runRSCABS: Runs RSCABS

In RSCABS: Rao-Scott Cochran-Armitage by Slices Trend Test

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.

Note

The outputted data frame will not show results for endpoints that did not meet selection criteria as determined by checkSelction. Also note that RSCABS is a step down procedure so analysis for an effect at an RSCORE will stop when a non-significant result is found.

Author(s)

Joe Swintek

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: 
#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')
	
## End(Not run)

RSCABS documentation built on May 1, 2020, 9:06 a.m.