From 90eaccaccc4ec8feb3c529168ebb0587b13c0632 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 28 Nov 2023 16:31:41 +0100
Subject: [PATCH 01/14] GIS file loading now handles missing table file #1 and
 simulation hbGPS output is created to aid testing #1

---
 R/hbGIS.R             | 95 +++++++++++++++++++++++++++++++++++--------
 inst/dev_code_hbGIS.R | 21 +++++++---
 2 files changed, 92 insertions(+), 24 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 1a8b064..ef5c561 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -37,6 +37,15 @@ hbGIS <- function(gisdir = "",
   Nlocations = length(locationNames)
   loca = vector("list", Nlocations)
   names(loca) = locationNames
+  # Initialise loca object which is a list that for each location
+  # has a list with four items:
+  # 1 - location shape
+  # 2 - location neighbourhood shape
+  # 3 - shape file to read 1
+  # 4 - shape file to read 2
+  # Sometimes neighbourhood is referred to as buffer
+  # For some location types such as parks some of these are missing,
+  # which for now is ok, those lists will be left empty.
   for (i in 1:Nlocations) {
     loca[[i]] = vector("list", 4)
     names(loca[[i]]) =  c(locationNames[i], paste0(locationNames[i], "_nbh"), 
@@ -48,6 +57,7 @@ hbGIS <- function(gisdir = "",
   find_file = function(path, namelowercase) {
     allcsvfiles = dir(path, recursive = TRUE, full.names = TRUE)
     file_of_interest = allcsvfiles[which(tolower(basename(allcsvfiles)) == namelowercase)]
+    if (length(file_of_interest) == 0) file_of_interest = NULL
     return(file_of_interest)
   }
   # Find shape files
@@ -55,33 +65,37 @@ hbGIS <- function(gisdir = "",
     findfile3 = find_file(path = gisdir, namelowercase = paste0(locationNames[jj], "_table.shp"))
     if (!is.null(findfile3)) {
       loca[[jj]][3] = findfile3
-    } else {
-      stop(paste0("unable to find ", findfile3))
+      loca[[jj]][[1]] = sf::read_sf(loca[[jj]][3]) #e.g. school or home
     }
     findfile4 = find_file(path = gisdir, namelowercase = paste0("loc_", locationNames[jj], "buffers.shp"))
-    if (!is.null(findfile3)) {
+    if (!is.null(findfile4)) {
       loca[[jj]][4] = findfile4
     } else {
-      stop(paste0("unable to find ", findfile4))
+      # If it is not a buffer file then it is space file, eg. public park
+      findfile4 = find_file(path = gisdir, namelowercase = paste0("loc_", locationNames[jj], ".shp"))
+      if (!is.null(findfile4)) {
+        loca[[jj]][4] = findfile4
+      }
+    }
+    # Only load shape file if it exists
+    if (!is.null(loca[[i]][4][[1]])) {
+      loca[[jj]][[2]] = sf::read_sf(loca[[jj]][4]) #e.g. school_nbh, home_nbh, or park
     }
-    loca[[jj]][[1]] = sf::read_sf(loca[[jj]][3]) #home_nbh
-    loca[[jj]][[2]] = sf::read_sf(loca[[jj]][4]) #school_nbh
   }
+  
   # Force id numbers to be character(
   locationNames = names(loca)
   for (i in 1:length(loca)) {
-    if (locationNames[i] != "home") {
-      loc_id = paste0(groupinglocation, "_id")
-    } else  if (locationNames[i] == "home") { # assumption that home is always the identifier for individuals
-      loc_id = "identifier"
-    } 
-    for (j in 1:2) {
-      loca[[i]][j][[1]][[loc_id]] = as.character(loca[[i]][j][[1]][[loc_id]])
+    if (!is.null(loca[[i]][3][[1]])) { # only consider locations with data
+      for (j in 1:2) {
+        loc_id = grep(pattern = "ID|identifier|_id", x = colnames(loca[[i]][j][[1]]))
+        if (length(loc_id) > 0) {
+          loca[[i]][j][[1]][[loc_id]] = as.character(loca[[i]][j][[1]][[loc_id]])
+        }
+      }
     }
   }
-  
-  # >>> TO DO: Check that public locations that are not linked to an ID can be loaded in code above <<<
-  
+
   #===============================================
   # hbGPS output (PALMS output)
   #===============================================
@@ -95,6 +109,47 @@ hbGIS <- function(gisdir = "",
   palms_country_files <- list.files(path = palmsdir, pattern = "*.csv", full.names = TRUE)
   # skip the combined file that palms generates
   palms_country_files = grep(pattern = "combined.csv", x = palms_country_files, invert = TRUE, value = TRUE)
+  if (length(palms_country_files) == 0) {
+    # Simulate hbGPS output (only for code developement purposes)
+    Nmin = 500
+    now = Sys.time()
+    dateTime = seq(now, now + ((Nmin - 1) * 60), by = 60)
+    example_object = loca[[1]][[2]][1,]
+    point_in_object = st_sample(x = example_object, size = 1)
+    xy = sf::st_coordinates(x = point_in_object)
+    
+    # latitude is for most of the time 1 lat degree away from location
+    # but for 30 minutes inside the location surround by 5 minute trips before and after
+    trip = seq(xy[1] - 1, xy[1] - 0.2, by = 0.2)
+    away = rep(xy[1] - 1, (Nmin/2) - 20)
+    lat = c(away, trip, rep(xy[1], 30), rev(trip), away)
+    lon = rep(xy[2], Nmin) # lon stays the same the entire time
+    tripNumber = c(rep(0, length(away)), rep(1, 5), rep(0, 30), rep(2, 5), rep(0, length(away)))
+    sedentaryBoutNumber = c(rep(1, length(away)), rep(0, 5), rep(2, 30), rep(0, 5), rep(3, length(away)))
+    tripType = rep(0, Nmin)
+    tripMOT = rep(0, Nmin)
+    tripType[which(diff(tripNumber) > 0)] = 1
+    tripType[which(diff(tripNumber) < 0)] = 4
+    tripMOT[which(tripNumber != 0)] = 3
+    hbGPSout = data.frame(identifier = "sim1",
+                          dateTime	= dateTime,
+                          dow = rep(5, Nmin),
+                          lat	= lat,
+                          lon	= lon,
+                          fixTypeCode	= rep(-1, Nmin),
+                          iov	= rep(2, Nmin), # all the time outdoor (indoor, outdoor, vehicle)
+                          tripNumber = tripNumber,
+                          tripType = tripType,
+                          tripMOT	= tripMOT,
+                          activity = rep(0, Nmin),
+                          activityIntensity = rep(0, Nmin),
+                          activityBoutNumber = rep(0, Nmin),
+                          sedentaryBoutNumber = sedentaryBoutNumber)
+    if (!dir.exists(palmsdir)) dir.create(palmsdir, recursive = TRUE)
+    palms_country_files = paste0(palmsdir, "/combined.csv")
+    write.csv(hbGPSout, file = palms_country_files, row.names = FALSE)
+  }
+
   # read and combine palms csv output files 
   csv_palms <- lapply(palms_country_files, FUN = readr::read_csv, col_types = list(
     identifier = readr::col_character(),
@@ -120,16 +175,20 @@ hbGIS <- function(gisdir = "",
   write.csv(palms_reduced_cleaned, PALMS_reduced_file)
   palms = palmsplusr::read_palms(PALMS_reduced_file, verbose = FALSE)
   palms$datetime = as.POSIXct(palms$datetime, format = "%d/%m/%Y %H:%M:%S", tz = "")
-  
+
   #===============================================
   # Load linkage file and identify which PALMS ids and home/school
   # ids are missing, but allow for publiclocations that are not linked
   # to an ID
   #===============================================
+  # >>> TO DO:
+  # >>> Allow for skipping of gislinkfile if it is missing
+  # >>> Allow for public locations that are not linked to an ID
+  
   participant_basis = read_csv(gislinkfile, show_col_types = FALSE)
   
