R/nparACT_auxfunctions2.R

In nparACT: Non-Parametric Measures of Actigraphy Data

nparACT_auxfunctions2 <- list(
  nparACT_plot_hourly = function(data, data_hrs, SR){
    a <- nrow(data) 
    hours <- nrow(data_hrs)
    days <- ceiling(hours/24)
    days_hours <- days*24
    
    daytime <- matrix(NA)
    time <- data$time
    time <- as.character(time)
    for (v in seq(1,a,(SR*60*60))){  
      daytime[v] <- time[v]
    }
    daytime <- na.omit(daytime)
    daytime <- as.character(daytime)
    
    temp = unlist(str_split(daytime, ' ') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 2) == 0 ] 
    temp = unlist(str_split(timeinfo, ':') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 3) == 1 ] 
    start.time <- as.numeric(timeinfo[1])  
    
    mf_labeller <- function(day_count){
      for (ee in 1:length(day_count)){
        if (day_count[ee] == 1){
          day_count[ee] <- "Days 1-2"
        } else if (day_count[ee] == 2){
          day_count[ee] <- "Days 3-4"
        } else if (day_count[ee] == 3){
          day_count[ee] <- "Days 5-6"
        } else if (day_count[ee] == 4){
          day_count[ee] <- "Days 7-8"
        } else if (day_count[ee] == 5){
          day_count[ee] <- "Days 9-10"
        } else if (day_count[ee] == 6){
          day_count[ee] <- "Days 11-12"
        } else if (day_count[ee] == 7){
          day_count[ee] <- "Days 13-14"
        } else if (day_count[ee] == 8){
          day_count[ee] <- "Days 15-16"
        } else if (day_count[ee] == 9){
          day_count[ee] <- "Days 17-18"
        } else if (day_count[ee] == 10){
          day_count[ee] <- "Days 19-20"
        } else if (day_count[ee] == 11){
          day_count[ee] <- "Days 21-22"
        } else if (day_count[ee] == 12){
          day_count[ee] <- "Days 23-24"
        } else if (day_count[ee] == 13){
          day_count[ee] <- "Days 25-26"
        } else if (day_count[ee] == 14){
          day_count[ee] <- "Days 27-28"
        } else if (day_count[ee] == 15){
          day_count[ee] <- "Days 29-30"
        }
      }
      return(day_count)
    }
    mf_labeller <- as_labeller(mf_labeller)
    

    fill <- rep(NA, start.time)
    
    data_hrs2 <- data_hrs
    data_hrs2 <- c(fill, data_hrs2)
    hours_plot <- length(data_hrs2)
    days_plot <- ceiling(hours_plot/24)
    days_hours_plot <- days_plot*24
    data_hrs2[days_hours_plot] <- NA 
    
    hours_count <- seq(1:24)
    hours_count <- rep(hours_count,days_plot)
    
    count_plot <- seq(1:48)-1 
    count_plot <- rep(count_plot, length.out = days_hours_plot)
    
    day_count <- NA 
    for (t in 1:(ceiling(days_plot/2))){
      day_count[((t-1)*48+1):(t*24*2)] <- rep(t,24)
    }
    day_count <- day_count[1:days_hours_plot]
    
    df_plot <- data.frame(day_count, count_plot, data_hrs2)
    
    p <- ggplot(df_plot, aes(x=count_plot, y = data_hrs2))+ 
      geom_bar(stat="identity", width = 1, position = position_dodge(width = 0.5))+
      theme_bw()+
      facet_grid(day_count ~ ., labeller = mf_labeller)+
      scale_x_discrete(expand = c(0,0), limits = c(seq(0:47)-1), breaks = seq(0,47,2))+
      expand_limits(x=-1)+
      xlab("Time \n (Start: 0am)")+
      ylab("Movement Intensity")+
      ggtitle("Actigraphy Plot (48 hrs)", subtitle = "Dual Day Display")+
      theme(plot.margin=unit(c(1,14,1,14),"cm"),
            axis.text.x = element_blank(),
            axis.title.x = element_text(face="bold", size=12),
            axis.title.y = element_text(face="bold", size=12, vjust = 1.2),
            plot.title = element_text(face="bold", size=14, vjust = 1))
    print(p)
  },
  
  nparACT_plot_hraverage = function(data, minaverage, start.time, a, SR){
    hraverage <- matrix(NA)
    for (i in 1:24){
      hraverage [i] <- mean(minaverage[(((i-1)*60)+1):(60*i)])
    }
    daytime <- matrix(NA)
    time <- data$time
    time <- as.character(time)
    for (v in seq(1,a,(SR*60*60))){  
      daytime[v] <- time[v]
    }
    daytime <- na.omit(daytime)
    daytime <- as.character(daytime)
    temp = unlist(str_split(daytime, ' ') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 2) == 0 ] 
    temp = unlist(str_split(timeinfo, ':') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 3) == 1 ] 
    start.time <- as.numeric(timeinfo[1])  
    
