Histopath: GUI for analysis of histopathological data

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

Description

This is the function call to start the GUI interface for StatCharrms

Usage

	Histopath()

Details

• Load Data Button: 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. The data must be in .csv to load it into Histopath.

• Specify Data Button: This is used to tell Histopath the names of the columns used to specify the data. Pushing the button bring up a new tab that needs to be navigated to. See addHistoSpec for details.

• Run RSCABS Button: Pressing this will perform the RSCABS analysis. The results will replace the current data in the display box.

• Run Other Analyses Button: Pressing this will perform the bring up a new window with the ability to perform other relevant analyses. See otherPath for details.

• Save Result Button: Used to save the results of the RSCABS analysis.

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 that row's endpoint treatment level, and RSCORE.
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

See the vignette for a full tutorial on how to use this function.

Author(s)

Joe Swintek

References

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

See Also

runRSCABS, otherPath, addHistoSpec

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