A data structure containing one or more Dose-Volume Histogram (DVH) objects
Objects from the Class
Objects can be created by calls of the form new("DVH.list", structures, ...).
Slots
structures:
List of DVH objects
Methods
[
Extract subset of DVH list based on pattern matching with structure names (regular expressions may be specified if desired, see regex for more details). Note that case-insensitive matching is supported using the "(?i)" prefix, such that DVHs["(?i)LIVER"] will match any combination of upper and lowercase letters spelling "liver".
[[
Extract single DVH object from DVH list
[[<-
Replace single DVH object in DVH list
[<-
Replace multiple elements of DVH list
$
Extract dose or volume parameter(s) from DVH objects within DVH list. Note that multiple parameters may be specified by use of the comma (e.g. $"V20Gy,D5%"). See DVH documentation ([] usage) for additional details. Note that this functionality can also be used to extract patient name(s) and/or identifier(s) (e.g. $patients or $ID).
as.list
Convert a DVH.list object to a list containing individual DVH objects. Note that the reverse conversion can be performed using the as command and specifying class="DVH.list".
c
Combine two or more DVH lists and/or DVH objects
lapply
Apply function to a list of DVH objects
length
Extract number of DVH objects in DVH list
mad
Compute the median absolute deviation (i.e. the median of the absolute deviations from the median) for all doses extracted from DVH object list
max
Compute the maximum dose contained within the DVH list
mean
Compute the mean DVH from all DVH objects within the list
median
Compute the median DVH from all DVH objects within the list
min
Compute the minimum dose contained within the DVH list
names
Extract structure names for DVH objects in DVH list
names<-
Assign structure name(s) to one or more DVH objects in DVH list
print
Display summary of DVH list
range
Compute the range (minimum and maximum doses) contained within the DVH list
rev
Return a DVH list whose DVH objects are in reverse order
sd
Compute the standard deviation for all doses extracted from DVH object list
show
Display summary of DVH list
sum
Compute the total (summed) DVH from all DVH objects within the list. Note that structures are assumed to be non-overlapping; any overlaps in structure volumes may generate inaccurate dose summation.
t.test
Apply Student's t-Test to compare two DVH lists (see also t.test)
var
Compute the variance for all doses extracted from DVH object list
wilcox.test
Apply Wilcoxon Rank Sum and Signed Rank Tests to compare two DVH lists (see also wilcox.test)
# Description of structure/slots in class
showClass("DVH.list")
data(list="RadOnc", package="RadOnc")
print(johndoe)
plot(johndoe[c("LIVER", "PTV")], plot.type="i", col=c("red","blue"), lty=1:2, lwd=1:2)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(RadOnc)
Loading required package: rgl
Loading required package: geometry
Loading required package: magic
Loading required package: abind
Loading required package: oro.dicom
oro.dicom: Rigorous - DICOM Input / Output (version = 0.5.0)
Loading required package: ptinpoly
Loading required package: misc3d
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RadOnc/DVH.list-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DVH.list-class
> ### Title: Class '"DVH.list"'
> ### Aliases: DVH.list DVH.list-class [,DVH.list-method [[,DVH.list-method
> ### [[<-,DVH.list-method $,DVH.list-method as.list,DVH.list-method
> ### c,DVH.list-method initialize,DVH.list-method lapply,DVH.list-method
> ### length,DVH.list-method mad,DVH.list-method max,DVH.list-method
> ### mean,DVH.list-method median,DVH.list-method min,DVH.list-method
> ### names,DVH.list-method names<-,DVH.list-method plot,DVH.list-method
> ### print,DVH.list-method quantile,DVH.list-method range,DVH.list-method
> ### rev,DVH.list-method sd,DVH.list-method show,DVH.list-method
> ### sum,DVH.list-method t.test,DVH.list-method var,DVH.list-method
> ### wilcox.test,DVH.list-method
> ### Keywords: classes
>
> ### ** Examples
>
> # Description of structure/slots in class
> showClass("DVH.list")
Class "DVH.list" [package "RadOnc"]
Slots:
Name: structures
Class: list
> data(list="RadOnc", package="RadOnc")
> print(johndoe)
[1] "List containing 10 DVH objects (LIVER, SMALL_BOWEL, DUODENUM, STOMACH, CTV, PTV, BODY, LEFT_KIDNEY, RIGHT_KIDNEY, CORD)"
> plot(johndoe[c("LIVER", "PTV")], plot.type="i", col=c("red","blue"), lty=1:2, lwd=1:2)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.