RSCABS (version 0.9.5)

runRSCABS: Runs RSCABS

Description

Runs the Rao-Scott adjusted Cochran-Armitage trend test by slices (RSCABS) analysis.

Usage

runRSCABS(Data, Treatment, Replicate='', Effects = '', test.type = "RS")

Arguments

Data

A standard data set in the tall format. Every row indicates an organism. The data set must contain columns for the treatment level and every tested histological endpoint.

Treatment

The name of the column that contains the information about the treatment level. Increasing values indicate higher treatments.

Replicate

The name of the column that contains the information about the replicate structure. If the replicate is not specified this will default to running "CA" as the test type.

Effects

The endpoint to be tested. Defaults to all columns that have integers less then 20. The analysis assumes that higher scores indicate a worse outcome.

test.type

Indicate the type of analysis to be performed. Use "RS" to select the Rao-Scott adjustment to the Cochran-Armitage test and "CA" to ignore the adjustment.

Value

Returns a list with the following values:

Response

The endpoint that is being tested.

Treatment

The treatment level.

R-Score

The severity score from the histology.

Statistic

The test statistic corresponding to that row's endpoint treatment level, and R-Score.

P-Value

The corresponding p-value

Signif

The significance flag where "." is a p-value > 0.05, "*" is a 0.01 < p-value <= 0.05, "**" for 0.001 < p-value <= 0.01, and "***" for p-value <= 0.001.

References

Green, John W. and Springer, Timothy A. and Saulnier, Amy N. and Swintek, Joe, (2014) Statistical analysis of histopathological endpoints. Environmental Toxicology and Chemistry, 33(5), 1108-1116

Examples

# NOT RUN {
	
# }
# NOT RUN {
## Not run: 
#Take the subset corresponding to F0-females of 16 weeks of age
data(exampleHistData)
exampleHistData.sub<-exampleHistData[which(exampleHistData$Generation=='F2' & 
	exampleHistData$Genotypic_Sex=='Female' & exampleHistData$Age=='16_wk' ),  ]
#Run RSCABS	
	exampleResults<-runRSCABS(exampleHistData.sub,'Treatment',
		'Replicate',test.type='RS')
	
# }