Merge branch 'master' of https://github.com/JulioV/moshi-aware

2019-11-05 16:18:43 -05:00 · 2019-11-05 16:18:43 -05:00 · df2a73fe1b
parent 70f3c336b5 13a6537b14
commit df2a73fe1b
46 changed files with 1583 additions and 8 deletions
--- a/2
+++ b/2
@ -8,6 +8,7 @@ rule all:
        expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
        expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
        expand("data/processed/{pid}/battery_deltas.csv", pid=config["PIDS"]),
+        expand("data/interim/{pid}/phone_valid_sensed_days.csv", pid=config["PIDS"]),
        expand("data/processed/{pid}/com_sms_{sms_type}_{day_segment}_{metric}.csv",
                            pid=config["PIDS"],
                            sms_type = config["COM_SMS"]["SMS_TYPES"],
@ -23,6 +24,7 @@ rule all:
                            call_type = config["COM_CALL"]["CALL_TYPE_TAKEN"],
                            segment = config["COM_CALL"]["DAY_SEGMENTS"],
                            metric = config["COM_CALL"]["METRICS_TAKEN"]),
+        expand("data/processed/{pid}/location_barnett_metrics.csv", pid=config["PIDS"]),
        # Reports
        expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
        expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"], sensor=config["SENSORS"]),
--- a/config.yaml
+++ b/config.yaml
@ -1,5 +1,5 @@
 # Valid database table names
-SENSORS: [messages, calls, battery]
+SENSORS: [applications_crashes, applications_foreground, applications_notifications, battery, bluetooth, calls, locations, messages, plugin_ambient_noise, plugin_device_usage, plugin_google_activity_recognition, screen]

 # Participants to include in the analysis
 # You must create a file for each participant
@ -10,13 +10,17 @@ PIDS: [p01, p02]
 DAY_SEGMENTS: &day_segments
  [daily, morning, afternoon, evening, night]

+# Global timezone
+TIMEZONE: &timezone
+  EST
+
 # Download data config
 DOWNLOAD_DATASET:
  GROUP: AAPECS

 # Readable datetime config
 READABLE_DATETIME:
-  FIXED_TIMEZONE: EST
+  FIXED_TIMEZONE: *timezone

 # Communication SMS features config
 COM_SMS:
@ -32,3 +36,12 @@ COM_CALL:
  DAY_SEGMENTS: *day_segments
  METRICS_MISSED: [count, distinctcontacts]
  METRICS_TAKEN: [count, distinctcontacts, meanduration, sumduration, hubermduration, varqnduration, entropyduration]
+
+PHONE_VALID_SENSED_DAYS:
+  BIN_SIZE: 5 # (in minutes)
+  MIN_VALID_HOURS: 20 # (out of 24)
+  MIN_BINS_PER_HOUR: 8 # (out of 60min/BIN_SIZE bins)
+
+BARNETT_LOCATION:
+  ACCURACY_LIMIT: 51 # filters location coordinates with an accuracy higher than this
+  TIMEZONE: *timezone
--- a/rules/features.snakefile
+++ b/rules/features.snakefile
@ -29,3 +29,14 @@ rule battery_deltas:
        "data/processed/{pid}/battery_deltas.csv"
    script:
        "../src/features/battery_deltas.R"
+
+rule location_barnett_metrics:
+    input:
+        "data/raw/{pid}/locations_with_datetime.csv"
+    params:
+        accuracy_limit = config["BARNETT_LOCATION"]["ACCURACY_LIMIT"],
+        timezone = config["BARNETT_LOCATION"]["TIMEZONE"]
+    output:
+        "data/processed/{pid}/location_barnett_metrics.csv"
+    script:
+        "../src/features/location_barnett_metrics.R"
--- a/rules/preprocessing.snakefile
+++ b/rules/preprocessing.snakefile
@ -19,3 +19,15 @@ rule readable_datetime:
        "data/raw/{pid}/{sensor}_with_datetime.csv"
    script:
        "../src/data/readable_datetime.R"
+
+rule phone_valid_sensed_days:
+    input:
+        all_sensors =  expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["SENSORS"])
+    params:
+        bin_size = config["PHONE_VALID_SENSED_DAYS"]["BIN_SIZE"],
+        min_valid_hours = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS"],
+        min_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_BINS_PER_HOUR"]
+    output:
+        "data/interim/{pid}/phone_valid_sensed_days.csv"
+    script:
+        "../src/data/phone_valid_sensed_days.R"
--- a/src/data/download_dataset.R
+++ b/src/data/download_dataset.R
@ -19,5 +19,5 @@ sensor_data <- sensor_data[order(sensor_data$timestamp),]

 # Droping duplicates on all columns except for _id
 sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), "_id")))
-write.table(sensor_data, sensor_file, row.names = FALSE, quote = FALSE, sep = ",")
+write.csv(sensor_data, sensor_file)
 dbDisconnect(stopDB)
--- a/src/data/phone_valid_sensed_days.R
+++ b/src/data/phone_valid_sensed_days.R
@ -0,0 +1,31 @@
+source("packrat/init.R")
+
+library(dplyr)
+
+all_sensors <- snakemake@input[["all_sensors"]]
+bin_size <- snakemake@params[["bin_size"]]
+min_valid_hours <- snakemake@params[["min_valid_hours"]]
+min_bins_per_hour <- snakemake@params[["min_bins_per_hour"]]
+output_file <- snakemake@output[[1]]
+
+# Load all sensors and extract timestamps
+all_sensor_data <- data.frame(timestamp = c())
+for(sensor in all_sensors){
+    sensor_data <- read.csv(sensor, stringsAsFactors = F) %>% select(local_date, local_hour, local_minute)
+    all_sensor_data <- rbind(all_sensor_data, sensor_data)
+}
+
+phone_valid_sensed_days <- all_sensor_data %>% 
+    mutate(bin = (local_minute %/% bin_size) * bin_size) %>% # bin rows into bin_size-minute bins
+    group_by(local_date, local_hour, bin) %>% 
+    summarise(minute_period = first(bin)) %>% #filter repeated bins (if rows were logged within bin_size minutes)
+    ungroup() %>% 
+    group_by(local_date, local_hour) %>% 
+    summarise(bins = n()) %>% # Count how many bins there are per hour
+    ungroup() %>% 
+    filter(bins >= min_bins_per_hour) %>% # Discard those hours where there were fewer than min_bins_per_hour
+    group_by(local_date) %>% 
+    summarise(valid_hours = n()) %>% # Count how many valid hours each day has
+    filter(valid_hours >= min_valid_hours) # Discard those days where there were fewer than min_valid_hours
+
+write.csv(phone_valid_sensed_days, output_file)
--- a/src/features/battery_deltas.R
+++ b/src/features/battery_deltas.R
@ -7,7 +7,7 @@ battery <- read.csv(snakemake@input[[1]])
 consumption <- battery %>%
    mutate(group = ifelse(lag(battery_status) != battery_status, 1, 0) %>% coalesce(0),
            group_id = cumsum(group) + 1) %>%
-    filter(battery_status == 3) %>%
+    filter(battery_status == 2 || battery_status == 3) %>%
    group_by(group_id) %>%
    summarize(battery_diff = first(battery_level) - last(battery_level),
            time_diff = (last(timestamp) - first(timestamp)) / (1000 * 60 * 60),
@ -16,6 +16,6 @@ consumption <- battery %>%
            local_start_date = first(local_date),
            local_end_date = last(local_date)) %>%
    select(-group_id) %>%
-    filter(time_diff > 0.1) # Avoids including quick discharge cycles
+    filter(time_diff > 0.1) # Avoids including quick cycles

 write.csv(consumption, snakemake@output[[1]])
--- a/src/features/location_barnett/AvgFlightDur.R
+++ b/src/features/location_barnett/AvgFlightDur.R
@ -0,0 +1,13 @@
+AvgFlightDur <-
+function(mat){
+  num=0
+  tot=0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==1){
+      tot=tot+mat[i,7]-mat[i,4]
+      num=num+1
+    }
+  }
+  if(num==0){return(0)}
+  return(tot/num)
+}
--- a/src/features/location_barnett/AvgFlightLen.R
+++ b/src/features/location_barnett/AvgFlightLen.R
@ -0,0 +1,13 @@
+AvgFlightLen <-
+function(mat){
+  num=0
+  tot=0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==1){
+      tot=tot+sqrt((mat[i,5]-mat[i,2])^2+(mat[i,6]-mat[i,3])^2)
+      num=num+1
+    }
+  }
+  if(num==0){return(0)}
+  return(tot/num)
+}
--- a/src/features/location_barnett/Collapse2Pause.R
+++ b/src/features/location_barnett/Collapse2Pause.R
@ -0,0 +1,9 @@
+Collapse2Pause <-
