cc {epicalc}R Documentation

Odds ratio calculation and graphing

Description

Odds ratio calculation and graphing

Usage

cc(outcome, exposure, decimal = 2, cctable = NULL, graph = TRUE, 
	design = "cohort") 
cci(caseexp, controlex, casenonex, controlnonex, cctable = NULL, 
	decimal = 2, graph = TRUE, design = "cohort") 
cs(outcome, exposure, cctable = NULL, decimal = 2)
csi(caseexp, controlex, casenonex, controlnonex, cctable = NULL, 
	decimal = 2) 
graph.casecontrol(caseexp, controlex, casenonex, controlnonex,
	 decimal=2) 
graph.prospective(caseexp, controlex, casenonex, controlnonex,
	 decimal=2) 
labelTable(outcome, exposure, cctable = NULL, cctable.dimnames = NULL) 
make2x2(caseexp, controlex, casenonex, controlnonex)

Arguments

cctable.dimnames Dimension names of the variables, usually omitted
decimal number of decimal places displayed
outcome, exposure two dichotomous variables
cctable A 2-by-2 table. If specified, will supercede the outcome and exposure variables
graph If TRUE (default), produces an odds ratio plot
design Specification for graph; can be "case control","case-control", "cohort" or "prospective"
caseexp Number of cases exposed
controlex Number of controls exposed
casenonex Number of cases not exosed
controlnonex Number of controls not exposed

Details

'cc' computes odds ratios and 95 percent confidence intervals from outcome and exposure variables. The results are based on the exact method.

'cci' is a variant of 'cc' where four numbers are entered manually.

'cs' is for cohort and cross-sectional studies. It computes the absolute risk, risk difference, and risk ratio. When the exposure is a risk factor, the attributable fraction exposure, attributable fraction population and number needed to harm (NNH) are also displayed in the output. When the exposure is a protective factor, protective efficacy or percent of risk reduced and number needed to treat (NNT) are displayed instead.

'csi' is a variant of 'cs' where four numbers are entered manually.

'make2x2' creates a 2-by-2 table using the above orientation.

'graph.casecontrol' and 'graph.prospective' draw a graph comparing the odds of exposure between cases and controls or odds of diseased between exposed and non-exposed.

These two graphic commands are automatically called by 'cc' and 'cci'.

Alternatively, a table saved from 'make2x2' can be supplied as the 'cctable' argument for the 'cc' command. The squares on the values of each group (case vs control and exposed vs unexposed) represent the relative sample sizes for each group.

Author(s)

Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>

See Also

'fisher.test', 'chisq.test' and 'mhor'

Examples

data(Oswego)
.data <- Oswego
attach(.data)

# The above lines generate a hypothetical data frame. 
# In reality, one just types 'use("Oswego.rec")', if the file is available.
cc(ill, chocolate)
cc(ill, chocolate, design="case-control")
cs(ill, chocolate) # The outcome variable should come first.

#    For the following table
#          chocolate
#    ill     FALSE TRUE
#     FALSE     7   22
#     TRUE     20   25
#
cci(25, 22, 20, 7)
graph.casecontrol(25, 22, 20, 7)
graph.prospective(25, 22, 20, 7)

#Alternatively
table1 <- make2x2(25,70,22,7)
cc(outcome=NULL, exposure=NULL, cctable=table1)
cs(outcome=NULL, exposure=NULL, cctable=table1)


[Package epicalc version 2.10.1.1 Index]