	The counts and fitted values of a marginal table
showTest	Show the Pearson Chi-square, the power divergence, etc.
showTests	Show all the stored tests of a CoCo object
showVertexOrder	Show the vertex ordering
sinkCoCo	Direct output to a file
summaryTable	Univariate summary statistics for table values

-- U --

Carcinoma of the uterine cervix