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Last data update: 2014.03.03

R: layout displaying the PoPLR analysis

vflayout_poplr

R Documentation

layout displaying the PoPLR analysis

Description

the function performs the PoPLR analysis (see poplr) with default values and presents the results in form of a A4 printout

Usage

vflayout_poplr( vf, grp = 3, nperm = 5000,
                            plotType = "vf", truncVal = 1,
                            type = "slr", typecomb = "fisher",
                            pwidth = 8.27, pheight = 11.69,
                            margin = 0.25, filename = NULL,
                            colorMapType = "pval", colorScale = NULL,
                            ringMapType  = NULL,  ringScale  = NULL,
                            imparedVision = 10, rangeNormal = NULL,
                            ffamily = "serif", sizetxt = 12,
                            sizetxtSmall = 8,
                            ffamilyvf = "serif", pointsize = 7,
                            outerSymbol = "circle", outerInch = 0.12,
                            innerSymbol = "circle", innerInch = outerInch / 1.9,
                            inch2axisunits = 12.528,
                            lengthLines = 0, thicknessLines = 0,
                            outerInchpoplr = 0.185,
                            innerInchpoplr = outerInchpoplr / 1.9,
                            lengthLinespoplr = 0, borderThickness = 1.5 )

Arguments

`vf`	`vf` object with threshold sensitivities, td, or pd values
`grp`	how many visual fields to group. Default is `3`
`nperm`	number of permutations. Default is `5000`
`plotType`	Type of plot to show. It can be visual sensitivities (`vf`), total-deviation values (`td`), or pattern-deviation values (`pd`)
`truncVal`	p-value cut-off for truncation. Default is `1`
`type`	Type of regression statistic: `slr` for simple linear regression and `rank` for Spearman correlation coefficient. Default is `slr`
`typecomb`	Combination type for p-values. Default is `fisher`
`pwidth`	width of the page (in inches). Default is `8.27`
`pheight`	height of the page (in inches). Default is `11.69`
`margin`	margins of the page (in inches). Default is `0.25`
`filename`	file name to save the printout as pdf. If it is saved to pdf, it won't be displayed in the screen. Default is `NULL`.
`colorMapType`	what does color map categorizes. It can be `pvals`, `slopes`, or years `blind`. Default is `pvals`
`colorScale`	Color mapping to use. Default is `NULL`. A different default is given depending on `colorMapType`
`ringMapType`	what concentric rings categorizes. It can be `pvals` or `slopes`, or years `blind`. Default is `NULL`, for which no rings are shown.
`ringScale`	Ring mapping to use. Default is `NULL`. A different default is given depending on `ringMapType`
`rangeNormal`	range to indicate which slopes are normal. All significance from data points within the range will be removed. Default is `NULL`.
`imparedVision`	sensitivity below which it is considered imparement. Default is `10`
`ffamily`	Family font for the text in the from. Default is `"Helvetica"`
`sizetxt`	Text size for main text in the form. Default is `12`
`sizetxtSmall`	Text size for details in the form. Default is `8`
`ffamilyvf`	Font family for text in lego plots. Default is `"Times"`
`pointsize`	Point size for text in lego plots. Default is `7`
`outerSymbol`	Type of outer symbol. Default is `"circle"`
`outerInch`	Inches of outer symbol. Default is `0.12`
`innerSymbol`	Type of inner symbol. Default is `"circle"`
`innerInch`	Inches of inner symbol. Default is `outerInch / 1.9`
`inch2axisunits`	Conversion factor inches to axis units. Default is `12.528`
`lengthLines`	Line length. Default is `0`
`thicknessLines`	Line thickness. Default is `0`
`outerInchpoplr`	Size of outer symbols for PoPLR gragh. Default is `0.185`
`innerInchpoplr`	Size of inner symbols for PoPLR gragh. Default is `outerInchpoplr / 1.9`
`lengthLinespoplr`	length of lines. Default is `0`
`borderThickness`	Border thickness. Default is `1.5`

Author(s)

Ivan Marin-Franch, Chaitanya Khadilkar

References

[1] N. O'Leary, B. C. Chauhan, and P. H. Artes. Visual field progression in glaucoma: estimating the overall significance of deterioration with permutation analyses of pointwise linear regression (PoPLR). Investigative Ophthalmology and Visual Science, 53, 2012

Examples

#vflayout_poplr( vf91016right )