   
-  # >>> TO DO: Allow for public locations that are not linked to an ID <<<
+  
   
   # Check for missing IDs -------------------------------------------------------------------------
   withoutMissingId = check_missing_id(participant_basis, palmsplus_folder, dataset_name, palms,
diff --git a/inst/dev_code_hbGIS.R b/inst/dev_code_hbGIS.R
index b220f4e..df4d48e 100644
--- a/inst/dev_code_hbGIS.R
+++ b/inst/dev_code_hbGIS.R
@@ -17,13 +17,22 @@ library(purrr)
 library(geosphere)
 library(lwgeom)
 
-hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/GIS",
-                 palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/hbGPSoutput",
-                 gislinkfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/Tables/participant_basis.csv",
-                 outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010",
-                 dataset_name = "NBBB2010",
-                 configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
+
+hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/loc_greenspace",
+      palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/hbGPSoutput",
+      gislinkfile = NULL,
+      outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023",
+      dataset_name = "JasperNov2023",
+      configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
 kkk
+# 
+# hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/GIS",
+#                  palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/hbGPSoutput",
+#                  gislinkfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/Tables/participant_basis.csv",
+#                  outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010",
+#                  dataset_name = "NBBB2010",
+#                  configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
+# kkk
 
 # Belgium dataset
 # hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/GIS",

From ab807e9e166937cf560db6a60d65e97e162a7dca Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Thu, 30 Nov 2023 15:23:35 +0100
Subject: [PATCH 02/14] adapting code to handle locations not linked to id

---
 R/build_days.R |  19 +++---
 R/hbGIS.R      | 156 +++++++++++++++++++++++++++++++++----------------
 2 files changed, 116 insertions(+), 59 deletions(-)

diff --git a/R/build_days.R b/R/build_days.R
index 3250f0a..49d9416 100644
--- a/R/build_days.R
+++ b/R/build_days.R
@@ -30,10 +30,10 @@
 #' @export
 # Code modified from https://thets.github.io/palmsplusr/
 build_days <- function(data = NULL, verbose = TRUE, 
-                           palmsplus_domains = NULL,
-                           palmsplus_fields = NULL,
-                           loca = NULL,
-                           participant_basis = NULL) {
+                       palmsplus_domains = NULL,
+                       palmsplus_fields = NULL,
+                       loca = NULL,
+                       participant_basis = NULL) {
   # Note:
   # home, school, home_nbh, school_nbh (or similar) need to be present, 
   # because the functions that are passed on assume that they exist
@@ -41,8 +41,10 @@ build_days <- function(data = NULL, verbose = TRUE,
   Nlocations = length(loca)
   identifier = NULL
   for (i in 1:Nlocations) {
-    txt = paste0(names(loca[[i]])[1], " = loca[[i]][[1]]")
-    eval(parse(text = txt))
+    for (j in 1:2) {
+      txt = paste0(names(loca[[i]])[j], " = loca[[i]][[j]]")
+      eval(parse(text = txt))
+    }
   }
   
   duration = datetime = name = domain_field = NULL
@@ -58,21 +60,20 @@ build_days <- function(data = NULL, verbose = TRUE,
   domain_args <- setNames("1", "total") %>% lapply(parse_expr)
   domain_args <- c(domain_args, setNames(domain_fields[[2]], domain_fields[[1]]) %>%
                      lapply(parse_expr))
-  
   data <- data %>%
     mutate(!!! domain_args) %>%
     mutate_if(is.logical, as.integer)
   
   fields <- palmsplus_fields %>% filter(domain_field == TRUE) %>% pull(name)
 
