Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
echo = TRUE,
python.reticulate = FALSE
)
## ----eval=FALSE---------------------------------------------------------------
# calculateCounts = function(data=c(), parameters=c()) {
# # data: 3 column matrix with acc data
# # parameters: the sample rate of data
# library("activityCounts")
# if (ncol(data) == 4) data= data[,2:4]
# mycounts = counts(data=data, hertz=parameters,
# x_axis=1, y_axis=2, z_axis=3,
# start_time = Sys.time())
# mycounts = mycounts[,2:4] #Note: do not provide timestamps to GGIR
# return(mycounts)
# }
## ----eval=FALSE---------------------------------------------------------------
# source("~/calculateCounts.R")
# myfun = list(FUN=calculateCounts,
# parameters= 30,
# expected_sample_rate= 30,
# expected_unit="g",
# colnames = c("countsX","countsY","countsZ"),
# outputres = 1,
# minlength = 1,
# outputtype="numeric",
# aggfunction = sum,
# timestamp=F,
# reporttype="scalar")
## ----eval=FALSE---------------------------------------------------------------
# library(GGIR)
# GGIR(datadir="~/myaccelerometerdata",
# outputdir="~/myresults",
# mode=1:2,
# epochvalues2csv = TRUE,
# do.report=2,
# myfun=myfun) #<= this is where object myfun is provided to GGIR
## ----eval=FALSE---------------------------------------------------------------
# dominant_frequency = function(data=c(), parameters=c()) {
# # data: 3 column matrix with acc data
# # parameters: the sample rate of data
# source_python("dominant_frequency.py")
# sf=parameters
# N = nrow(data)
# ws = 5 # windowsize
# if (ncol(data) == 4) data= data[,2:4]
# data = data.frame(t= floor(seq(0,(N-1)/sf,by=1/sf)/ws),
# x=data[,1], y=data[,2], z=data[,3])
# df = aggregate(data, by = list(data$t),
# FUN=function(x) {return(dominant_frequency(x,sf))})
# df = df[,-c(1:2)]
# return(df)
# }
# }
## ----eval=FALSE---------------------------------------------------------------
# library("reticulate")
# use_virtualenv("~/myvenv", required = TRUE) # Local Python environment
# py_install("numpy", pip = TRUE)
#
## ----eval=FALSE---------------------------------------------------------------
# source("~/dominant_frequency.R")
# myfun = list(FUN=dominant_frequency,
# parameters= 30,
# expected_sample_rate= 30,
# expected_unit="g",
# colnames = c("domfreqX", "domfreqY", "domfreqZ"),
# minlength = 5,
# outputres = 5,
# outputtype="numeric",
# aggfunction = median
# timestamp=F,
# reporttype="scalar")
## ----eval=FALSE---------------------------------------------------------------
# library(GGIR)
# GGIR(datadir="~/myaccelerometerdata",
# outputdir="~/myresults",
# mode=1:2,
# epochvalues2csv = TRUE,
# do.report=2,
# myfun=myfun,
# do.parallel = FALSE)
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