+function(mat){
+  cent=colMeans(mat[,2:3],na.rm=TRUE)
+  if(!is.na(mat[nrow(mat),7])){
+    return(c(2,cent[1],cent[2],mat[1,4],NA,NA,mat[nrow(mat),7]))
+  }else{
+    return(c(2,cent[1],cent[2],mat[1,4],NA,NA,mat[nrow(mat),4]))    
+  }
+}
--- a/src/features/location_barnett/DailyMobilityPlots.R
+++ b/src/features/location_barnett/DailyMobilityPlots.R
@ -0,0 +1,42 @@
+DailyMobilityPlots <-
+function(mobmat,obj,tz,filename){
+  curdate=strsplit(as.character(as.POSIXct(mobmat[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+  curtime=strsplit(strsplit(as.character(as.POSIXct(mobmat[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][2],":")
+  subsetinds_v = list()
+  daystr_v = c(curdate)
+  dayind=1
+  subsetinds = c(1)
+  for(i in 2:nrow(mobmat)){
+    nexdate=strsplit(as.character(as.POSIXct(mobmat[i,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+    if(nexdate == curdate && i<nrow(mobmat)){
+      subsetinds=c(subsetinds,i)
+    }else{
+      subsetinds_v[[dayind]]=subsetinds
+      dayind=dayind+1
+      if(mobmat[i-1,1]==2 && (mobmat[i-1,7]-mobmat[i-1,4])/(60*60*24)>1){
+        ii=1
+        middate = strsplit(as.character(as.POSIXct(mobmat[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        while(middate!=nexdate){
+          subsetinds_v[[dayind]]=i-1
+          dayind=dayind+1
+          if(middate!=daystr_v[length(daystr_v)]){
+            daystr_v=c(daystr_v,middate)        
+          }          
+          ii=ii+1
+          middate = strsplit(as.character(as.POSIXct(mobmat[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        }
+      }
+      curdate=nexdate
+      subsetinds=c(i-1,i)
+      if(curdate!=daystr_v[length(daystr_v)] && length(daystr_v)<length(subsetinds_v)){
+        daystr_v=c(daystr_v,curdate)        
+      }
+    }
+  }  
+  plot.flights(mobmat,diminch=4,outfile=paste("FlightsPlot_full_",filename,".pdf",sep=""),xrang=plotlimits(mobmat)$xrang,yrang=plotlimits(mobmat)$yrang)
+  for(i in 1:length(daystr_v)){
+    submat=matrix(mobmat[subsetinds_v[[i]],],ncol=7)
+    plot.flights(submat,diminch=4,outfile=paste("FlightsPlot_",daystr_v[i],"_ZOOMOUT_",filename,".pdf",sep=""),xrang=plotlimits(mobmat)$xrang,yrang=plotlimits(mobmat)$yrang)      
+    plot.flights(submat,diminch=4,outfile=paste("FlightsPlot_",daystr_v[i],"_ZOOMIN_",filename,".pdf",sep=""))      
+  }
+}
--- a/src/features/location_barnett/DailyRoutineIndex.R
+++ b/src/features/location_barnett/DailyRoutineIndex.R
@ -0,0 +1,25 @@
+DailyRoutineIndex <-
+function(indday,mobmat,subsetinds_v,subsetdayofweek_v,subsetstarttime_v,tz,CENTERRAD){
+  submat=matrix(mobmat[subsetinds_v[[indday]],],ncol=7)
+  daydist_v = rep(NA,length(subsetinds_v))
+  for(i in 1:length(subsetinds_v)){
+    if(i == indday){next}
+    daydist_v[i]=DayDist(indday,i,mobmat,subsetinds_v,subsetstarttime_v,tz,CENTERRAD)
+  }
+  if(length(which(!is.na(daydist_v)))==0){
+    circscore=NA
+  }else{
+    circscore = mean(daydist_v,na.rm=T)    
+  }
+  if(subsetdayofweek_v[indday] == "Saturday" || subsetdayofweek_v[indday] == "Sunday"){
+    IDcompare = c(which(subsetdayofweek_v=="Saturday"),which(subsetdayofweek_v=="Sunday"))
+  }else{
+    IDcompare = c(which(subsetdayofweek_v=="Monday"),which(subsetdayofweek_v=="Tuesday"),which(subsetdayofweek_v=="Wednesday"),which(subsetdayofweek_v=="Thursday"),which(subsetdayofweek_v=="Friday"))
+  }
+  if(length(IDcompare)==0 || length(which(!is.na(daydist_v[IDcompare])))==0){
+    wkscore=NA
+  }else{
+    wkscore = mean(daydist_v[IDcompare],na.rm=T)    
+  }
+  return(list('cscore'=circscore,'wscore'=wkscore))
+}
--- a/src/features/location_barnett/DayDist.R
+++ b/src/features/location_barnett/DayDist.R
@ -0,0 +1,42 @@
+DayDist <-
+function(i1,i2,mobmat,subsetinds_v,subsetstarttime_v,tz,CENTERRAD){
+  chkpts=subsetstarttime_v[i1]+seq(from=30*60,by=60*60,length.out=24)
+  chkpts2=subsetstarttime_v[i2]+seq(from=30*60,by=60*60,length.out=24)
+  mat1=matrix(mobmat[subsetinds_v[[i1]],],ncol=7)
+  mat2=matrix(mobmat[subsetinds_v[[i2]],],ncol=7)
+  SamePlace = rep(NA,24)
+  for(i in 1:24){
+    loc1=LocationAt(mat1,chkpts[i])
+    if(is.null(loc1)){
+      next
+    }
+    IDs=c(which(abs(mat2[,4]-chkpts[i])%%(60*60*24)<30*60),which(abs(mat2[,4]-chkpts[i])%%(60*60*24)>(60*60*24)-30*60))
+    if(length(IDs)>0){
+      CanBe0=FALSE
+      for(j in 1:length(IDs)){
+        if(mat2[IDs[j],1]<=3){
+          CanBe0 = TRUE
+          if(sqrt((mat2[IDs[j],2]-loc1$x)^2+(mat2[IDs[j],3]-loc1$y)^2)<CENTERRAD){
+            SamePlace[i]=1
+          }
+        }
+      }
+      if(CanBe0 && is.na(SamePlace[i])){
+        SamePlace[i]=0
+      }
+    }else{
+      for(j in 1:nrow(mat2)){
+        if(!is.na(mat2[j,4])&&!is.na(mat2[j,7])&& mat2[j,4]<chkpts2[i] && mat2[j,7]>chkpts2[i]){
+          if(mat2[j,1]!=4 && sqrt((mat2[j,2]-loc1$x)^2+(mat2[j,3]-loc1$y)^2)<CENTERRAD){
+            SamePlace[i]=1
+          }else{
+            SamePlace[i]=0
+          }
+          break
+        }
+      }
+    }
+  }
+  if(length(which(!is.na(SamePlace)))==0){return(NA)}
+  return(mean(SamePlace,na.rm=T))
+}
--- a/src/features/location_barnett/DistanceTravelled.R
+++ b/src/features/location_barnett/DistanceTravelled.R
@ -0,0 +1,10 @@
+DistanceTravelled <-
+function(mat){
+  dt=0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==1){
+      dt=dt+sqrt((mat[i,5]-mat[i,2])^2+(mat[i,6]-mat[i,3])^2)
+    }
+  }
+  return(dt)
+}
--- a/src/features/location_barnett/ExtractFlights.R
+++ b/src/features/location_barnett/ExtractFlights.R
@ -0,0 +1,71 @@
+ExtractFlights <-
+function(mat,r,w){
+  out = c()  
+  if(!is.matrix(mat)){
+    out=matrix(c(3,mat[1],mat[2],mat[3],NA,NA,NA),nrow=1)
+    colnames(out)=c("code","lon1","lat1","t1","lon2","lat2","t2")
+    return(out)
+  }
+  nextline = rep(NA,6)
+  nextline[1:3]=mat[1,]
+  curind = 1
+  while(TRUE){
+    nexind = curind+1
+    if(nexind==nrow(mat)){
+      nextline[4:6]=mat[nexind,]
+      out=rbind(out,nextline)
+      break
+    }
+    while(TRUE){
+      if(!IsFlight(mat[curind:nexind,],r,w)){
+        break
+      }
+      nexind=nexind+1
+      if(nexind>nrow(mat)){
+        break
+      }
+    }
+    if(nexind==curind+1 && curind!=nrow(mat)){
+      nextline[3]=mat[nexind,3]
+      mat=mat[-nexind,]
+    }else{
+      nextline[4:6]=mat[nexind-1,]
+      out=rbind(out,nextline)
+      nextline=rep(NA,6)
+      curind=nexind-1
+      nextline[1:3]=mat[curind,]
+    }
+    if(nexind>nrow(mat)){break}
+  }
+  outp=c()
+  if(out[1,3]>min(mat[,3])){
+    outp=rbind(outp,c(2,out[1,1],out[1,2],min(mat[,3]),NA,NA,out[1,3]))
+    if(nrow(out)==1){
+      outp[1,7]=out[1,6]
+      return(outp)
+    }
+  }
+  if(nrow(out)==1){
+    outp=rbind(outp,c(1,out))
+    return(outp)
+  }
+  for(i in 1:(nrow(out)-1)){
+    outp=rbind(outp,c(1,out[i,]))
+    if(out[i,6]<out[i+1,3]){
+      outp=rbind(outp,c(2,out[i,4],out[i,5],out[i,6],NA,NA,out[i+1,3]))
+    }
+  }
+  # convert flights with distance 0 into pauses
+  IDf=which(outp[,1]==1)
+  IDp=which((outp[IDf,2]-outp[IDf,5])^2+(outp[IDf,3]-outp[IDf,6])^2==0)
+  if(length(IDp)>0){
+    for(i in 1:length(IDp)){
+      outp[IDf[IDp[i]],1]=2
+      outp[IDf[IDp[i]],5]=NA
+      outp[IDf[IDp[i]],6]=NA
+    }
+  }
+  outp=rbind(outp,c(1,out[nrow(out),]))
+  colnames(outp)=c("code","lon1","lat1","t1","lon2","lat2","t2")
+  return(outp)
+}
--- a/src/features/location_barnett/ExtractTimePeriod.R
+++ b/src/features/location_barnett/ExtractTimePeriod.R
@ -0,0 +1,8 @@
+ExtractTimePeriod <-
+function(tstart,tend,out){
+  tstart = as.POSIXct(tstart)
+  tend = as.POSIXct(tend)