-    data <- data %>%
+  data <- data %>%
     st_set_geometry(NULL) %>%
     dplyr::select(identifier, datetime, any_of(domain_names), all_of(fields)) %>%
     mutate(duration = 1) %>%
     mutate_at(vars(-identifier,-datetime), ~ . * palms_epoch(data) / 60) %>%
     group_by(identifier, date = as.Date(datetime)) %>%
     dplyr::select(-datetime)
-
+  
   x <- list()
   for (i in domain_names) {
     x[[i]] <- data %>%
diff --git a/R/hbGIS.R b/R/hbGIS.R
index ef5c561..a9a18aa 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -61,24 +61,28 @@ hbGIS <- function(gisdir = "",
     return(file_of_interest)
   }
   # Find shape files
+  locationNames_nbh = locationNames_table = NULL
   for (jj in 1:Nlocations) {
     findfile3 = find_file(path = gisdir, namelowercase = paste0(locationNames[jj], "_table.shp"))
     if (!is.null(findfile3)) {
       loca[[jj]][3] = findfile3
       loca[[jj]][[1]] = sf::read_sf(loca[[jj]][3]) #e.g. school or home
+      locationNames_table = c(locationNames_table, locationNames[jj])
     }
     findfile4 = find_file(path = gisdir, namelowercase = paste0("loc_", locationNames[jj], "buffers.shp"))
     if (!is.null(findfile4)) {
       loca[[jj]][4] = findfile4
+      locationNames_nbh = c(locationNames_nbh, locationNames[jj])
     } else {
       # If it is not a buffer file then it is space file, eg. public park
       findfile4 = find_file(path = gisdir, namelowercase = paste0("loc_", locationNames[jj], ".shp"))
       if (!is.null(findfile4)) {
         loca[[jj]][4] = findfile4
+        locationNames_nbh = c(locationNames_nbh, locationNames[jj])
       }
     }
     # Only load shape file if it exists
-    if (!is.null(loca[[i]][4][[1]])) {
+    if (!is.null(loca[[jj]][4][[1]])) {
       loca[[jj]][[2]] = sf::read_sf(loca[[jj]][4]) #e.g. school_nbh, home_nbh, or park
     }
   }
@@ -128,7 +132,7 @@ hbGIS <- function(gisdir = "",
     sedentaryBoutNumber = c(rep(1, length(away)), rep(0, 5), rep(2, 30), rep(0, 5), rep(3, length(away)))
     tripType = rep(0, Nmin)
     tripMOT = rep(0, Nmin)
-    tripType[which(diff(tripNumber) > 0)] = 1
+    tripType[which(diff(tripNumber) > 0) + 1] = 1
     tripType[which(diff(tripNumber) < 0)] = 4
     tripMOT[which(tripNumber != 0)] = 3
     hbGPSout = data.frame(identifier = "sim1",
@@ -172,34 +176,31 @@ hbGIS <- function(gisdir = "",
   # Write to csv and read using read_palms to format the object as expected from the rest of the code
   PALMS_reduced_file = normalizePath(paste0(palmsplus_folder, "/", stringr::str_interp("PALMS_${dataset_name}_reduced.csv")))
   # if (verbose) cat(paste0("\nCheck PALMS_reduced_file: ", PALMS_reduced_file))
-  write.csv(palms_reduced_cleaned, PALMS_reduced_file)
+  write.csv(palms_reduced_cleaned, PALMS_reduced_file, row.names = FALSE)
   palms = palmsplusr::read_palms(PALMS_reduced_file, verbose = FALSE)
   palms$datetime = as.POSIXct(palms$datetime, format = "%d/%m/%Y %H:%M:%S", tz = "")
-
   #===============================================
   # Load linkage file and identify which PALMS ids and home/school
   # ids are missing, but allow for publiclocations that are not linked
   # to an ID
   #===============================================
-  # >>> TO DO:
-  # >>> Allow for skipping of gislinkfile if it is missing
-  # >>> Allow for public locations that are not linked to an ID
-  
-  participant_basis = read_csv(gislinkfile, show_col_types = FALSE)
-  
-  
-  
-  
-  # Check for missing IDs -------------------------------------------------------------------------
-  withoutMissingId = check_missing_id(participant_basis, palmsplus_folder, dataset_name, palms,
-                                      loca, groupinglocation = groupinglocation,
-                                      verbose = verbose)
-  palms = withoutMissingId$palms
-  participant_basis = withoutMissingId$participant_basis
-  loca = withoutMissingId$loca
-  write.csv(participant_basis, paste0(palmsplus_folder, "/", stringr::str_interp("participant_basis_${dataset_name}.csv"))) # store file for logging purposes only
-  if (length(participant_basis) == 0 || nrow(participant_basis) == 0) {
-    stop("\nParticipant basis file does not include references for the expected recording IDs")
+  if (length(gislinkfile) > 0) {
+    participant_basis = read_csv(gislinkfile, show_col_types = FALSE)
+    
+    
+    # Check for missing IDs -------------------------------------------------------------------------
+    withoutMissingId = check_missing_id(participant_basis, palmsplus_folder, dataset_name, palms,
+                                        loca, groupinglocation = groupinglocation,
+                                        verbose = verbose)
+    palms = withoutMissingId$palms
+    participant_basis = withoutMissingId$participant_basis
+    loca = withoutMissingId$loca
+    write.csv(participant_basis, paste0(palmsplus_folder, "/", stringr::str_interp("participant_basis_${dataset_name}.csv"))) # store file for logging purposes only
+    if (length(participant_basis) == 0 || nrow(participant_basis) == 0) {
+      stop("\nParticipant basis file does not include references for the expected recording IDs")
+    }
+  } else {
+    participant_basis = ""
   }
   
