R/PA_summary.R

In YukunZhang/PAactivPAL: Summarize Daily Physical Activity from 'activPAL' Accelerometer Data

#' Physical Activity Summary-Summations
#'
#' Summarize activity measures
#' @param final_dat cleaned final data that is between record getup time and sleep time
#' @return \code{hours_worn_total} Total worn hours
#' @return \code{sed_hour}  Total sedantary hours
#' @return \code{stand_hour} Total stand hours
#' @return \code{step_hour} Total step hours
#' @return \code{num_changes_from_sed_to_non_sed} Numbers of changing from sedantary to non sadantary status
#' @return \code{step_count_total} Total Step count
#' @return \code{num_hour_over_3_METs} Number of hours that Metabolic Equivalent of Task (MET) is over 3
#' @return \code{MET_hours}  Total METs
#' @return \code{table} A table that shows all above results
#' @details All numbers are calculated in the given time period (day, hour, etc_)_ Total sedentary/standing/stepping hours are obtained from the summation of the duration times for sedentary/standing/stepping activities in the given time period_

#' @examples  data(sampledata);PA_summary(sampledata)
#' @export
PA_summary=function (final_dat) {

  dat=final_dat
  if(is.numeric(dat$Time)==F) ####if  is.numeric(dat$Time)==F, we need further modification of time in next step
  {
    ee<-as.character(dat$Time)
    max_length<-max(nchar(ee))
    ee[nchar(ee)!=max_length]<-"#1899-12-30 00:00:00#"
    #### use character type, may not be good
    ee_new<- (as.numeric( as.POSIXlt( substr(ee, 2, max_length-1 )  )    )+2209190400)/24/60/60
    #### use interval type, this is the best
    start_ee<-  min(which(dat[,2]>0))-1
    if (start_ee>1)
    {
      ee_new_int_type <-c( ee_new[1:((start_ee)-1)],ee_new[start_ee]+(dat$DataCount[start_ee:nrow(dat)]/10/24/60/60)  )
    }else
    {    ee_new_int_type <-ee_new[start_ee]+(dat$DataCount[start_ee:nrow(dat)]/10/24/60/60)
    } #### if interval type has large difference with character type, use character type
    int_dif_char<-which(abs(ee_new-ee_new_int_type)>0.1 )
    ee_new_int_type[int_dif_char]<-ee_new[int_dif_char]
    ####
    dat<-cbind(ee_new_int_type,dat[,2:6])
  }
  final_dat<-dat[,c(1,3,4,6)]
  colnames(final_dat)<-c("date_time","Interval","ActivityCode", "METs")
  final_dat=final_dat[final_dat$date_time!=0.625,] #delete rows with time as #1899-12-30 00:00:00#

  temp_mat=final_dat
  ###################################################
  #time_char<-as.POSIXlt(record_getup_time[ll]*24*60*60, origin = ISOdatetime(1899,12,30,0,0,0))
  hour_char<-as.numeric(format(as.POSIXlt(temp_mat$date_time*24*60*60, origin = ISOdatetime(1899,12,30,0,0,0)),"%H"))
  ###
  temp_sed<-subset(temp_mat,temp_mat$ActivityCode==0)$Interval
  length_temp_sed<-length(temp_sed)
#   month<-as.numeric(format(time_char,"%m"))
#   day<-as.numeric(format(time_char,"%d"))
#   year<-as.numeric(format(time_char,"%Y"))
  hours_worn_total<- sum(temp_mat$Interval)/60/60
  #hours_awake<- (record_sleep_time[ll]-record_getup_time[ll])*24
  sed_hour<- sum(temp_sed) /60/60
  stand_hour<- sum(subset(temp_mat,temp_mat$ActivityCode==1)$Interval) /60/60
  step_hour<- sum(subset(temp_mat,temp_mat$ActivityCode==2)$Interval) /60/60
  num_changes_from_sed_to_non_sed<- length_temp_sed
  ######## Code update here !
  step_count_total<- 2*nrow(subset(temp_mat,temp_mat$ActivityCode==2))  ##### in the event file, one row with ActivityCode==2 means two steps
  ########
 # gini_index<- gini(temp_sed)
  num_hour_over_3_METs<-  sum(temp_mat$Interval[(temp_mat$METs/temp_mat$Interval)*60*60>3])/60/60
  MET_hours<- sum(temp_mat$METs)
  #valid_day<-ifelse( (hours_worn_total<10 & hours_worn_total/hours_awake>0_8 & step_count_total>200) | (hours_worn_total>=10 & step_count_total>200 ),1,0    )
  #dayofweek<-as.numeric(format(time_char,"%w"))
  #weekday_or_weekend<- ifelse( dayofweek!=0 & dayofweek!=6,1,0)
  #table1<-c(person,group_char,www,month,day,year,hours_worn_total,hours_awake,sed_hour,stand_hour,step_hour,num_changes_from_sed_to_non_sed,step_count_total,num_hour_over_3_METs,MET_hours,valid_day,dayofweek,weekday_or_weekend)
  table<-cbind(hours_worn_total,sed_hour,stand_hour,step_hour,num_changes_from_sed_to_non_sed,step_count_total,num_hour_over_3_METs,MET_hours)
  colnames(table)<-c("hours_worn_total","sed_hour","stand_hour","step_hour","num_changes_from_sed_to_non_sed","step_count_total","num_hour_over_3_METs","MET_hours")

  out=list(hours_worn_total=hours_worn_total, sed_hour=sed_hour, stand_hour=stand_hour, step_hour=step_hour, num_changes_from_sed_to_non_sed=num_changes_from_sed_to_non_sed,step_count_total=step_count_total,num_hour_over_3_METs=num_hour_over_3_METs,MET_hours=MET_hours,table=table)

 #table1_label<-c("id","group","week","month","day","year","hours_worn_total","hours_awake","sed_hour","stand_hour","step_hour","num_changes_from_sed_to_non_sed","step_count_total","num_hour_over_3_METs","MET_hours","valid_day","dayofweek","weekday_or_weekend")
  #num_hour_over_3_METs=num_hour_over_3_METs
  return(out)
}