    for_hraverage_plot.time <- rep(seq(1,24),2)
    seq <- seq(start.time, length.out = 24)
    if (seq[1] == 0){
      seq[1] = 24 ## changed 21 12 16, accounts for case in which start time is midnight
    }
    hraverage_plot_time <- for_hraverage_plot.time[seq]
    hraverage_plot_time[hraverage_plot_time==24] <- 0
    hraverage_plot_df <- data.frame (hraverage_plot_time, hraverage)
    
    ppp <- ggplot(hraverage_plot_df, aes(x=hraverage_plot_time, y = hraverage))+ 
      geom_bar(stat="identity", width = 1, position = position_dodge(width = 0.5))+
      theme_bw()+
      scale_x_discrete(expand = c(0,0), limits = c(seq(0:23)-1), breaks = seq(0,23))+
      expand_limits(x=-1)+
      xlab("Time \n (Start: 0am)")+
      ylab("Movement Intensity")+
      ggtitle("Actigraphy Plot (24 hrs)", subtitle = "Average across days")+
      theme(plot.margin=unit(c(1,2,1,2),"cm"),
            axis.text.x = element_blank(),
            axis.title.x = element_text(face="bold", size=12),
            axis.title.y = element_text(face="bold", size=12, vjust = 1.2),
            plot.title = element_text(face="bold", size=14, vjust = 1))
    print(ppp)
  },
  
  nparACT_plot_minaverage = function(data, minaverage, start.time, a, SR){
    daytime <- matrix(NA)
    time <- data$time
    time <- as.character(time)
    for (v in seq(1,a,(SR*60*60))){  
      daytime[v] <- time[v]
    }
    daytime <- na.omit(daytime)
    daytime <- as.character(daytime)
    
    temp = unlist(str_split(daytime, ' ') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 2) == 0 ] 
    temp = unlist(str_split(timeinfo, ':') )
    temp_nums = 1:length(temp)
    timeinfo = temp[ (temp_nums %% 3) == 1 ] 
    start.time_h <- as.numeric(timeinfo[1])
    start.time_min <- as.numeric(temp[2]) ## changed 21 12 16 -> select start minute, was [1] for hour previously
    
    for_minaverage_plot.time <- rep(seq(1,1440),2)
    seq <- seq(start.time_h*60+start.time_min, length.out = 1440) ## 21 12 16: was start.time*60 when input was hours only
    if (seq[1] == 0){  ## changed 21 12 16, accounts for case in which start time is midnight
      seq[1] = 1440
    }
    minaverage_plot_time <- for_minaverage_plot.time[seq] # time info, vectors will be joined in next step
    
    minaverage_plot_df <- data.frame (minaverage_plot_time, minaverage)
    
    pp <- ggplot(minaverage_plot_df, aes(x=minaverage_plot_time, y = minaverage))+ 
      geom_bar(stat="identity", width = 1, position = position_dodge(width = 0.5))+
      theme_bw()+
      scale_x_discrete(limits = c(seq(1:1440)), breaks = seq(1,1440,60))+
      expand_limits(x=c(-30,1470))+
      xlab("Time \n (Start: 0am)")+
      ylab("Movement Intensity")+
      ggtitle("Actigraphy Plot (24 hrs)", subtitle = "Average across days")+
      theme(plot.margin=unit(c(1,2,1,2),"cm"),
            axis.text.x = element_blank(),
            axis.title.x = element_text(face="bold", size=12),
            axis.title.y = element_text(face="bold", size=12, vjust = 1.2),
            plot.title = element_text(face="bold", size=14, vjust = 1))
    print(pp)
  },
  
  nparACT_plot_hraverage_GA_loop = function(matrix_hraverage){
    GA_hraverage <- colMeans(matrix_hraverage, na.rm = T)
    GA_hraverage_plot_time <- seq(1,24)-1
    
    GA_hraverage_plot_df <- data.frame (GA_hraverage_plot_time, GA_hraverage)
    
    p <- ggplot(GA_hraverage_plot_df, aes(x=GA_hraverage_plot_time, y = GA_hraverage))+ 
      geom_bar(stat="identity", width = 1, position = position_dodge(width = 0.5))+
      theme_bw()+
      scale_x_discrete(expand = c(0,0), limits = c(seq(0:23)-1), breaks = seq(0,23))+
      expand_limits(x=-1)+
      xlab("Time \n (Start: 0am)")+
      ylab("Movement Intensity")+
      ggtitle("Grand Average Actigraphy Plot (24 hrs)", subtitle = "Average across days")+
      theme(plot.margin=unit(c(1,2,1,2),"cm"),
            axis.text.x = element_blank(),
            axis.title.x = element_text(face="bold", size=12),
            axis.title.y = element_text(face="bold", size=12, vjust = 1.2),
            plot.title = element_text(face="bold", size=14, vjust = 1))
    print(p)
  }
)