   #===============================================
@@ -234,41 +235,96 @@ hbGIS <- function(gisdir = "",
   CONF = read.csv(config, sep = ",")
   CONF$start_criteria = ""
   CONF$end_criteria = ""
-  # add standard location based fields to CONF object:
+  #=====================================================
+  # Expand CONF with standard location based fields
+  #=====================================================
+  # palmsplus_domain:
+  #-------------------
+  # ignore stored definition as we no longer use this
+  
+  CONF = CONF[which(CONF[,1] != "palmsplus_domain"), ] 
+  element1 = ifelse(length(locationNames_table) > 0, yes = paste0("!", paste0("at_", locationNames_table, collapse = " & !"), " & "), no = "")
+  CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+                             "transport",
+                            paste0(element1, "(pedestrian | bicycle | vehicle)"),
+                             TRUE, NA, "", "")
+  CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+                             "other",
+                             paste0(element1, "(!pedestrian & !bicycle & !vehicle)", # removed because theorectically possible
+                                    ifelse(test = length(locationNames_nbh) > 0, yes = " & ", no = ""),
+                                    paste0("!", paste0("at_", locationNames_nbh, "_nbh", collapse = " & !"))),
+                             TRUE, NA, "", "")
   for (i in 1:Nlocations) {
-    if (locationNames[i] == "home") {
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+    # palmsplus_domain:
+    #-------------------
+    if (locationNames[i] %in% locationNames_table) {
+      CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+                                 locationNames[i],
                                  paste0("at_", locationNames[i]), 
-                                 paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                        locationNames[i],", identifier == i), identifier)"),
-                                 NA, "", "", "")
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
-                                 paste0("at_", locationNames[i], "_nbh"), 
-                                 paste0("palms_in_polygon(datai, polygons = dplyr::filter(",
-                                        locationNames[i], "_nbh, identifier == i), identifier)"),
-                                 NA, "", "", "")
+                                 TRUE,
+                                 NA, "", "")
+    } else if (locationNames[i] %in% locationNames_nbh) {
+      # condition that only needs to be used if table element is present
+      at_table = ifelse(test = locationNames[i] %in% locationNames_table == TRUE, yes = paste0("!at_", locationNames[i], " &"), no = "")
+      CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+                                 paste0(locationNames[i], "_nbh"),
+                                 paste0(at_table, " at_", locationNames[i], "_nbh", 
+                                        " & (!vehicle)"), # removed !pedestrian & !bicycle &  because unclear why these are not possible in a neighbourhood, e.g. park
+                                 TRUE,
+                                 NA, "", "")
+    }
+    # palmsplus_field:
+    #-------------------
+    if (!is.null(loca[[i]][[1]])) {
+      # only do this if there is table data (meaning that location is linked to participant basis file)
+      if (locationNames[i] == "home") {
+        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+                                   paste0("at_", locationNames[i]), 
+                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                                          locationNames[i],", identifier == i), identifier)"),
+                                   NA, "", "", "")
+        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+                                   paste0("at_", locationNames[i], "_nbh"), 
+                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(",
+                                          locationNames[i], "_nbh, identifier == i), identifier)"),
+                                   NA, "", "", "")
+      } else {
+        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+                                   paste0("at_", locationNames[i]), 
+                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                                          locationNames[i],",", locationNames[i],
+                                          "_id == participant_basis %>% filter(identifier == i) %>% pull(",
+                                          locationNames[i], "_id)))"),
+                                   NA, "", "", "")
+        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+                                   paste0("at_", locationNames[i], "_nbh"), 
+                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                                          locationNames[i], "_nbh,", locationNames[i],
+                                          "_id == participant_basis %>% filter(identifier == i) %>% pull(",
+                                          locationNames[i], "_id)))"),
+                                   NA, "", "", "")
+      }
     } else {
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
-                                 paste0("at_", locationNames[i]), 
-                                 paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                        locationNames[i],",", locationNames[i],
-                                        "_id == participant_basis %>% filter(identifier == i) %>% pull(",
-                                        locationNames[i], "_id)))"),
-                                 NA, "", "", "")
+      # palmsplus_domain:
+      #-------------------
+      # locations not in linkagefile
+      # Note palms_in_polygon allows for aggregating polygons based by variable
       CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
                                  paste0("at_", locationNames[i], "_nbh"), 
-                                 paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                        locationNames[i], "_nbh,", locationNames[i],
-                                        "_id == participant_basis %>% filter(identifier == i) %>% pull(",
-                                        locationNames[i], "_id)))"),
+                                 paste0("suppressMessages(any(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
                                  NA, "", "", "")
     }
+    reference_location = ifelse("home" %in% locationNames, yes = "home", no = locationNames[1])
     for (j in 1:Nlocations) {
+      #add nbh if table is missing
+      element2 = ifelse(test = is.null(loca[[j]][[1]]), yes = "_nbh", no = "")
+      # trajectory_location:
+      #-------------------
       CONF[nrow(CONF) + 1, ] = c("trajectory_location",
-                                 paste0(locationNames[i], "_", locationNames[i]),
-                                 paste0("at_", locationNames[i]), NA, "at_home",
-                                 paste0("at_", locationNames[i]),
-                                 paste0("at_", locationNames[j]))
+                                 paste0(locationNames[i], element2, "_", locationNames[i], element2),
+                                 paste0("at_", locationNames[i]), NA, paste0("at_", reference_location, element2),
+                                 paste0("at_", locationNames[i], element2),
+                                 paste0("at_", locationNames[j], element2))
     }
     CONF = CONF[!duplicated(CONF),]
   }
@@ -310,7 +366,7 @@ hbGIS <- function(gisdir = "",
   
