| Type: | Package |
| Title: | Depth-Dependent Binocular Visual Fields Simulation |
| Version: | 0.1.1 |
| Author: | Ping Liu [aut, cre], Andrew Turpin [aut] |
| Maintainer: | Ping Liu <ping.liu@unimelb.edu.au> |
| URL: | https://people.eng.unimelb.edu.au/aturpin/opi/index.html |
| Description: | Simulation and visualization depth-dependent integrated visual fields. Visual fields are measured monocularly at a single depth, yet real-life activities involve predominantly binocular vision at multiple depths. The package provides functions to simulate and visualize binocular visual field impairment in a depth-dependent fashion from monocular visual field results based on Ping Liu, Allison McKendrick, Anna Ma-Wyatt, Andrew Turpin (2019) <doi:10.1167/tvst.9.3.8>. At each location and depth plane, sensitivities are linearly interpolated from corresponding locations in monocular visual field and returned as the higher value of the two. Its utility is demonstrated by evaluating DD-IVF defects associated with 12 glaucomatous archetypes of 24-2 visual field pattern in the included 'shiny' apps. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| Depends: | R (≥ 3.1.0) |
| Imports: | plotrix, gtools, shiny |
| Suggests: | knitr, rmarkdown, testthat |
| RoxygenNote: | 6.1.1 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2020-03-04 06:04:11 UTC; virliu |
| Repository: | CRAN |
| Date/Publication: | 2020-03-10 10:20:02 UTC |
Calculates an array of integrated visual fields
Description
binovfcal calculates an array of integrated visual fields given required parameters.
Usage
binovfcal(leftvf, rghtvf, lefttheta, righttheta, distplanes, pd = NULL,
gender = NULL, m_xs = seq(-27, 27, length.out = 10), m_ys = seq(21,
-21, -6), c_xs = seq(-57, 57, 6), db_cutoff = 25)
Arguments
leftvf |
A matrix of left monocular visual field |
rghtvf |
A matrix of right monocular visual field |
lefttheta |
A number angle of convergence for the left eye in radian |
righttheta |
A number angle of convergence for the right eye in radian |
distplanes |
A vector of object distances in mm. |
pd |
Pupil distance in mm |
gender |
A string of either "male" or "female" |
m_xs |
Horizontal coordinates for monocular visual field for the 24-2 pattern |
m_ys |
Vertical coordinates for monocular visual field for the 24-2 pattern |
c_xs |
Horizontal coordinates for integrated visual field (from -57 to 57 degree with 6 degree spacing) |
db_cutoff |
cutoff value default to 25 dB above which the simulated threshold value is returned (NA otherwise) when there threshold value is present only for one eye |
Value
An array of binocular visual fields for the distances specified by distplanes vector.
Warning
the value of either pd or gender has to be provided the unit of pd and fixdist must be the same, default to mm.
Examples
rghtvf <- matrix(c(
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 0, 30, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA
), ncol=10, byrow=TRUE)
leftvf <- rghtvf[, 10:1]
binovfcal(leftvf, rghtvf, -.045, .045, c(1000, 1010), pd=62)
Calculates the angle of convergence
Description
caltheta calculates the angle of convergence (radians) for left or right eye to fixate at a designated fixation distance.
Usage
caltheta(fixdist, pd = NULL, gender = NULL, eye = c("left", "right"))
Arguments
fixdist |
A two element vector of fixation distance in mm in Cartesian coordinates. |
pd |
A number of pupil distance in mm. |
gender |
A string of either "male" or "female" |
eye |
A string specifying either "left" or "right" eye. |
Value
The angle of convergence in radians that respective eye with a pupil distance of pd rolls to fixate at fixation distance of fixdist.
Warning
the value of either pd or gender has to be provided the unit of pd and fixdist must be the same and is default to mm.
