visualFields (version 0.4.3)

vflayout_poplr: 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

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

See Also

vflayout, vflayout_legoplot, poplr, hist_poplr, poplr_cstat, poplr_pstat, vfplot_poplr

Examples

#vflayout_poplr( vf91016right )