+  INDs=intersect(which(apply(out[,c(4,7)],1,function(x) max(x,na.rm=T))>=tstart),which(out[,4]<=tend))
+  suboutmat=out[INDs,]  
+  return(suboutmat)
+}
--- a/src/features/location_barnett/GPS2MobMat.R
+++ b/src/features/location_barnett/GPS2MobMat.R
@ -0,0 +1,78 @@
+GPS2MobMat <-
+function(locations_df,itrvl=10,accuracylim=51,r=NULL,w=NULL,tint_m=NULL,tint_k=NULL){
+  if(is.null(r)){
+    r=sqrt(itrvl)
+  }
+  cat("Read GPS coordinates...\n")
+  mat=as.matrix(locations_df)
+  colnames(mat)=c("timestamp","latitude","longitude","altitude","accuracy")
+  mat=data.frame(mat)
+  mat = mat[order(mat[,1]),]
+  mat=mat[which(mat$accuracy<accuracylim),]
+  if(!is.null(tint_k) && !is.null(tint_m)){
+    t0 = mat$timestamp[1]/1000;
+    mat=mat[which((mat$timestamp/1000-t0)%%(tint_k+tint_m)<tint_k),]    
+  }
+  if(is.null(w)){
+    w=mean(mat$accuracy)+itrvl
+  }
+  tstart=mat[1,1]/1000
+  tend=mat[nrow(mat),1]/1000
+  avgmat = matrix(NA,nrow=ceiling((tend-tstart)/itrvl)+2,ncol=4)
+  IDam = 1
+  count = 0
+  nextline=c(1,tstart+itrvl/2,mat[1,2],mat[1,3]) 
+  numitrvl=1
+  cat("Collapse data within",itrvl,"second intervals...\n")
+  for(i in 2:nrow(mat)){
+    #ProgressBar(nrow(mat)-1,i-1)
+    if(mat[i,1]/1000<tstart+itrvl){
+      nextline[3]=nextline[3]+mat[i,2]
+      nextline[4]=nextline[4]+mat[i,3]
+      numitrvl=numitrvl+1
+    }else{
+      nextline[3]=nextline[3]/numitrvl
+      nextline[4]=nextline[4]/numitrvl
+      #avgmat=rbind(avgmat,nextline)
+      avgmat[IDam,]=nextline
+      count=count+1
+      IDam=IDam+1
+      nummiss=floor((mat[i,1]/1000-(tstart+itrvl))/itrvl)
+      if(nummiss>0){
+        #avgmat = rbind(avgmat,c(4,tstart+itrvl/2,tstart+itrvl*(nummiss+1)+itrvl/2,NA))
+        avgmat[IDam,] = c(4,tstart+itrvl/2,tstart+itrvl*(nummiss+1)+itrvl/2,NA)
+        count=count+1
+        IDam=IDam+1
+      }
+      tstart=tstart+itrvl*(nummiss+1)
+      nextline[1]=1
+      nextline[2]=tstart+itrvl/2
+      nextline[3]=mat[i,2]
+      nextline[4]=mat[i,3]
+      numitrvl=1
+    }
+  }
+  avgmat = avgmat[1:count,]
+  avgmat=cbind(avgmat[,1:4],NA,NA)
+  ID1 = which(avgmat[,1]==1)
+  cat("Convert from Lat/Lon to X/Y...\n")
+  obj=LatLong2XY(avgmat[ID1,3],avgmat[ID1,4])
+  avgmat[ID1,5:6]=cbind(obj$x_v,obj$y_v)
+  outmat=c()
+  curind=1
+  cat("Convert from X/Y to flights/pauses...\n")
+  for(i in 1:nrow(avgmat)){
+    #ProgressBar(nrow(avgmat),i)
+    if(avgmat[i,1]==4){
+      outmat=rbind(outmat,ExtractFlights(avgmat[curind:(i-1),c(5,6,2)],r,w),
+                   c(avgmat[i,1],NA,NA,avgmat[i,2],NA,NA,avgmat[i,3]))
+      curind=i+1
+    }
+  }  
+  if(curind<=nrow(avgmat)){  
+    outmat=rbind(outmat,ExtractFlights(avgmat[curind:nrow(avgmat),c(4,3,2)],r,w))
+  }
+  rownames(outmat)=NULL
+  colnames(outmat)=c("Code","x0","y0","t0","x1","y1","t1")
+  return(outmat)
+}
--- a/src/features/location_barnett/GPSmobility-internal.R
+++ b/src/features/location_barnett/GPSmobility-internal.R
@ -0,0 +1,127 @@
+.Random.seed <-
+c(403L, 532L, 1313347924L, 1871810394L, 1011383459L, 542971573L, 
+-1187392539L, -1841977675L, 1217131604L, -1944452603L, 1098034341L, 
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+1331187882L, 1481475622L, 892770178L, -1889921295L, -1870961089L, 
+-2137441515L, 1504371917L, 1834797012L, 1264278039L, 1648781970L, 
+-2140624793L, 53578265L, 1201061792L, 1516041549L, -216621021L, 
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+-1773470008L, -1939021033L, 1778465361L, 532321917L, 1286568102L
+)
--- a/src/features/location_barnett/GetMobilityFeaturesMat.R
+++ b/src/features/location_barnett/GetMobilityFeaturesMat.R
@ -0,0 +1,151 @@
+GetMobilityFeaturesMat <-
+function(mobmat,obj,mobmatmiss,tz,CENTERRAD,ITRVL){
+  #### Get significant locations
+  slout=SigLocs(mobmat,obj,CENTERRAD,tz=tz)
+  IDhome=which(slout[,4]==1)
+  if(length(IDhome)==0){IDhome=1}
+  homex=slout[IDhome,1];homey=slout[IDhome,2]
+  #### Partion mobmat data into daily subsets: create subsetinds_v and daystr_v.
+  curdate=strsplit(as.character(as.POSIXct(mobmat[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+  curtime=strsplit(strsplit(as.character(as.POSIXct(mobmat[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][2],":")
+  subsetinds_v = list()
+  subsetdayofweek_v = c()
+  subsetstarttime_v = c()
+  daystr_v = c(curdate)
+  dayind=1
+  subsetinds = c(1)
+  if(nrow(mobmat)<2){
+    outmat=NULL
+    return(list(outmat,slout))
+  }
+  for(i in 2:nrow(mobmat)){
+    nexdate=strsplit(as.character(as.POSIXct(mobmat[i,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+    if(nexdate == curdate && i<nrow(mobmat)){
+      subsetinds=c(subsetinds,i)
+    }else{
+      subsetinds_v[[dayind]]=subsetinds
+      subsetdayofweek_v = c(subsetdayofweek_v,weekdays(as.Date(curdate)))
+      subsetstarttime_v = c(subsetstarttime_v,as.numeric(as.POSIXct(paste(curdate," 00:00:00",sep=""),tz=tz,origin="1970-01-01")))
+      dayind=dayind+1          
+      if(mobmat[i-1,1]==2 && (mobmat[i-1,7]-mobmat[i-1,4])/(60*60*24)>1){
+        ii=1
+        middate = strsplit(as.character(as.POSIXct(mobmat[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        while(middate!=nexdate){
+          subsetdayofweek_v = c(subsetdayofweek_v,weekdays(as.Date(middate)))
+          subsetstarttime_v = c(subsetstarttime_v,as.numeric(as.POSIXct(paste(middate," 00:00:00",sep=""),tz=tz,origin="1970-01-01")))
+          subsetinds_v[[dayind]]=i-1
+          dayind=dayind+1
+          if(middate!=daystr_v[length(daystr_v)]){
+            daystr_v=c(daystr_v,middate)        
+          }          
+          ii=ii+1
+          middate = strsplit(as.character(as.POSIXct(mobmat[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        }
+      }
+      curdate=nexdate
+      subsetinds=c(i-1,i)
+      if(curdate!=daystr_v[length(daystr_v)]&& !(length(daystr_v)==length(subsetinds_v) && nrow(mobmat)==i)){
+        daystr_v=c(daystr_v,curdate)        
+      }
+    }
+  }
+  #### Partion mobmatmiss data into daily subsets: create subsetinds_v and daystr_v.
+  curdate=strsplit(as.character(as.POSIXct(mobmatmiss[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+  curtime=strsplit(strsplit(as.character(as.POSIXct(mobmatmiss[1,4],tz=tz,origin="1970-01-01"))," ")[[1]][2],":")
+  subsetindsmiss_v = list()
+  daystrmiss_v=c(curdate)
+  dayind=1
+  subsetinds = c(1)
+  for(i in 2:nrow(mobmatmiss)){
+    nexdate=strsplit(as.character(as.POSIXct(mobmatmiss[i,4],tz=tz,origin="1970-01-01"))," ")[[1]][1]
+    if(nexdate == curdate && i<nrow(mobmatmiss)){
+      subsetinds=c(subsetinds,i)
+    }else{
+      curdate=nexdate
+      subsetindsmiss_v[[dayind]]=subsetinds
+      if(curdate!=daystrmiss_v[length(daystrmiss_v)] && !(length(daystrmiss_v)==length(subsetindsmiss_v) && nrow(mobmatmiss)==i)){
+        daystrmiss_v=c(daystrmiss_v,curdate)        
+      }
+      subsetinds=c(i-1,i)
+      dayind=dayind+1
+      if(mobmatmiss[i-1,1]==2 && (mobmatmiss[i-1,7]-mobmatmiss[i-1,4])/(60*60*24)>1){
+        ii=1
+        middate = strsplit(as.character(as.POSIXct(mobmatmiss[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        while(middate!=nexdate){
+          subsetindsmiss_v[[dayind]]=i-1
+          dayind=dayind+1
+          if(middate!=daystrmiss_v[length(daystrmiss_v)]){
+            daystrmiss_v=c(daystrmiss_v,middate)        
+          }          
+          ii=ii+1
+          middate = strsplit(as.character(as.POSIXct(mobmatmiss[i-1,4]+(60*60*24)*ii,tz=tz,origin="1970-01-01"))," ")[[1]][1]
+        }
+      }
+    }
+  }
+  ##### intersect mobmat and mobmatmiss to ignore missing data
+  IDkeep=c()
+  IDkeepmiss=c()
+  for(i in 1:length(daystr_v)){
