Description Usage Arguments Value Note Author(s) References Examples

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

1 | ```
runRSCABS(Data, Treatment, Replicate='', Effects = '', test.type = "RS")
``` |

`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. |

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. |

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.

Joe Swintek

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

1 2 3 4 5 6 7 8 9 10 11 | ```
## 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)
``` |

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