   Nlocation_objects = NULL
   for (i in 1:Nlocations) {
-    Nlocation_objects = c(Nlocation_objects, length(loca[[i]][[1]]), length(loca[[i]][[2]]))
+    Nlocation_objects = c(Nlocation_objects, length(loca[[i]][[2]])) # at least a nbh object is expected #length(loca[[i]][[1]]), 
   }
   if (verbose) cat("\n<<< building palmsplus...\n")
   if (length(palms) > 0 & length(palmsplus_fields) &

From a6f130241b437748313321a4425a0e0034aac8a7 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Thu, 30 Nov 2023 15:26:58 +0100
Subject: [PATCH 03/14] tidying up syntax

---
 R/hbGIS.R | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index a9a18aa..4ee5269 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -27,6 +27,7 @@ hbGIS <- function(gisdir = "",
   publiclocation = "park"
   groupinglocation = "school"
   lon = identifier = palms = NULL # . = was also included, but probably wrong
+  
   #===============================================
   # GIS files
   #===============================================
@@ -179,6 +180,7 @@ hbGIS <- function(gisdir = "",
   write.csv(palms_reduced_cleaned, PALMS_reduced_file, row.names = FALSE)
   palms = palmsplusr::read_palms(PALMS_reduced_file, verbose = FALSE)
   palms$datetime = as.POSIXct(palms$datetime, format = "%d/%m/%Y %H:%M:%S", tz = "")
+  
   #===============================================
   # Load linkage file and identify which PALMS ids and home/school
   # ids are missing, but allow for publiclocations that are not linked
@@ -228,9 +230,6 @@ hbGIS <- function(gisdir = "",
     config <- system.file("testfiles_hbGIS/config_hbGIS.csv", package = "hbGIS")[1]
   }
   
-  
-  # >>> TO DO: Add fields for public places <<<
-  
   # adding fields
   CONF = read.csv(config, sep = ",")
   CONF$start_criteria = ""
@@ -254,6 +253,7 @@ hbGIS <- function(gisdir = "",
                                     ifelse(test = length(locationNames_nbh) > 0, yes = " & ", no = ""),
                                     paste0("!", paste0("at_", locationNames_nbh, "_nbh", collapse = " & !"))),
                              TRUE, NA, "", "")
+  
   for (i in 1:Nlocations) {
     # palmsplus_domain:
     #-------------------
@@ -273,6 +273,7 @@ hbGIS <- function(gisdir = "",
                                  TRUE,
                                  NA, "", "")
     }
+    
     # palmsplus_field:
     #-------------------
     if (!is.null(loca[[i]][[1]])) {
@@ -328,6 +329,7 @@ hbGIS <- function(gisdir = "",
     }
     CONF = CONF[!duplicated(CONF),]
   }
+  
   palmsplusr_field_rows = which(CONF$context == "palmsplus_field")
   palmsplus_fields = tibble(name = CONF$name[palmsplusr_field_rows],
                             formula = CONF$formula[palmsplusr_field_rows],
@@ -337,24 +339,24 @@ hbGIS <- function(gisdir = "",
   palmsplus_domains = tibble(name = CONF$name[palmsplusr_domain_rows],
                              formula = CONF$formula[palmsplusr_domain_rows],
                              domain_field = CONF$domain_field[palmsplusr_domain_rows])
-  # #=============================
-  # # trajectory_fields
+  #=============================
+  # trajectory_fields
   trajectory_field_rows = which(CONF$context == "trajectory_field")
   trajectory_fields = tibble(name = CONF$name[trajectory_field_rows],
                              formula = CONF$formula[trajectory_field_rows],
                              after_conversion = CONF$after_conversion[trajectory_field_rows])
-  # #=============================
-  # # multimodal_fields
+  #=============================
+  # multimodal_fields
   multimodal_fields_rows = which(CONF$context == "multimodal_field")
   multimodal_fields = tibble(name = CONF$name[multimodal_fields_rows],
                              formula = CONF$formula[multimodal_fields_rows])
-  # #=============================
-  # # trajectory locations
+  #=============================
+  # trajectory locations
   trajectory_location_rows = which(CONF$context == "trajectory_location")
   trajectory_locations = tibble(name = CONF$name[trajectory_location_rows],
                                 start_criteria = CONF$start_criteria[trajectory_location_rows],
                                 end_criteria = CONF$end_criteria[trajectory_location_rows])
-  # save(palms, loca, participant_basis, file = "~/projects/fontys/state_1_gui.RData")
+  
   # Run palmsplusr ----------------------------------------------------------
   fns = c(paste0(palmsplus_folder, "/", dataset_name, "_palmsplus.csv"),
           paste0(palmsplus_folder, "/", dataset_name, "_days.csv"),
@@ -368,6 +370,7 @@ hbGIS <- function(gisdir = "",
   for (i in 1:Nlocations) {
     Nlocation_objects = c(Nlocation_objects, length(loca[[i]][[2]])) # at least a nbh object is expected #length(loca[[i]][[1]]), 
   }
+  
   if (verbose) cat("\n<<< building palmsplus...\n")
   if (length(palms) > 0 & length(palmsplus_fields) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {
@@ -382,6 +385,7 @@ hbGIS <- function(gisdir = "",
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
+  
   if (verbose) cat("\n<<< building days...")
   if (length(palmsplus) > 0 & length(palmsplus_domains) > 0 & length(palmsplus_fields) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {
@@ -398,13 +402,11 @@ hbGIS <- function(gisdir = "",
     } else {
       if (verbose) cat(paste0("  WARNING: no days object produced."))
     }
-    
-    # sf::st_write(palmsplus, dsn = paste0(palmsplus_folder, "/", dataset_name, "_palmsplus.shp"), append = FALSE)
-    
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
   if (verbose) cat(">>>\n")
+  
   trajectory_locations = trajectory_locations[order(trajectory_locations$name),]
   if (verbose) cat("\n<<< building trajectories...\n")
   if (length(palmsplus) > 0 & length(trajectory_fields) > 0) {
@@ -426,6 +428,7 @@ hbGIS <- function(gisdir = "",
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
+  
   if (verbose) cat("\n<<< building multimodal...\n")
   if (length(palmsplus) > 0 & length(multimodal_fields) > 0 & length(trajectory_locations) > 0) {
     multimodal <- build_multimodal(data = trajectories,