+    for(j in 1:length(daystrmiss_v)){
+      if(daystr_v[i]==daystrmiss_v[j]){
+        IDkeep=c(IDkeep,i)
+        IDkeepmiss=c(IDkeepmiss,j)
+        break
+      }
+    }
+  }
+  if(length(IDkeep)==0){
+    outmat=NULL
+    return(list(outmat,slout))
+  }
+  daystr_v=daystr_v[IDkeep]
+  subsetinds_v=subsetinds_v[IDkeep]
+  subsetdayofweek_v=subsetdayofweek_v[IDkeep]
+  subsetstarttime_v=subsetstarttime_v[IDkeep]
+  daystrmiss_v=daystrmiss_v[IDkeepmiss]
+  subsetindsmiss_v=subsetindsmiss_v[IDkeepmiss]
+  ##### Compute mobility features for each day
+  Nfeatures=15
+  outmat=matrix(,nrow=length(daystr_v),ncol=Nfeatures)
+  colnames(outmat)=c("Hometime","DistTravelled","RoG","MaxDiam","MaxHomeDist","SigLocsVisited","AvgFlightLen","StdFlightLen","AvgFlightDur","StdFlightDur","ProbPause","SigLocEntropy","MinsMissing","CircdnRtn","WkEndDayRtn")
+  rownames(outmat)=daystr_v
+  for(i in 1:length(daystr_v)){
+    if(length(subsetinds_v[[i]])==0){next}
+    submat=matrix(mobmat[subsetinds_v[[i]],],ncol=7)
+    if(submat[1,1]==2 && submat[1,4]<subsetstarttime_v[[i]]){
+      submat[1,4]=subsetstarttime_v[[i]]
+    }
+    if(submat[nrow(submat),1]==2 && submat[nrow(submat),7]>subsetstarttime_v[[i]]+60*60*24){
+      submat[nrow(submat),7]=subsetstarttime_v[[i]]+60*60*24
+    }
+    submatmiss=matrix(mobmatmiss[subsetindsmiss_v[[i]],],ncol=7)
+    if(submatmiss[1,1]==4 && submatmiss[1,4]<subsetstarttime_v[[i]]){
+      submatmiss[1,4]=subsetstarttime_v[[i]]
+    }
+    if(submatmiss[nrow(submatmiss),1]==4 && submatmiss[nrow(submatmiss),7]>subsetstarttime_v[[i]]+60*60*24){
+      submatmiss[nrow(submatmiss),7]=subsetstarttime_v[[i]]+60*60*24
+    }
+    if(nrow(submat)==0 || length(which(slout$home==1))==0){
+      outmat[i,]=c(rep(NA,12),1440,rep(NA,2))
+    }else{
+      outmat[i,1]=Hometime(submat,slout,CENTERRAD=200)    
+      outmat[i,2]=DistanceTravelled(submat)
+      outmat[i,3]=RadiusOfGyration(submat,ITRVL)
+      outmat[i,4]=MaxDiam(submat)
+      outmat[i,5]=MaxHomeDist(submat,homex,homey)
+      outmat[i,6]=SigLocsVisited(submat,slout,CENTERRAD)
+      outmat[i,7]=AvgFlightLen(submat)
+      outmat[i,8]=StdFlightLen(submat)
+      outmat[i,9]=AvgFlightDur(submat)
+      outmat[i,10]=StdFlightDur(submat)
+      outmat[i,11]=ProbPause(submat)
+      outmat[i,12]=SigLocEntropy(submat,slout,CENTERRAD)
+      outmat[i,13]=MinsMissing(submatmiss)
+      DRIout=DailyRoutineIndex(i,mobmat,subsetinds_v,subsetdayofweek_v,subsetstarttime_v,tz,CENTERRAD)
+      outmat[i,14]=DRIout$cscore
+      outmat[i,15]=DRIout$wscore      
+    }
+  }
+  return(list(outmat,slout))
+}
--- a/src/features/location_barnett/GuessPause.R
+++ b/src/features/location_barnett/GuessPause.R
@ -0,0 +1,134 @@
+GuessPause <-
+function(mat,mindur=300,r=75){
+  cat("Inferring pauses...\n")
+  flatmat=c()
+  collapse=FALSE
+  inds=1
+  incr=1
+  tcur=mat[inds,4]
+  while(TRUE){
+    if(!is.na(mat[inds+incr,7])){
+      tnex=mat[inds+incr,7]
+    }else{
+      tnex=mat[inds+incr,4]
+    }
+    if(tnex-tcur>=mindur){
+      if(mat[inds+incr,1]==1){
+        maxr=MaxRadius(rbind(mat[inds:(inds+incr),2:3],mat[inds:(inds+incr),5:6]))
+      }else{
+        maxr=MaxRadius(mat[inds:(inds+incr),2:3])        
+      }
+      if(maxr>r && !collapse){
+        inds=inds+1
+        tcur=mat[inds,1]
+        incr=0
+      }
+      if(maxr>r && collapse){
+        if(mat[inds+incr-1,1]==4){
+          if(inds<inds+incr-2){
+            flatmat=rbind(flatmat,c(inds,inds+incr-2))                                
+          }
+        }else{
+          flatmat=rbind(flatmat,c(inds,inds+incr-1))          
+        }
+        inds=inds+incr
+        tcur=mat[inds,1]
+        incr=0
+        collapse=FALSE
+      }
+      if(maxr<=r){
+        collapse=TRUE
+      }
+    }
+    incr=incr+1
+    if(inds+incr>nrow(mat)){
+      if(maxr<=r && tnex-tcur>=mindur){
+        flatmat=rbind(flatmat,c(inds,inds+incr-1))
+      }
+      break
+    }
+  }
+  if(nrow(flatmat)==0){
+    return(mat)
+  }else{
+    outmat=c()
+    if(flatmat[1,1]>1){
+      outmat=mat[1:(flatmat[1,1]-1),]
+    }
+    for(i in 1:nrow(flatmat)){
+      #ProgressBar(nrow(flatmat),i)
+      outmat=rbind(outmat,Collapse2Pause(mat[flatmat[i,1]:flatmat[i,2],]))
+      if(i<nrow(flatmat) && flatmat[i,2]<flatmat[i+1,1]-1){
+        outmat=rbind(outmat,mat[(flatmat[i,2]+1):(flatmat[i+1,1]-1),])
+      }
+    }    
+    if(flatmat[nrow(flatmat),2]<nrow(mat)){
+      outmat=rbind(outmat,mat[(flatmat[nrow(flatmat),2]+1):nrow(mat),])
+    }
+  }
+  if(nrow(outmat)==1){
+    rownames(outmat)=NULL
+    colnames(outmat)=c("Code","x0","y0","t0","x1","y1","t1")
+    return(outmat)
+  }
+  # Group together adjacent pauses, averaging their location
+  flatmat2=c()
+  outmat2=c()
+  collapse=FALSE
+  for(i in 2:nrow(outmat)){
+    if(outmat[i,1]!=2 && !collapse){
+      next
+    }else if(outmat[i,1]!=2 && collapse){
+      collapse=FALSE
+      flatmat2=rbind(flatmat2,c(cstart,i-1))
+    }else  if(outmat[i,1]==2 && outmat[i-1,1]==2 && !collapse){
+      cstart=i-1
+      collapse=TRUE
+    }else if(outmat[i,1]==2 && collapse){
+      next
+    }
+  }
+  if(collapse && outmat[nrow(outmat),1]==2){
+    flatmat2=rbind(flatmat2,c(cstart,nrow(outmat)))
+  }
+  if(is.null(flatmat2)){
+    outmat2=outmat
+  }else{
+    flatmat2=matrix(flatmat2,ncol=2)
+    outmat2=c()
+    if(flatmat2[1,1]>1){
+      outmat2=outmat[1:(flatmat2[1,1]-1),]
+    }
+    for(i in 1:nrow(flatmat2)){
+      outmat2=rbind(outmat2,Collapse2Pause(outmat[flatmat2[i,1]:flatmat2[i,2],]))
+      if(i<nrow(flatmat2) && flatmat2[i,2] < flatmat2[i+1,1]-1){
+        outmat2=rbind(outmat2,outmat[(flatmat2[i,2]+1):(flatmat2[i+1,1]-1),])
+      }
+    }
+    if(flatmat2[nrow(flatmat2),2]<nrow(outmat)){
+      outmat2=rbind(outmat2,outmat[(flatmat2[nrow(flatmat2),2]+1):nrow(outmat),])
+    }
+  }
+  # Set flight endpoints equal to pause endpoints
+  if(outmat2[1,1]==1 && outmat2[2,1]==2){
+    outmat2[1,5]=outmat2[2,2]
+    outmat2[1,6]=outmat2[2,3]
+  }
+  for(i in 2:(nrow(outmat2)-1)){
+    if(outmat2[i,1]==1 && outmat2[i-1,1]==2){
+      outmat2[i,2]=outmat2[i-1,2]
+      outmat2[i,3]=outmat2[i-1,3]
+    }
+    if(outmat2[i,1]==1 && outmat2[i+1,1]==2){
+      outmat2[i,5]=outmat2[i+1,2]
+      outmat2[i,6]=outmat2[i+1,3]
+    }
+  }
+  if(outmat2[nrow(outmat2)-1,1]==2 && outmat2[nrow(outmat2),1]==1){
+    outmat2[nrow(outmat2),2]=outmat2[nrow(outmat2)-1,2]
+    outmat2[nrow(outmat2),3]=outmat2[nrow(outmat2)-1,3]
+  }
+  rownames(outmat2)=NULL
+  colnames(outmat2)=c("Code","x0","y0","t0","x1","y1","t1")
+  return(outmat2)
+}
--- a/src/features/location_barnett/Hometime.R
+++ b/src/features/location_barnett/Hometime.R
@ -0,0 +1,13 @@
+Hometime <-
+function(mat,slout,CENTERRAD){
+  IDhome=which(slout$home==1)
+  xcenter=slout[IDhome,1]
+  ycenter=slout[IDhome,2]
+  tottime=0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==2 && sqrt((mat[i,2]-xcenter)^2+(mat[i,3]-ycenter)^2)<CENTERRAD){ ### error missing value where true/false needed
+      tottime=tottime+mat[i,7]-mat[i,4]
+    }
+  }
+  return(tottime/60)
+}
--- a/src/features/location_barnett/InitializeParams.R
+++ b/src/features/location_barnett/InitializeParams.R
@ -0,0 +1,58 @@
+InitializeParams <-
+function(out){
+  ID1=which(out[,1]==1)
+  ID2=which(out[,1]==2)
+  ID3=which(out[,1]==3)
+  ID4=which(out[,1]==4)
+  
+  # probability of a pause after a flight
+  ID1p1=ID1+1    
+  if(length(ID1)>0 && ID1[length(ID1)]==nrow(out)){  
+    ID1p1=ID1p1[-length(ID1p1)]
+  }
+  allts=apply(out,1,function(xx) mean(xx[c(4,7)]))
+  allxs=out[,2]
+  allys=out[,3]
+  ind11=ID1p1[which(out[ID1p1,1]==1)]
