R/median.cadence.bands.file.R

In PALkitchen/activPAL: Advanced Processing and Chart Generation from activPAL Events Files

median.cadence.bands.file <-
  function(events_file, file_uid, upright_bout = FALSE){
    #' @import dplyr
    lower_bound <- c(10,60,600)
    upper_bound <- c(60,600,86400)

    events_file <- group.stepping.by.upright.bout(events_file)
    events_file <- events_file[which(events_file$activity == 2 & events_file$interval >= lower_bound[1]),]
    events_file$cadence <- events_file$steps / (events_file$interval / 60)
    longest_stepping <- events_file %>%
      filter(activity == 2) %>%
      group_by(upright_bout) %>%
      summarise(max_stepping = max(interval))
    events_file <- left_join(events_file, longest_stepping, by = c("upright_bout"))
    events_file[is.na(events_file)] <- 0

    if(nrow(events_file) == 0){
      median_cadence_by_group <- as.data.frame(matrix(nrow = 3, ncol = 3))
      colnames(median_cadence_by_group) <- c("uid","group","median_cadence")
      median_cadence_by_group$uid <- file_uid
      median_cadence_by_group[1,]$group <- "< 1 minute"
      median_cadence_by_group[2,]$group <- "1 - 10 minutes"
      median_cadence_by_group[3,]$group <- "10 minutes +"
      median_cadence_by_group$median_cadence <- 0
      return(median_cadence_by_group)
    }
    events_file$group <- ""
    for (i in (1:length(lower_bound))){
      if(upright_bout){
        in_group <- which(events_file$max_stepping >= lower_bound[i] & events_file$max_stepping < upper_bound[i])
      }else{
        in_group <- which(events_file$interval >= lower_bound[i] & events_file$interval < upper_bound[i])
      }
      if(length(in_group) > 0 ){
        # Convert the maximum and minimum duration into a label
        duration_label <- paste(lubridate::seconds_to_period(lower_bound[i]),"to",lubridate::seconds_to_period(upper_bound[i]))
        duration_label <- gsub("d"," day",duration_label)
        duration_label <- gsub("S"," seconds",duration_label)
        duration_label <- gsub("M"," minutes",duration_label)
        duration_label <- gsub("H"," hours",duration_label)
        duration_label <- gsub(" 0 seconds","",duration_label)
        duration_label <- gsub(" 0 minutes","",duration_label)
        duration_label <- gsub(" 0 hours","",duration_label)
        duration_label <- gsub(" 1 minutes"," 1 minute",duration_label)
        duration_label <- gsub(" 1 hours"," 1 hour",duration_label)
        events_file[in_group,]$group <- duration_label
      }
    }

    median_cadence_by_group <- events_file %>% dplyr::group_by(.data$uid, .data$group) %>%
      dplyr::summarise(median_cadence = weighted.median(.data$cadence,.data$steps))
    if(length(which(median_cadence_by_group$group == "10 minutes to 1 day")) > 0){
      median_cadence_by_group[which(median_cadence_by_group$group == "10 minutes to 1 day"),]$group <- "10 minutes +"
    }
    if(length(which(median_cadence_by_group$group == "1 minutes to 10 minutes")) > 0){
      median_cadence_by_group[which(median_cadence_by_group$group == "1 minutes to 10 minutes"),]$group <- "1 - 10 minutes"
    }
    if(length(which(median_cadence_by_group$group == "10 seconds to 1 minute")) > 0){
      median_cadence_by_group[which(median_cadence_by_group$group == "10 seconds to 1 minute"),]$group <- "< 1 minute"
    }
    return(median_cadence_by_group)
  }

median.stepping.cadence.bands.file <-
  function(events_file){
    #' @import dplyr
    #' @import tidyr
    lower_bound <- c(10,60)
    upper_bound <- c(60,86400)

    events_file <- events_file[which(events_file$activity == 2 & events_file$interval >= lower_bound[1]),]
    events_file$cadence <- events_file$steps / (events_file$interval / 60)
    events_file$group <- ""
    for (i in (1:length(lower_bound))){
      in_group <- which(events_file$interval >= lower_bound[i] & events_file$interval < upper_bound[i])
      if(length(in_group) > 0 ){
        # Convert the maximum and minimum duration into a label
        duration_label <- paste(lubridate::seconds_to_period(lower_bound[i]),"to",lubridate::seconds_to_period(upper_bound[i]))
        duration_label <- gsub("d"," day",duration_label)
        duration_label <- gsub("S"," seconds",duration_label)
        duration_label <- gsub("M"," minutes",duration_label)
        duration_label <- gsub("H"," hours",duration_label)
        duration_label <- gsub(" 0 seconds","",duration_label)
        duration_label <- gsub(" 0 minutes","",duration_label)
        duration_label <- gsub(" 0 hours","",duration_label)
        duration_label <- gsub(" 1 minutes"," 1 minute",duration_label)
        duration_label <- gsub(" 1 hours"," 1 hour",duration_label)
        events_file[in_group,]$group <- duration_label
      }
    }

    median_cadence_by_group <- events_file %>% dplyr::group_by(.data$uid, .data$group) %>%
      dplyr::summarise(median_cadence = weighted.median(.data$cadence,.data$interval))
    median_cadence_by_group[which(median_cadence_by_group$group == "1 minutes to 1 day"),]$group <- "1 minute +"
    median_cadence_by_group[which(median_cadence_by_group$group == "10 seconds to 1 minute"),]$group <- "< 1 minute"
    return(median_cadence_by_group)
  }