From 1e5eba717e8e9b661305005adbe3af6a0ecfd904 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Thu, 30 Nov 2023 16:46:47 +0100
Subject: [PATCH 04/14] fix dummy data, fix st_contains call

---
 R/hbGIS.R | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 4ee5269..166ec83 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -117,7 +117,7 @@ hbGIS <- function(gisdir = "",
   if (length(palms_country_files) == 0) {
     # Simulate hbGPS output (only for code developement purposes)
     Nmin = 500
-    now = Sys.time()
+    now = as.POSIXct("2023-11-30 10:00:00 CET")
     dateTime = seq(now, now + ((Nmin - 1) * 60), by = 60)
     example_object = loca[[1]][[2]][1,]
     point_in_object = st_sample(x = example_object, size = 1)
@@ -127,8 +127,8 @@ hbGIS <- function(gisdir = "",
     # but for 30 minutes inside the location surround by 5 minute trips before and after
     trip = seq(xy[1] - 1, xy[1] - 0.2, by = 0.2)
     away = rep(xy[1] - 1, (Nmin/2) - 20)
-    lat = c(away, trip, rep(xy[1], 30), rev(trip), away)
-    lon = rep(xy[2], Nmin) # lon stays the same the entire time
+    lon = c(away, trip, rep(xy[1], 30), rev(trip), away)
+    lat = rep(xy[2], Nmin) # lon stays the same the entire time
     tripNumber = c(rep(0, length(away)), rep(1, 5), rep(0, 30), rep(2, 5), rep(0, length(away)))
     sedentaryBoutNumber = c(rep(1, length(away)), rep(0, 5), rep(2, 30), rep(0, 5), rep(3, length(away)))
     tripType = rep(0, Nmin)
@@ -312,7 +312,7 @@ hbGIS <- function(gisdir = "",
       # Note palms_in_polygon allows for aggregating polygons based by variable
       CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
                                  paste0("at_", locationNames[i], "_nbh"), 
-                                 paste0("suppressMessages(any(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
+                                 paste0("suppressMessages(colSums(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
                                  NA, "", "", "")
     }
     reference_location = ifelse("home" %in% locationNames, yes = "home", no = locationNames[1])
@@ -370,7 +370,6 @@ hbGIS <- function(gisdir = "",
   for (i in 1:Nlocations) {
     Nlocation_objects = c(Nlocation_objects, length(loca[[i]][[2]])) # at least a nbh object is expected #length(loca[[i]][[1]]), 
   }
-  
   if (verbose) cat("\n<<< building palmsplus...\n")
   if (length(palms) > 0 & length(palmsplus_fields) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {
@@ -385,7 +384,6 @@ hbGIS <- function(gisdir = "",
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
-  
   if (verbose) cat("\n<<< building days...")
   if (length(palmsplus) > 0 & length(palmsplus_domains) > 0 & length(palmsplus_fields) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {

From b4f15ffb915ddc4da4e87bf94b76ff25c581dfcc Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Thu, 30 Nov 2023 16:47:07 +0100
Subject: [PATCH 05/14] edits to development scripts

---
 inst/dev_code_hbGIS.R | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/inst/dev_code_hbGIS.R b/inst/dev_code_hbGIS.R
index df4d48e..ead1284 100644
--- a/inst/dev_code_hbGIS.R
+++ b/inst/dev_code_hbGIS.R
@@ -18,30 +18,30 @@ library(geosphere)
 library(lwgeom)
 
 
-hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/loc_greenspace",
-      palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/hbGPSoutput",
-      gislinkfile = NULL,
-      outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023",
-      dataset_name = "JasperNov2023",
-      configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
-kkk
-# 
-# hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/GIS",
-#                  palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/hbGPSoutput",
-#                  gislinkfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/Tables/participant_basis.csv",
-#                  outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010",
-#                  dataset_name = "NBBB2010",
-#                  configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
+# hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/loc_greenspace",
+#       palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023/hbGPSoutput",
+#       gislinkfile = NULL,
+#       outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JasperNov2023",
+#       dataset_name = "JasperNov2023",
+#       configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
 # kkk
+# 
+hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/GIS",
+                 palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/hbGPSoutput",
+                 gislinkfile = NULL, # "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/Tables/participant_basis.csv",
+                 outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010",
+                 dataset_name = "NBBB2010",
+                 configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_palmsplusr.csv")
+kkk
 
 # Belgium dataset
-# hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/GIS",
-#       palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/hbGPSoutput",
-#       gislinkfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/Tables/participant_basis.csv",
-#       outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata",
-#       dataset_name = "BEtestdata",
-#       configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/config_palmsplusr.csv")
-
+hbGIS(gisdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/GIS/",
+      palmsdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/hbGPSoutput",
+      gislinkfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/Tables/participant_basis.csv",
+      outputdir = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata",
+      dataset_name = "BEtestdata",
+      configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/BEtestdata/config_palmsplusr.csv")
+jkjj
 # hbGIS(gisdir = "/media/vincent/projects/Habitus/palmsplusr/testdata/GIS",
 #                  palmsdir = "/media/vincent/projects/Habitus/palmsplusr/testdata/PALMS_output/",
 #                  gislinkfile = "/media/vincent/projects/Habitus/palmsplusr/testdata/Tables/participant_basis.csv",