+  ind12=ID1p1[which(out[ID1p1,1]==2)]
+  l1=length(ind11)
+  l2=length(ind12)
+  if(l1+l2>0){
+    phatall=l2/(l1+l2)    
+  }
+  if(l1+l2==0){phatall=length(ID2)/(length(ID1)+length(ID2))}
+  #flight distances
+  fd=apply(out[ID1,],1,function(xx) sqrt((xx[2]-xx[5])^2+(xx[3]-xx[6])^2))
+  
+  # flight times: ft
+  ft=apply(out[ID1,],1,function(xx) (xx[7]-xx[4]))
+  fxs=out[ID1,2]
+  fys=out[ID1,3]
+  # flight angles range [0,2pi]: fa
+  #fa=apply(out[ID1,],1,function(xx) atan((xx[6]-xx[3])/(xx[5]-xx[2]))-((sign(xx[6]-xx[3])-1)/2)*pi)
+  fa=rep(0,length(ID1))
+  yvals=out[ID1,6]-out[ID1,3]
+  xvals=out[ID1,5]-out[ID1,2]
+  IDyg0=which(yvals>=0)
+  IDxg0=which(xvals>=0)
+  IDyl0=which(yvals<0)
+  IDxl0=which(xvals<0)  
+  IDgg=intersect(IDyg0,IDxg0)
+  IDlg=intersect(IDyg0,IDxl0)
+  IDgl=intersect(IDyl0,IDxg0)
+  IDll=intersect(IDyl0,IDxl0)
+  fa[IDgg]=atan(yvals[IDgg]/xvals[IDgg])
+  fa[IDgl]=atan(yvals[IDgl]/xvals[IDgl])+2*pi
+  fa[IDlg]=atan(yvals[IDlg]/xvals[IDlg])+pi
+  fa[IDll]=atan(yvals[IDll]/xvals[IDll])+pi
+  # flight time stamps: fts
+  fts=out[ID1,4]
+  
+  # pause times
+  pt=apply(matrix(out[ID2,],ncol=7),1,function(xx) xx[7]-xx[4])
+  pxs=out[ID2,2]
+  pys=out[ID2,3]
+  #pause time stamp: pts
+  pts=out[ID2,4]  
+  return(list(ID1=ID1,ID2=ID2,ID3=ID3,ID4=ID4,ID1p1=ID1p1,allts=allts,ind11=ind11,ind12=ind12,phatall=phatall,fd=fd,ft=ft,fa=fa,fts=fts,pt=pt,pts=pts,fxs=fxs,fys=fys,pxs=pxs,pys=pys,allxs=allxs,allys=allys))  
+}
--- a/src/features/location_barnett/IsFlight.R
+++ b/src/features/location_barnett/IsFlight.R
@ -0,0 +1,33 @@
+IsFlight <-
+function(mat,r,w){
+  num=nrow(mat)
+  if(sqrt((mat[1,1]-mat[num,1])^2+(mat[1,2]-mat[num,2])^2)<r){
+    return(FALSE)
+  }
+  if(min(sqrt((mat[2:num,1]-mat[1:(num-1),1])^2+(mat[2:num,2]-mat[1:(num-1),2])^2))<r){
+    return(FALSE)
+  }
+  if(num==2){
+    return(TRUE)
+  }
+  if(mat[1,1]==mat[num,1]){
+    if(max(abs(mat[2:(num-1),1]))>w){
+      return(FALSE)
+    }else{
+      return(TRUE)
+    }
+  }
+  if(mat[1,1]>mat[num,1]){
+    mat=mat[num:1,]
+  }
+  mat[,1]=mat[,1]-mat[1,1]
+  mat[,2]=mat[,2]-mat[1,2]
+  theta=-atan(mat[num,2]/mat[num,1])
+  A=matrix(c(cos(theta),-sin(theta),sin(theta),cos(theta)),nrow=2,byrow=TRUE)
+  rotpts=A%*%t(matrix(mat[2:(num-1),1:2],ncol=2))
+  if(max(abs(rotpts[2,]))>w){
+    return(FALSE)
+  }else{
+    return(TRUE)
+  }
+}
--- a/src/features/location_barnett/LatLong2XY.R
+++ b/src/features/location_barnett/LatLong2XY.R
@ -0,0 +1,19 @@
+LatLong2XY <-
+function(lat_v,lon_v,R=6.371*10^6){
+  th0 = min(lon_v)
+  th1 = max(lon_v)
+  ph0 = min(lat_v)
+  ph1 = max(lat_v)
+  d1 = 2*pi*R*((ph1-ph0)*2*pi/360)/(2*pi)
+  d2 = 2*pi*(R*sin(pi/2-ph1*2*pi/360))*((th1-th0)*2*pi/360)/(2*pi)
+  d3 = 2*pi*(R*sin(pi/2-ph0*2*pi/360))*((th1-th0)*2*pi/360)/(2*pi)
+  x_v=rep(0,length(lon_v))
+  y_v=rep(0,length(lat_v))
+  for(i in 1:length(lat_v)){
+    w1=(lat_v[i]-ph0)/(ph1-ph0)
+    w2=(lon_v[i]-th0)/(th1-th0)
+    x_v[i]=w1*abs(d3-d2)/2+w2*(d3*(1-w1)+d2*w1)
+    y_v[i]=w1*d1*sin(acos(abs((d3-d2)/(2*d1))))
+  }
+  return(list("x_v"=x_v,"y_v"=y_v))
+}
--- a/src/features/location_barnett/LocationAt.R
+++ b/src/features/location_barnett/LocationAt.R
@ -0,0 +1,15 @@
+LocationAt <-
+function(mat,tt){
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]<=2){
+      if(mat[i,4]<=tt && mat[i,7]>=tt){
+        return(list('x'=mat[i,2],'y'=mat[i,3]))
+      }
+    }else if(mat[i,1]==3){
+      if(mat[i,4]==tt){
+        return(list('x'=mat[i,2],'y'=mat[i,3]))
+      }      
+    }
+  }
+  return(NULL)
+}
--- a/src/features/location_barnett/MaxDiam.R
+++ b/src/features/location_barnett/MaxDiam.R
@ -0,0 +1,6 @@
+MaxDiam <-
+function(mat){
+  IDmv=which(mat[,1]<=2)
+  if(length(IDmv)<2){return(0)}
+  return(max(dist(mat[IDmv,2:3])))
+}
--- a/src/features/location_barnett/MaxDistBetweenTrajectories.R
+++ b/src/features/location_barnett/MaxDistBetweenTrajectories.R
@ -0,0 +1,29 @@
+MaxDistBetweenTrajectories <-
+function(mat1,mat2,t_gap=1){
+  mat1=matrix(mat1,ncol=7);mat2=matrix(mat2,ncol=7)
+  t0=mat1[1,4];t1=mat2[nrow(mat2),7]
+  t_mesh = seq(t0,t1,t_gap)
+  d_v = rep(0,length(t_mesh))
+  for(i in 1:length(t_mesh)){
+    ID1=intersect(which(mat1[,4]<=t_mesh[i]),which(mat1[,7]>=t_mesh[i]))[1]
+    if(mat1[ID1,1]==2){
+      x1=mat1[ID1,2]
+      y1=mat1[ID1,3]
+    }else{
+      w1=(t_mesh[i]-mat1[ID1,4])/(mat1[ID1,7]-mat1[ID1,4])
+      x1=mat1[ID1,2]*(1-w1)+mat1[ID1,5]*w1
+      y1=mat1[ID1,3]*(1-w1)+mat1[ID1,6]*w1
+    }
+    ID2=intersect(which(mat2[,4]<=t_mesh[i]),which(mat2[,7]>=t_mesh[i]))[1]
+    if(mat2[ID2,1]==2){
+      x2=mat2[ID2,2]
+      y2=mat2[ID2,3]
+    }else{
+      w2=(t_mesh[i]-mat2[ID2,4])/(mat2[ID2,7]-mat2[ID2,4])
+      x2=mat2[ID2,2]*(1-w2)+mat2[ID2,5]*w2
+      y2=mat2[ID2,3]*(1-w2)+mat2[ID2,6]*w2
+    }
+    d_v[i] = sqrt((x1-x2)^2+(y1-y2)^2)
+  }
+  return(max(d_v))
+}
--- a/src/features/location_barnett/MaxHomeDist.R
+++ b/src/features/location_barnett/MaxHomeDist.R
@ -0,0 +1,10 @@
+MaxHomeDist <-
+function(mat,homex,homey){
+  IDmv=which(mat[,1]<=2)
+  if(length(IDmv)==0){return(NA)}
+  dfhome=rep(NA,length(IDmv))
+  for(i in 1:length(IDmv)){
+    dfhome[i]=sqrt((mat[IDmv[i],2]-homex)^2+(mat[IDmv[i],3]-homey)^2)
+  }
+  return(max(dfhome))
+}
--- a/src/features/location_barnett/MaxRadius.R
+++ b/src/features/location_barnett/MaxRadius.R
@ -0,0 +1,5 @@
+MaxRadius <-
+function(mat){
+  cent=colMeans(mat,na.rm=TRUE)
+  return(max(apply(mat,1,function(x) sqrt((x[1]-cent[1])^2+(x[2]-cent[2])^2)),na.rm=TRUE))
+}
--- a/src/features/location_barnett/MinsMissing.R
+++ b/src/features/location_barnett/MinsMissing.R
@ -0,0 +1,10 @@
+MinsMissing <-
+function(mat){
+  tot=0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==4){
+      tot = tot+mat[i,7]-mat[i,4]
+    }
+  }
+  return(tot/60)
+}
--- a/src/features/location_barnett/MobilityFeatures.R
+++ b/src/features/location_barnett/MobilityFeatures.R
@ -0,0 +1,56 @@
+MobilityFeatures <-
+function(locations_df,
+                            ACCURACY_LIM=51, ### meters GPS accuracy
+                            ITRVL=10, ### seconds (data concatenation)
+                            nreps=1, ### simulate missing data numer of times
+                            tz="", ### time zone of data, defaults to current time zone
+                            CENTERRAD=200, ### meters radius from significant locations considered
+                            wtype="GLR",
+                            spread_pars=c(10,1),
+                            minpausedur=300,
+                            minpausedist=60,
+                            rad_fp=NULL,
+                            wid_fp=NULL
+){
+  mobmatmiss=GPS2MobMat(locations_df,itrvl=ITRVL,accuracylim=ACCURACY_LIM,r=rad_fp,w=wid_fp)
+  mobmat = GuessPause(mobmatmiss,mindur=minpausedur,r=minpausedist)
+  obj=InitializeParams(mobmat)
+  qOKmsg=MobmatQualityOK(mobmat,obj)
+  if(qOKmsg!=""){
+    cat(qOKmsg,"\n")
+    return(NULL)
+  }
+  lsmf = list()
+  lssigloc = list()
+  for(repnum in 1:nreps){
+    if(repnum==1){
+      cat("Sim #: 1")
+    }else if(repnum<=nreps-1){
+      cat(paste(" ",repnum,sep=""))
+    }else{
+      cat(paste(" ",nreps,"\n",sep=""))
+    }
+    out3=SimulateMobilityGaps(mobmat,obj,wtype,spread_pars)
+    IDundef=which(out3[,1]==3)
+    if(length(IDundef)>0){
+      out3=out3[-IDundef,]      
+    }
+    obj3=InitializeParams(out3)
+    out_GMFM=GetMobilityFeaturesMat(out3,obj3,mobmatmiss,tz,CENTERRAD,ITRVL)
+    lsmf[[repnum]]=out_GMFM[[1]]
+    lssigloc[[repnum]]=out_GMFM[[2]]
+  }
+  cat("\n\n")
+  if(length(lsmf)!=0){
+    featavg = lsmf[[1]]
+    if(nreps>1){