Examples
caltheta(c(600, 0), pd=65, eye="left")
caltheta(c(600, 0), gender="male", eye="left")
Creates a color scheme for visual field plots
Description
colfunc creates a color scheme visualising the dB values in visual field matrices with darker color corresponding to lower dB values
Usage
colfunc(n = 35)
Arguments
n |
A positive integer specifying the number of color gradients used in visual field plots and is default to 35 |
Value
A color mapping function
Examples
colfunc(35)
Generates a color legend for visual field plots
Description
colorkey generates a color legend for dB values in visual field plots with darker colors corresponding to lower dB values (e.g., black = 0dB, bright yellow >= 35dB)
Usage
colorkey()
Value
a color legend for dB values in visual field plots
Examples
colorkey()
Color-codes dB values
Description
get_color returns the color of a visual field location given its dB value (e.g., black = 0dB, white = 35dB)
Usage
get_col(db)
Arguments
db |
A number of sensitivity threshold in dB |
Value
the color of a visual field location in hcl color space with darker colors corresponding to lower dB values
Examples
get_col(25)
Color-codes dB values
Description
get_inv_col returns the color of a visual field location given its dB value, (e.g., white < 15dB, black > 15dB)
Usage
get_inv_col(db)
Arguments
db |
A number of sensitivity threshold in dB |
Value
either white or black color for a visual field location
Examples
get_inv_col(25)
Makes a visual field matrix
Description
makevf Makes a visual field matrix from a vector of 54 elements for the 24-2 test results
Usage
makevf(vfvector, eye = c("left", "right"))
Arguments
vfvector |
A vector of length 54. The 54 data points for the 24-2 pattern have to be ordered from superior nasal to inferior temporal. |
eye |
A string of either "left" or "right" |
Value
A matrix of 8 rows and 10 columns
Examples
vfvector <- rep(35, 54)
makevf(vfvector, 'left')
Plots visual field
Description
plotvf plots a figure of a visual field matrix with sensitivity threshold values
Usage
plotvf(xs, vf, title = "")
Arguments
xs |
A vector of horizontal coordinates. The length of it must be either 10 for a monocular or 25 for a binocular visual field plot. |
vf |
A matrix of either a left/right monocular visual field or a binocular visual field sensitivity values |
title |
A string for the name of the plot. |
Value
A plot of a monocular or binocular visual field.
Warning
the length of xs and the number of columns of the vf must be the same and with a value of either 10 or 20.
Examples
m_xs <- seq(-27, 27, length.out = 10)
rghtvf <- matrix(c(
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 0, 30, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA
), ncol=10, byrow=TRUE)
plotvf(m_xs, rghtvf, title='right visual field')
Plots visual field
Description
plotvf_2 plots a figure of a binocular visual field matrix with sensitivity threshold values with missing locations
Usage
plotvf_2(xs, vf, vf_norm, title = "")
Arguments
xs |
A vector of binocular visual field horizontal coordinates. The length of it must be 20 for a binocular visual field plot |
vf |
A matrix of a binocular visual field sensitivity values |
vf_norm |
A matrix a binocular healthy visual field sensitivity values for a specified distance plane |
title |
A string for the name of the plot |
Value
A plot of a monocular or binocular visual field
Warning
the length of xs and the number of columns of the vf must be the same and with a value of either 25.
Examples
c_xs <- seq(-57, 57, length.out = 20)
cvf <- matrix(c(
NA, NA, NA, NA, NA, NA, NA, NA, 30, 20, 20, 30, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 30, 20, 0, 0, 20, 30, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 20, 0, 0, 20, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 20, 20, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA, NA
), ncol=20, byrow=TRUE)
cvf_norm <- matrix(c(
NA, NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, 30, 30, 30, 30, NA, NA, NA, NA, NA, NA, NA, NA
), ncol=20, byrow=TRUE)
plotvf_2(c_xs, cvf, cvf_norm, title='integrated visual field')
Plots binocular visual field rays
Description
plotvfray plots a figure showing how the left and right visual field sensitivity threshold data interact in the simulated binocular visual field.
Usage
plotvfray(leftvf, rghtvf, lefttheta, righttheta, fixdist, distplane)
Arguments
leftvf |
An 8 by 10 matrix of sensitivity threshold data for the left visual field |
rghtvf |
An 8 by 10 matrix of sensitivity threshold data for the right visual field |
lefttheta |
A number left eye rotating angle in radian |
righttheta |
A number right eye rotating angle in radian |
fixdist |
A 2 element vector the coordinates of the fixation point in cartesian system in mm. |
distplane |
A number object distance in mm range from 0 to a maximum of 1500 mm. |
Value
A plot of binocular visual field rays from a top view with left eye on the top.
Warning
the unit of fixdist, pd and distplane must be in mm.
Examples
rghtvf <- matrix(c(
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 30, 30, NA,
30, 30, 30, 30, 30, 30, 30, 0, 30, NA,
NA, 30, 30, 30, 30, 30, 30, 30, 30, NA,
NA, NA, 30, 30, 30, 30, 30, 30, NA, NA,
NA, NA, NA, 30, 30, 30, 30, NA, NA, NA
), ncol=10, byrow=TRUE)
leftvf <- rghtvf[, 10:1]
plotvfray(leftvf, rghtvf, -.05, .05, c(700, 0), 1000)
Rotates a point (x,y) by an angle
Description
rotate calculates the coordinates for a point (x,y) after it rotates by an angle theta (radian)
Usage
rotate(xy, theta = 0)
Arguments
xy |
A vector of length 2 representing the coordinates of a point in cartesian system |
theta |
A number rotating angle in radian |
Value
Coordinates of the point after the rotation
Examples
rotate(c(1000, 0), theta=pi/6)
Runs shiny applications included in the package
Description
rundemo(demo) runs a shiny application provided in the package
Usage
rundemo(demo)
Arguments
demo |
A shiny application name. There are two applications i.e., "app", "app2" included in the package |
Value
the called shiny application in a new browser
Examples
## Not run:
rundemo("app2.R")
## End(Not run)