From c81d9eccc8119220c0d0ac17f924a40c72a146ee Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Mon, 4 Dec 2023 16:43:03 +0100
Subject: [PATCH 06/14] fix trajectory locations, code did not correctly loop
 over combinations of locations

---
 R/hbGIS.R | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 166ec83..7236d11 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -242,14 +242,14 @@ hbGIS <- function(gisdir = "",
   # ignore stored definition as we no longer use this
   
   CONF = CONF[which(CONF[,1] != "palmsplus_domain"), ] 
-  element1 = ifelse(length(locationNames_table) > 0, yes = paste0("!", paste0("at_", locationNames_table, collapse = " & !"), " & "), no = "")
+  element3 = ifelse(length(locationNames_table) > 0, yes = paste0("!", paste0("at_", locationNames_table, collapse = " & !"), " & "), no = "")
   CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
                              "transport",
-                            paste0(element1, "(pedestrian | bicycle | vehicle)"),
+                            paste0(element3, "(pedestrian | bicycle | vehicle)"),
                              TRUE, NA, "", "")
   CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
                              "other",
-                             paste0(element1, "(!pedestrian & !bicycle & !vehicle)", # removed because theorectically possible
+                             paste0(element3, "(!pedestrian & !bicycle & !vehicle)", # removed because theorectically possible
                                     ifelse(test = length(locationNames_nbh) > 0, yes = " & ", no = ""),
                                     paste0("!", paste0("at_", locationNames_nbh, "_nbh", collapse = " & !"))),
                              TRUE, NA, "", "")
@@ -318,18 +318,20 @@ hbGIS <- function(gisdir = "",
     reference_location = ifelse("home" %in% locationNames, yes = "home", no = locationNames[1])
     for (j in 1:Nlocations) {
       #add nbh if table is missing
+      element1 = ifelse(test = is.null(loca[[i]][[1]]), yes = "_nbh", no = "")
       element2 = ifelse(test = is.null(loca[[j]][[1]]), yes = "_nbh", no = "")
+      element4 = ifelse(test = is.null(loca[[reference_location]][[1]]), yes = "_nbh", no = "")
       # trajectory_location:
       #-------------------
       CONF[nrow(CONF) + 1, ] = c("trajectory_location",
-                                 paste0(locationNames[i], element2, "_", locationNames[i], element2),
-                                 paste0("at_", locationNames[i]), NA, paste0("at_", reference_location, element2),
-                                 paste0("at_", locationNames[i], element2),
+                                 paste0(locationNames[i], element1, "_", locationNames[j], element2),
+                                 paste0("at_", locationNames[i]), NA,
+                                 paste0("at_", reference_location, element4),
+                                 paste0("at_", locationNames[i], element1),
                                  paste0("at_", locationNames[j], element2))
     }
     CONF = CONF[!duplicated(CONF),]
   }
-  
   palmsplusr_field_rows = which(CONF$context == "palmsplus_field")
   palmsplus_fields = tibble(name = CONF$name[palmsplusr_field_rows],
                             formula = CONF$formula[palmsplusr_field_rows],
@@ -408,15 +410,13 @@ hbGIS <- function(gisdir = "",
   trajectory_locations = trajectory_locations[order(trajectory_locations$name),]
   if (verbose) cat("\n<<< building trajectories...\n")
   if (length(palmsplus) > 0 & length(trajectory_fields) > 0) {
-    
     trajectories <- build_trajectories(data = palmsplus,
                                        trajectory_fields = trajectory_fields,
                                        trajectory_locations = trajectory_locations)
     if (length(trajectories) > 0) {
       write_csv(trajectories,  file = fns[3])
-      shp_file = paste0(palmsplus_folder, "/", dataset_name, "_trajecories.shp")
+      shp_file = paste0(palmsplus_folder, "/", dataset_name, "_trajectories.shp")
       if (file.exists(shp_file)) file.remove(shp_file) # remove because st_write does not know how to overwrite
-      
       sf::st_write(obj = trajectories, dsn = shp_file)
       if (verbose) cat(paste0("  N rows in trajectories object: ", nrow(trajectories)))
     } else {
@@ -426,7 +426,6 @@ hbGIS <- function(gisdir = "",
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
-  
   if (verbose) cat("\n<<< building multimodal...\n")
   if (length(palmsplus) > 0 & length(multimodal_fields) > 0 & length(trajectory_locations) > 0) {
     multimodal <- build_multimodal(data = trajectories,

From ae95c88fc0da07c005bb0066c4d8754cb865be90 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 12:42:52 +0100
Subject: [PATCH 07/14] replace deprecate dependencies

---
 NAMESPACE      | 1 -
 R/build_days.R | 6 +++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index dc7df75..78f74cf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -19,7 +19,6 @@ importFrom(geosphere,distGeo)
 importFrom(purrr,reduce)
 importFrom(readr,read_csv)
 importFrom(readr,write_csv)
-importFrom(rlang,UQ)
 importFrom(rlang,parse_expr)
 importFrom(stats,as.formula)
 importFrom(stats,end)
diff --git a/R/build_days.R b/R/build_days.R
index 49d9416..3af30e2 100644
--- a/R/build_days.R
+++ b/R/build_days.R
@@ -24,7 +24,7 @@
 #'
 #' @import dplyr
 #' @import sf
-#' @importFrom rlang parse_expr UQ
+#' @importFrom rlang parse_expr
 #' @importFrom purrr reduce
 #'
 #' @export
@@ -77,8 +77,8 @@ build_days <- function(data = NULL, verbose = TRUE,
   x <- list()
   for (i in domain_names) {
     x[[i]] <- data %>%
-      filter(UQ(as.name(i)) > 0) %>%
-      dplyr::select(-one_of(domain_names), duration) %>%
+      filter(!!(as.name(i)) > 0) %>%
+      dplyr::select(-any_of(domain_names), duration) %>%
       summarise_all(~ sum(.)) %>%
       ungroup() %>%
       rename_at(vars(-identifier, -date), ~ paste0(i, "_", .))