+      for(i in 2:nreps){
+        featavg=featavg+lsmf[[i]]
+      }    
+      featavg=featavg/nreps
+    }    
+  }else{
+    featavg=NULL
+  }
+  return(list('mobmat'=mobmat,'mobmatmiss'=mobmatmiss,'featsims'=lsmf,'siglocsims'=lssigloc,'featavg'=featavg))
+}
--- a/src/features/location_barnett/MobmatQualityOK.R
+++ b/src/features/location_barnett/MobmatQualityOK.R
@ -0,0 +1,14 @@
+MobmatQualityOK <-
+function(mobmat,obj){
+  msg=""
+  if(!is.matrix(mobmat)){
+    msg = "Mobmat not a matrix. Removing individual from analysis.\n"
+  }
+  if(length(obj$ID1)==0){
+    msg= "No flights in mobmat. Removing individual from analysis.\n"
+  }
+  if(length(obj$ID2)==0){
+    msg= "No pauses in mobmat. Removing individual from analysis.\n"
+  }
+  return(msg)
+}
--- a/src/features/location_barnett/ProbPause.R
+++ b/src/features/location_barnett/ProbPause.R
@ -0,0 +1,14 @@
+ProbPause <-
+function(mat){
+  tpause = 0 
+  tflight = 0
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==1){
+      tflight = tflight + mat[i,7]-mat[i,4]
+    }
+    if(mat[i,1]==2){
+      tpause = tpause + mat[i,7]-mat[i,4]
+    }
+  }
+  return(tpause/(tpause+tflight))
+}
--- a/src/features/location_barnett/ProgressBar.R
+++ b/src/features/location_barnett/ProgressBar.R
@ -0,0 +1,30 @@
+ProgressBar <-
+function (maxn, ind){
+  if(maxn<51){
+    if (ind == 1) {
+      cat("|1%--------------------50%--------------------100%|\n")
+      cat("|")
+      return()
+    }else{
+      numprint=floor(50*ind/maxn)-floor(50*(ind-1)/maxn)
+      if(numprint>0){
+        for(i in 1:numprint){
+          cat("|")
+        }
+      }
+    }
+  }else{
+    if (ind == 1) {
+      cat("|1%--------------------50%--------------------100%|\n")
+      cat("|")
+      return()
+    }
+    if (maxn == ind) {
+      cat("|\n")
+      return()
+    }
+    if (floor(50 * ind/maxn) != floor(50 * (ind - 1)/maxn)) {
+      cat("|")
+    }    
+  }
+}
--- a/src/features/location_barnett/RadiusOfGyration.R
+++ b/src/features/location_barnett/RadiusOfGyration.R
@ -0,0 +1,36 @@
+RadiusOfGyration <-
+function(mat,ITRVL){
+  mat=matrix(mat,ncol=7)
+  IDskip=which(mat[,1]==4)
+  if(length(IDskip)>0){
+    mat=matrix(mat[-IDskip,],ncol=7)
+  }
+  N=nrow(mat)
+  w_v=rep(0,N)
+  x_v=rep(0,N)
+  y_v=rep(0,N)
+  for(i in 1:N){
+    if(mat[i,1]==4){
+      next
+    } 
+    if(mat[i,1]==3){
+      x_v[i]=mat[i,2]
+      y_v[i]=mat[i,3]
+      w_v[i]=ITRVL
+    }
+    if(mat[i,1]==1){
+      x_v[i]=mean(mat[i,c(2,5)])
+      y_v[i]=mean(mat[i,c(3,6)])
+      w_v[i]=mat[i,7]-mat[i,4]
+    }
+    if(mat[i,1]==2){
+      x_v[i]=mat[i,2]
+      y_v[i]=mat[i,3]
+      w_v[i]=mat[i,7]-mat[i,4]
+    }
+  }
+  sumw_v=sum(w_v)
+  xavg=sum(w_v*x_v)/sumw_v
+  yavg=sum(w_v*y_v)/sumw_v
+  return(sqrt(sum(((x_v-xavg)^2+(y_v-yavg)^2)*w_v)/sumw_v))
+}
--- a/src/features/location_barnett/RandomBridge.R
+++ b/src/features/location_barnett/RandomBridge.R
@ -0,0 +1,101 @@
+RandomBridge <-
+function(x0,y0,x1,y1,t0,t1,fd,ft,fts,fa,fw,probp,pt,pts,pw,allts,allw,ind11,ind12,i_ind,pxs,pys,fxs,fys,allxs,allys,wtype,canpause,niter=100,spread_pars){
+  success=FALSE
+  for(i in 1:niter){
+    outmat=c()
+    curx=x0
+    cury=y0
+    curt=t0
+    tarrive=t0
+    while(TRUE){
+      ## new
+      varmult=1
+      while(TRUE){
+        if(wtype=="TL"){          
+          fw=dt(spread_pars[1]*(fts-curt)/(varmult*(t1-t0)),df=spread_pars[2])
+          pw=dt(spread_pars[1]*(pts-curt)/(varmult*(t1-t0)),df=spread_pars[2])
+          allw=dt(spread_pars[1]*(allts-curt)/(varmult*(t1-t0)),df=spread_pars[2])          
+        }else if(wtype=="GL"){
+          fw=dt(spread_pars[1]*sqrt((fxs-curx)^2+(fys-cury)^2)/(50*varmult),df=spread_pars[2])
+          pw=dt(spread_pars[1]*sqrt((pxs-curx)^2+(pys-cury)^2)/(50*varmult),df=spread_pars[2])
+          allw=dt(spread_pars[1]*sqrt((allxs-curx)^2+(allys-cury)^2)/(50*varmult),df=spread_pars[2])
+        }else if(wtype=="GLR"){ 
+          fw=dt(spread_pars[1]*sqrt((fxs-curx)^2+(fys-cury)^2)/(50*varmult),df=spread_pars[2])*dt(spread_pars[1]*apply(cbind(abs((fts-curt))%%(60*60*24),(60*60*24)-abs((fts-curt))%%(60*60*24)),1,min)/(varmult*(t1-t0)),df=spread_pars[2])
+          pw=dt(spread_pars[1]*sqrt((pxs-curx)^2+(pys-cury)^2)/(50*varmult),df=spread_pars[2])*dt(spread_pars[1]*apply(cbind(abs((pts-curt))%%(60*60*24),(60*60*24)-abs((pts-curt))%%(60*60*24)),1,min)/(varmult*(t1-t0)),df=spread_pars[2])
+          allw=dt(spread_pars[1]*sqrt((allxs-curx)^2+(allys-cury)^2)/(50*varmult),df=spread_pars[2])*dt(spread_pars[1]*apply(cbind(abs((allts-curt))%%(60*60*24),(60*60*24)-abs((allts-curt))%%(60*60*24)),1,min)/(varmult*(t1-t0)),df=spread_pars[2])
+        }
+        if(length(pts)>0 && length(fts)>0 && sum(fw)>0 && sum(pw)>0){break}
+        if(length(pts)==0 && length(fts)>0 && sum(fw)>0){break}
+        if(length(fts)==0 && length(pts)>0 && sum(pw)>0){break}
+        varmult=varmult*2
+      }
+      s11=sum(allw[ind11],na.rm=T)
+      s12=sum(allw[ind12],na.rm=T)
+      if(s11+s12==0){phatcur=probp}else{phatcur=s12/(s11+s12)}
+      probp=phatcur      
+      ## end
+      
+      if(canpause && runif(1)<probp){ #pause happens
+        canpause=FALSE
+        p_samp=sample(pt,1,prob=pw)
+        if(curt+p_samp<t1){
+          nextline = c(2,curx,cury,curt,NA,NA,curt+p_samp)
+          curt=curt+p_samp
+          outmat=rbind(outmat,nextline)
+        }else{
+          break
+        }
+      }else{ #flight happens
+        canpause=TRUE
+        IDsamp = sample(1:length(fa),1,prob=fw)
+        a_samp = fa[IDsamp]
+        d_samp = fd[IDsamp]
+        t_samp = ft[IDsamp]
+        if(curt+t_samp<t1){
+          nexx=curx+cos(a_samp)*d_samp
+          nexy=cury+sin(a_samp)*d_samp
+          if(is.nan(nexx)){break}
+          nextline = c(1,curx,cury,curt,nexx,nexy,curt+t_samp)      
+          curt=curt+t_samp
+          curx=nexx
+          cury=nexy
+          outmat=rbind(outmat,nextline)
+          tarrive=curt
+        }else{
+          break
+        }
+      }
+    }    
+    if(tarrive>t0){
+      success=TRUE
+      break
+    }
+  }
+  if(!success){
+    return(c(1,x0,y0,t0,x1,y1,t1))
+    return(NULL)
+  }else{
+    curx=x0
+    cury=y0
+    for(i in 1:nrow(outmat)){
+      if(outmat[i,1]==1){
+        outmat[i,2]=curx
+        outmat[i,3]=cury
+        curt=outmat[i,7]
+        w=(tarrive-curt)/(tarrive-t0)
+        outmat[i,5]=outmat[i,5]*w+x1*(1-w)
+        outmat[i,6]=outmat[i,6]*w+y1*(1-w)
+        curx=outmat[i,5]
+        cury=outmat[i,6]
+      }else{
+        curt=outmat[i,4]
+        outmat[i,2]=curx
+        outmat[i,3]=cury
+      }
+    }
+    outmat[nrow(outmat),7]=t1
+    rownames(outmat)=NULL
+    colnames(outmat)=c("Code","x0","y0","t0","x1","y1","t1")
+    return(outmat)
+  }
+}
--- a/src/features/location_barnett/SigLocEntropy.R
+++ b/src/features/location_barnett/SigLocEntropy.R
@ -0,0 +1,22 @@
+SigLocEntropy <-
+function(mat,slout,CENTERRAD){
+  tp = rep(0,nrow(slout))
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]==2){
+      for(j in 1:nrow(slout)){
+        if(sqrt((slout[j,1]-mat[i,2])^2+(slout[j,2]-mat[i,3])^2)<CENTERRAD){
+          tp[j] = tp[j] + mat[i,7]-mat[i,4]
+        }
+      } 
+    }
+  }
+  tot=0
+  if(sum(tp)==0){return(0)}
+  for(i in 1:nrow(slout)){
+    p=tp[i]/sum(tp)
+    if(p>0){
+      tot=tot-p*log(p)
+    }
+  }
+  return(tot)
+}
--- a/src/features/location_barnett/SigLocs.R
+++ b/src/features/location_barnett/SigLocs.R
@ -0,0 +1,68 @@
+SigLocs <-
+function(mobmat,obj,CENTERRAD=125,MINPAUSETIME=600,tz=""){
+  if(length(obj$ID2)==0){
+    warning("No pauses in mobmat within function SigLocs!")
