Nothing
## ----Installing and loading packages,eval=FALSE--------------------------
# install.packages("GENEAread",repos = "http://cran.us.r-project.org")
# install.packages("devtools",repos = "http://cran.us.r-project.org")
# install.packages("changepoint",repos = "http://cran.us.r-project.org")
# install.packages("signal",repos = "http://cran.us.r-project.org")
# install.packages("mmap",repos = "http://cran.us.r-project.org")
# install.packages("misc3d",repos = "http://cran.us.r-project.org")
# install.packages("rgl",repos = "http://cran.us.r-project.org")
# install.packages("mapproj",repos = "http://cran.us.r-project.org")
#
# library(GENEAread)
# library(devtools)
# library(changepoint)
# library(signal)
# library(mmap)
# library(misc3d)
# library(rgl)
# library(mapproj)
## ----Installing GENEAclassify,eval=FALSE---------------------------------
# setwd("/Users/owner/Documents/GENEActiv")
# # You will need to change this to the directory where you saved the tar.gz file
# install.packages("GENEAclassify_1.4.1.tar.gz", repos=NULL, type="source")
#
# #' Or using a GitHub authentication key which will go in the brackets of auth_token
#
# install_github("https://github.com/JossLangford/GENEAclassify_1.41.git",
# auth_token = "7f0051aaca453eaabf0e60d49bcf752c0fea0668")
#
# #' Once the package has been installed load in the library
# library(GENEAclassify)
## ----Installing GENEAsphere,eval=FALSE-----------------------------------
# # Again install GENEAsphere either from source or GitHub
# setwd("/Users/owner/Documents/GENEActiv")
# # You will need to change this to the directory where you saved the tar.gz file
# install.packages("GENEAsphere_1.0.tar.gz", repos=NULL, type="source")
#
# ## If installing from GitHub please run these lines
# install_github("https://github.com/JossLangford/GENEAsphere.git",
# auth_token = "7f0051aaca453eaabf0e60d49bcf752c0fea0668")
#
# library(GENEAsphere)
## ----Reading in the data,eval=FALSE--------------------------------------
# setwd("/Users/owner/Documents/GENEActiv/GENEAsphereDemo")
# # You will need to change this to the directory containing the data file.
# # Here I have analysed the first day for.
# AccData = read.bin("jl_left wrist_010094_2012-01-30 20-39-54.bin", start = "3:00", end = "1 3:00")
# SegData = getSegmentedData("jl_left wrist_010094_2012-01-30 20-39-54.bin", start = "3:00", end = "1 3:00")
## ----viewing data objects,eval=FALSE-------------------------------------
# names(AccData)
# head(AccData)
# head(AccData$data.out) # Raw data output
# names(SegData)
# head(SegData)
## ----Plot of acceleration against Time,eval=FALSE------------------------
# plot(AccData$data.out[1:1000,1],AccData$data.out[1:1000,2],
# title="Time against X acceleration",
# xlab="Time",ylab="X Acceleration",type="l")
## ---- eval = FALSE-------------------------------------------------------
# plot.AccData(x, what = ("sd"))
# plot.AccData(x, what = ("mean"))
# plot.AccData(x, what = ("temperature"))
# plot.AccData(x, what = ("light"))
# plot.AccData(x, what = ("voltage"))
## ---- eval = FALSE-------------------------------------------------------
# plotTLM(x, start = NULL, end = NULL)
## ----STFT plot,eval=FALSE------------------------------------------------
#
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE)
#
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE,reassign = TRUE)
#
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE, type = "mv")
#
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE, type = "sum")
# # Changing the window size
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE, win=100)
#
# stft(AccData, start=0.45, end=0.5, plot.it=TRUE, win=1000)
#
## ----postionals plot,eval=FALSE------------------------------------------
# positionals(AccData, start=0.45, end= 0.5, length = NULL, filter=2
# ,bw = TRUE , legend = TRUE, max.points = 1e6, density = FALSE)
## ----plotsphere plot,eval=FALSE------------------------------------------
# plotSphere(AccData, start=0, end= 0.5, length = NULL, time.format = "auto",
# density = F, arrow = T, add= F)
## ----loading in the segmentation csv,eval=FALSE--------------------------
# segmentationCSV="~/GENEAclassification/jl_left wrist_010094_2012-01-30 20-39-54_segmented.csv"
#
# # I find it useful to load in the csv to the workspace so that the rows I'm going to plot can be seen.
# csv=read.table(segmentationCSV,sep=",")
## ----running plotSegmentSphere,eval=FALSE--------------------------------
# plotRows=c(1:5) # Segments 1 and 5.
# plotSegmentSphere(segmentationCSV, plotRows, levels = c(0.9, 0.75, 0.5, 0.25, 0.1), singlePlot = TRUE, col = heat.colors(5),
# alpha = c(0.03, 0.05, 0.1, 0.2, 0.3), arrow = FALSE, nsims = 1000)
## ----plotSegmentFlat,eval=FALSE------------------------------------------
# plotSegmentFlat(segmentationCSV, plotRows,
# col = c("red",heat.colors(5, alpha = c(0.3, 0.2, 0.1, 0.05, 0.03))),
# singlePlot = TRUE, nsims= 1000)
## ----plotSegmentProjection,eval=FALSE------------------------------------
# plotSegmentProjection(segmentationCSV, plotRows, projection = "aitoff",
# col = "red", singlePlot = TRUE, nsims = 1000)
## ----plotSegmentEllipse,eval=FALSE---------------------------------------
# plotSegmentEllipse(segmentationCSV, plotRows, projection = "aitoff",
# col = "red", singlePlot = TRUE, confidenceLevel = 0.05,
# alpha = thresholds, wrap = FALSE, greyGrid = FALSE)
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