+    return(NULL)
+  }else if(length(obj$ID2)==1){
+    outmat=data.frame('x'=mobmat[obj$ID2[1],2],'y'=mobmat[obj$ID2[1],3],'timepresent'=c(0),'home'=c(1))
+    nrowfc=1
+  }else{  
+    ptred=floor(obj$pt/MINPAUSETIME)
+    if(length(which(ptred>0))<2){
+      warning("No pauses long enough in mobmat within function SigLocs!")
+      return(NULL)
+    }
+    pmat=c()
+    for(i in 1:length(obj$ID2)){
+      if(ptred[i]>0){
+        pmat=rbind(pmat,matrix(rep(mobmat[obj$ID2[i],2:3],ptred[i]),ncol=2,byrow=T))
+      }
+    }  
+    kmeansk_v=2:length(which(ptred>0))
+    lsfit = list()
+    for(i in 1:length(kmeansk_v)){
+      kmeansk = kmeansk_v[i]
+      fit = kmeans(pmat,centers=kmeansk)
+      lsfit[[i]]=fit
+      if(min(dist(fit$centers))<CENTERRAD*2 || i==length(kmeansk_v)){
+        if(i>1){
+          kmeansk=kmeansk_v[i-1]
+          fit = lsfit[[i-1]]      
+        }
+        break
+      }
+    }
+    nrowfc = nrow(fit$centers)
+    outmat=data.frame('x'=fit$centers[,1],'y'=fit$centers[,2],'timepresent'=rep(0,nrow(fit$centers)),'home'=rep(0,nrow(fit$centers)))
+  }
+  #Determine time spent at these significant locations
+  for(i in 1:length(obj$ID2)){
+    for(j in 1:nrowfc){
+      if(sqrt((mobmat[obj$ID2[i],2]-outmat$x[j])^2+(mobmat[obj$ID2[i],3]-outmat$y[j])^2)<CENTERRAD){
+        outmat[j,3]=outmat[j,3]+obj$pt[i]
+      }
+    }
+  }
+  #Determine which is home (where is the night spent)
+  for(i in 1:length(obj$ID2)){
+    xx=as.POSIXct((mobmat[obj$ID2[i],7]+mobmat[obj$ID2[i],4])/2,tz=tz,origin="1970-01-01")
+    hourofday = as.numeric(strsplit(strsplit(as.character(xx),":")[[1]][1]," ")[[1]][2])
+    if(hourofday>=21 || hourofday<6){
+      for(j in 1:nrowfc){
+        if(sqrt((mobmat[obj$ID2[i],2]-outmat$x[j])^2+(mobmat[obj$ID2[i],3]-outmat$y[j])^2)<CENTERRAD){
+          outmat[j,4]=outmat[j,4]+obj$pt[i]
+        }
+      }      
+    }
+  }
+  IDmax =order(outmat[,4],decreasing=T)[1] 
+  outmat[,4]=rep(0,nrow(outmat))
+  outmat[IDmax,4]=1
+  outmat=outmat[order(outmat[,3],decreasing=T),]
+  IDrm=which(outmat[,3]==0)
+  if(length(IDrm)>0){
+    outmat=outmat[-IDrm,]
+  }
+  rownames(outmat)=NULL
+  return(outmat)
+}
--- a/src/features/location_barnett/SigLocsVisited.R
+++ b/src/features/location_barnett/SigLocsVisited.R
@ -0,0 +1,14 @@
+SigLocsVisited <-
+function(mat,slout,CENTERRAD){
+  places_visited = rep(0,nrow(slout))
+  for(i in 1:nrow(mat)){
+    if(mat[i,1]<=3){
+      for(j in 1:nrow(slout)){
+        if(sqrt((slout[j,1]-mat[i,2])^2 + (slout[j,2]-mat[i,3])^2)<CENTERRAD){
+          places_visited[j]=1
+        }
+      }
+    }
+  }
+  return(sum(places_visited))
+}
--- a/src/features/location_barnett/SimulateMobilityGaps.R
+++ b/src/features/location_barnett/SimulateMobilityGaps.R
@ -0,0 +1,41 @@
+SimulateMobilityGaps <-
+function(suboutmat,obj,wtype="TL",spread_pars=c(1,10)){
+  ind11=obj$ind11;ind12=obj$ind12;fd=obj$fd;ft=obj$ft;fts=obj$fts;fa=obj$fa;pt=obj$pt;pts=obj$pts;allts=obj$allts;phatall=obj$phatall;fxs=obj$fxs;fys=obj$fys;pxs=obj$pxs;pys=obj$pys;allxs=obj$allxs;allys=obj$allys
+  if(nrow(suboutmat)==0){
+    return(suboutmat)
+  }
+  foutmat=c()
+  for(i in 1:nrow(suboutmat)){
+    if(suboutmat[i,1]==1){
+      curx=suboutmat[i,5]
+      cury=suboutmat[i,6]
+      foutmat=rbind(foutmat,suboutmat[i,])
+    }else  if(suboutmat[i,1]<=3){
+      curx=suboutmat[i,2] 
+      cury=suboutmat[i,3]
+      foutmat=rbind(foutmat,suboutmat[i,])
+    }
+    if(suboutmat[i,1]==4 && i>1 && i<nrow(suboutmat)){
+      varmult=1
+      while(TRUE){
+        fw=dnorm((fts-mean(c(suboutmat[i,4],suboutmat[i,7])))/(varmult*(suboutmat[i,7]-suboutmat[i,4])))
+        pw=dnorm((pts-mean(c(suboutmat[i,4],suboutmat[i,7])))/(varmult*(suboutmat[i,7]-suboutmat[i,4])))
+        allw=dnorm((allts-mean(c(suboutmat[i,4],suboutmat[i,7])))/(varmult*(suboutmat[i,7]-suboutmat[i,4])))
+        if(length(pts)>0 && length(fts)>0 && sum(fw)>0 && sum(pw)>0){break}
+        if(length(pts)==0 && length(fts)>0 && sum(fw)>0){break}
+        if(length(fts)==0 && length(pts)>0 && sum(pw)>0){break}
+        varmult=varmult*2
+      }
+      s11=sum(allw[ind11],na.rm=T)
+      s12=sum(allw[ind12],na.rm=T)
+      if(s11+s12==0){phatcur=phatall}else{phatcur=s12/(s11+s12)}
+      if(wtype=="LI"){
+        foutmat=rbind(foutmat,c(1,curx,cury,suboutmat[i,4],suboutmat[i+1,2],suboutmat[i+1,3],suboutmat[i,7]))
+      }else{
+        rbout=matrix(RandomBridge(x0=curx,y0=cury,x1=suboutmat[i+1,2],y1=suboutmat[i+1,3],t0=suboutmat[i,4],t1=suboutmat[i,7],fd=fd,ft=ft,fts=fts,fa=fa,fw=fw,probp=phatcur,pt=pt,pts=pts,pw=pw,allts=allts,allw=allw,ind11=ind11,ind12=ind12,i_ind=i,pxs=pxs,pys=pys,fxs=fxs,fys=fys,allxs=allxs,allys=allys,wtype=wtype,canpause=suboutmat[i-1,1]==1,niter=100,spread_pars=spread_pars),ncol=7)
+        foutmat=rbind(foutmat,rbout)        
+      }
+    }
+  }  
+  return(foutmat)
+}
--- a/src/features/location_barnett/StdFlightDur.R
+++ b/src/features/location_barnett/StdFlightDur.R
@ -0,0 +1,11 @@
+StdFlightDur <-
+function(mat){
+  ID1=which(mat[,1]==1)
+  if(length(ID1)==0){return(0)}
+  try1=try(sd(as.numeric(mat[ID1,7]-mat[ID1,4])),silent=TRUE)
+  if(class(try1) == "try-error" || is.na(try1)){
+    return(0)
+  }else{
+    return(try1)
+  }
+}
--- a/src/features/location_barnett/StdFlightLen.R
+++ b/src/features/location_barnett/StdFlightLen.R
@ -0,0 +1,11 @@
+StdFlightLen <-
+function(mat){
+  ID1=which(mat[,1]==1)
+  if(length(ID1)<=1){return(0)}
+  try1=try(sd(as.numeric(sqrt((mat[ID1,6]-mat[ID1,3])^2+(mat[ID1,5]-mat[ID1,2])^2))),silent=TRUE)
+  if(class(try1) == "try-error" || is.na(try1)){
+    return(0)
+  }else{
+    return(try1)
+  }
+}
--- a/src/features/location_barnett/WriteSurveyAnswers2File.R
+++ b/src/features/location_barnett/WriteSurveyAnswers2File.R
@ -0,0 +1,35 @@
+WriteSurveyAnswers2File <-
+function(fildir,survey_id,SID){
+  try1=try(setwd(fildir),silent=TRUE)
+  if(class(try1) == "try-error"){
+    warning(paste(fildir,"does not exist."))
+    return(NULL)
+  }
+  filelist <- list.files(pattern = "\\.csv$")
+  if(length(filelist)==0){return(NULL)}
+  date_v=substr(filelist,1,10)
+  ## keep only the last survey of each day
+  IDkeep=length(date_v)
+  curdate = date_v[length(date_v)]
+  for(i in length(date_v):1){
+    nexdate=date_v[i]
+    if(curdate!=nexdate){
+      IDkeep=c(IDkeep,i)
+      curdate=nexdate
+    }
+  }
+  IDkeep=rev(IDkeep)
+  
+  outmat=c()
+  for(i in IDkeep){
+    x=read.csv(filelist[i],fileEncoding="UTF-8")
+    outmat=rbind(outmat,c(date_v[i],x$answer))
+  }
+  try1=try(colnames(outmat)<-c("Date",paste(as.character(x$question.text)," (",as.character(x$question.answer.options),")",sep="")),silent=TRUE)
+  if(class(try1) == "try-error"){
+    warning(paste("Survey non-constant over time for ID:",SID))
+    return(NULL)
+  }  
+  write.table(outmat,paste("SurveyAnswers_",survey_id,"_",SID,".txt",sep=""),quote=F,col.names=T,row.names=F,sep="\t")
+  return("success")
+}
--- a/src/features/location_barnett/plot.flights.R
+++ b/src/features/location_barnett/plot.flights.R
@ -0,0 +1,96 @@
+plot.flights <-
+function(mat,xrang=NULL,yrang=NULL,diminch=6,add2plot=FALSE,addlegend=TRUE,outfile=NULL,title=NULL){
+  #col24hour_v=c("#253494","#2c7fb8","#41b6c4","#7fcdbb","#c7e9b4","#ffffcc","#fed976","#feb24c","#fd8d3c","#fc4e2a","#e31a1c","#b10026","#7a0177","#ae017e","#dd3497","#f768a1","#fa9fb5","#fcc5c0","#edf8fb","#ccece6","#99d8c9","#66c2a4","#2ca25f","#006d2c")
+  col24hour_v=c(c("#08306b","#08519c","#2171b5","#4292c6","#6baed6","#9ecae1","#fcbba1","#fc9272","#fb6a4a","#ef3b2c","#cb181d","#99000d"),rev(c("#08306b","#08519c","#2171b5","#4292c6","#6baed6","#9ecae1","#fcbba1","#fc9272","#fb6a4a","#ef3b2c","#cb181d","#99000d")))  
+  if(nrow(mat)==0){
+    return(NULL)
+  }
+  if(add2plot){outfile=NULL}
+  write2file=FALSE
+  if(!is.null(outfile)){
+    write2file=TRUE
+  }
+  if(write2file){
+    pdf(outfile,width=diminch*11/10,height=diminch)
+  }
+  if(is.null(xrang)){
+    xrang=plotlimits(mat)$xrang
+  }
+  if(is.null(yrang)){
+    yrang=plotlimits(mat)$yrang
+  }
+  if(xrang[2]-xrang[1]>yrang[2]-yrang[1]){
+    dif=((xrang[2]-xrang[1])-(yrang[2]-yrang[1]))
+    yrang[2] = yrang[2]+dif/2
+    yrang[1] = yrang[1]-dif/2
+  }else{
+    dif=((yrang[2]-yrang[1])-(xrang[2]-xrang[1]))
+    xrang[2] = xrang[2]+dif/2
+    xrang[1] = xrang[1]-dif/2    
+  }
+  xrang[1]=xrang[1]-(xrang[2]-xrang[1])/10
+  if(!add2plot){
+    if(!is.null(title)){
+      par(mai=c(0,0,.4,0))      
+      plot(NA,xlim=xrang
+           ,ylim=yrang
+           ,xaxt="n"
+           ,yaxt="n"
+           ,xlab=""
+           ,ylab=""
+           ,bty="n"
+           ,main=title)  
+    }else{
+      par(mai=c(0,0,0,0))      
+      plot(NA,xlim=xrang
+           ,ylim=yrang
+           ,xaxt="n"
+           ,yaxt="n"
+           ,xlab=""
+           ,ylab=""
+           ,bty="n"
+           ,main="")        
+    }
+    xleg1=xrang[1]      
+    xleg2=xleg1+(xrang[2]-xrang[1])/30
+    yincr=(yrang[2]-yrang[1])/40
+    legtext=c(" 6AM"," 12PM"," 6PM"," 12AM")
+    if(addlegend){
+      for(i in 1:24){
+        polygon(c(xleg1,xleg1,xleg2,xleg2),c(yrang[1]+(i-1)*yincr,yrang[1]+i*yincr,yrang[1]+i*yincr,yrang[1]+(i-1)*yincr),col=col24hour_v[i])
+        if(i%%6==0){
+          text(xleg2,yrang[1]+i*yincr,legtext[floor(i/6)],adj=0,cex=.5)        
+        }
+      }
+      points(xleg1,yrang[1]+26*yincr,cex=2,pch=16)
+      text(xleg2,yrang[1]+26*yincr,">4 hrs",adj=0,cex=.5)
+      points(xleg1,yrang[1]+28*yincr,cex=1,pch=16)
+      text(xleg2,yrang[1]+28*yincr,"1 hr",adj=0,cex=.5)
+      points(xleg1,yrang[1]+30*yincr,cex=.5,pch=16)
+      text(xleg2,yrang[1]+30*yincr,"<30 mins",adj=0,cex=.5)
+      #text(xleg1,yrang[1]+32.3*yincr,"Pause\nDuration",adj=0,cex=.5)
+      legdist=10^floor(log10((yrang[2]-yrang[1])/5))
+      lines(c(xrang[1],xrang[1]),c(yrang[2],yrang[2]-legdist))
+      lines(c(xrang[1]-(xrang[2]-xrang[1])/120,xrang[1]+(xrang[2]-xrang[1])/120),c(yrang[2],yrang[2]))
+      lines(c(xrang[1]-(xrang[2]-xrang[1])/120,xrang[1]+(xrang[2]-xrang[1])/120),c(yrang[2]-legdist,yrang[2]-legdist))
+      if(log10(legdist)<3){
+        text(xrang[1]+(xrang[2]-xrang[1])/50,yrang[2]-legdist/2,paste(as.character(legdist),"m"),cex=.5,srt=270,adj=c(.5,0))      
+      }else{
+        text(xrang[1]+(xrang[2]-xrang[1])/50,yrang[2]-legdist/2,paste(as.character(legdist/1000),"km"),cex=.5,srt=270,adj=c(.5,0))      
+      }      
+    }
+  }
+  for(i in 1:nrow(mat)){
+    hour=as.numeric(strsplit(strsplit(as.character(as.POSIXct(mean(c(mat[i,4],mat[i,7]),na.rm=T),origin='1970-01-01'))," ")[[1]][2],":")[[1]][1])
+    if(mat[i,1]==1){
+      lines(c(mat[i,2],mat[i,5]),c(mat[i,3],mat[i,6]),col=col24hour_v[hour+1])
+    }
+    if(mat[i,1]==2){
+      pwidth=max(.5,min(sqrt(2*(mat[i,7]-mat[i,4])/7200),2))
+      points(mat[i,2],mat[i,3],pch=19,col=paste(col24hour_v[hour+1],"CC",sep=""),cex=pwidth)
+    }
+  }  
+  if(write2file){
+    dev.off()
+  }
+}
--- a/src/features/location_barnett/plotlimits.R
+++ b/src/features/location_barnett/plotlimits.R
@ -0,0 +1,14 @@
+plotlimits <-
+function(mat,defaultdist=100){
+  xrang=range(c(mat[which(mat[,1]<=2),2],mat[which(mat[,1]<=1),5]))
+  yrang=range(c(mat[which(mat[,1]<=2),3],mat[which(mat[,1]<=1),6]))
+  if(xrang[2]==xrang[1]){
+    xrang[2]=xrang[2]+defaultdist/2
+    xrang[1]=xrang[1]-defaultdist/2
+  }
+  if(yrang[2]==yrang[1]){
+    yrang[2]=yrang[2]+defaultdist/2
+    yrang[1]=yrang[1]-defaultdist/2
+  }
+  return(list(xrang=xrang,yrang=yrang))
+}
--- a/src/features/location_barnett_metrics.R
+++ b/src/features/location_barnett_metrics.R
@ -0,0 +1,22 @@
+library(dplyr)
+
+# Load Ian Barnett's code. Taken from https://scholar.harvard.edu/ibarnett/software/gpsmobility
+file.sources = list.files(c("src/features/location_barnett"), pattern="*.R$", full.names=TRUE, ignore.case=TRUE)
+sapply(file.sources,source,.GlobalEnv)
+
+accuracy_limit <- snakemake@params[["accuracy_limit"]]
+timezone <- snakemake@params[["timezone"]]
+
+location <- read.csv(snakemake@input[[1]], stringsAsFactors = F) %>%
+  select(timestamp, latitude = double_latitude, longitude = double_longitude, altitude = double_altitude, accuracy)
+
+if (nrow(location) > 0){
+    features <- MobilityFeatures(location, ACCURACY_LIM = accuracy_limit, tz = timezone)
+
+    # Copy index (dates) as a column 
+    outmatrix = cbind(rownames(features$featavg), features$featavg)
+    colnames(outmatrix)=c("local_date",tolower(colnames(features$featavg)))
+    write.csv(outmatrix,snakemake@output[[1]], row.names = F)
+} else {
+    write.csv(data.frame(),snakemake@output[[1]])
+}