From a7191ca071dcfaf5e863c9b80dd60dd84f98cc98 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 13:20:17 +0100
Subject: [PATCH 08/14] add count of visits to a domain per day

---
 R/build_days.R | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/R/build_days.R b/R/build_days.R
index 3af30e2..29c96a5 100644
--- a/R/build_days.R
+++ b/R/build_days.R
@@ -86,5 +86,24 @@ build_days <- function(data = NULL, verbose = TRUE,
   
   result <- x %>%
     reduce(left_join, by = c("identifier" = "identifier", "date" = "date"))
+  
+  # Count the number of segments per domain per day per identifier
+  segmentcount = function(x) {
+    x = as.numeric(unlist(x)) # x is a tibble column, so first convert to numeric vector
+    return(length(which(rle(x)$values != 0)))
+  }
+  
+  for (dom in domain_names) {
+    if (dom != "total") {
+      result[, dom] <- NA
+      for (id in unique(result$identifier)) {
+        for (date in as.Date(unique(result$date[which(result$identifier == id)]))) {
+          CNT = segmentcount(data[which(data$identifier == id & data$date == date), dom])
+          result[which(result$identifier == id & result$date == date), dom] = CNT
+        }
+      }
+      names(result)[which(names(result) == dom)] = paste0(dom, "_segmentcount")
+    }
+  }
   return(result)
 }

From e5f42d01adf13410ff1469149a3261f7fdb14b7e Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 17:48:53 +0100
Subject: [PATCH 09/14] handle sublocations in GIS files, these are now
 included in day and palmsplus output file, but not in trajectory and
 multimodal file #1

---
 R/hbGIS.R | 129 +++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 94 insertions(+), 35 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 7236d11..23f8bf2 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -24,8 +24,9 @@ hbGIS <- function(gisdir = "",
                   dataset_name = "",
                   configfile = "",
                   verbose = TRUE) {
-  publiclocation = "park"
   groupinglocation = "school"
+  writeshp = FALSE
+  splitGIS = TRUE
   lon = identifier = palms = NULL # . = was also included, but probably wrong
   
   #===============================================
@@ -56,20 +57,25 @@ hbGIS <- function(gisdir = "",
   
   # Helper function to find shape files
   find_file = function(path, namelowercase) {
-    allcsvfiles = dir(path, recursive = TRUE, full.names = TRUE)
-    file_of_interest = allcsvfiles[which(tolower(basename(allcsvfiles)) == namelowercase)]
+    allshpfiles = dir(path, recursive = TRUE, full.names = TRUE, pattern = "shp")
+    file_of_interest = allshpfiles[which(tolower(basename(allshpfiles)) == namelowercase)]
     if (length(file_of_interest) == 0) file_of_interest = NULL
     return(file_of_interest)
   }
   # Find shape files
   locationNames_nbh = locationNames_table = NULL
+  ignore4trajectories = NULL
   for (jj in 1:Nlocations) {
+    # files with _table at the end of their name indicate that it is
+    # a location for which entries exist in the GIS-Person linkage file
     findfile3 = find_file(path = gisdir, namelowercase = paste0(locationNames[jj], "_table.shp"))
     if (!is.null(findfile3)) {
       loca[[jj]][3] = findfile3
       loca[[jj]][[1]] = sf::read_sf(loca[[jj]][3]) #e.g. school or home
       locationNames_table = c(locationNames_table, locationNames[jj])
     }
+    # files with "loc_" and "buffers" in their name are assumed to be the areas surrounding
+    # the table files (if exist)
     findfile4 = find_file(path = gisdir, namelowercase = paste0("loc_", locationNames[jj], "buffers.shp"))
     if (!is.null(findfile4)) {
       loca[[jj]][4] = findfile4
@@ -84,12 +90,43 @@ hbGIS <- function(gisdir = "",
     }
     # Only load shape file if it exists
     if (!is.null(loca[[jj]][4][[1]])) {
-      loca[[jj]][[2]] = sf::read_sf(loca[[jj]][4]) #e.g. school_nbh, home_nbh, or park
+      shp_dat = sf::read_sf(loca[[jj]][4]) #e.g. school_nbh, home_nbh, or park
+      # Check whether there are multiple polygons in the shapefile:
+      nshp = nrow(shp_dat)
+      loca[[jj]][[2]] = shp_dat # look at all sublocations combined either way
+      if (nshp > 1 & splitGIS == TRUE) {
+        collect_na = NULL
+        # Treat each polygon as a separate location
+        for (gi in 1:nshp) {
+          fn_4 = as.character(unlist(loca[[jj]][4]))
+          gi2 = Nlocations + gi
+          loca[[gi2]] = vector("list", 4)
+          objectname = as.character(st_drop_geometry(shp_dat[gi, "OBJECTID"]))
+          if (objectname == "NA") collect_na = c(collect_na, gi)
+          loca[[gi2]][[2]] = shp_dat[gi, ]
+          loca[[gi2]][[4]] = fn_4
+          newname = paste0(locationNames[jj], objectname)
+          names(loca[[gi2]]) =  c(newname,
+                                 paste0(newname, "_nbh"), 
+                                 paste0(newname, "_tablefile"),
+                                 paste0(newname, "_locbufferfile"))
+          locationNames = c(locationNames, newname)
+          names(loca)[[gi2]] = newname
+          locationNames_nbh = c(locationNames_nbh, newname)
+          ignore4trajectories = c(ignore4trajectories, newname)
+        }
+        if (length(collect_na) > 0) {
+          shp_dat = shp_dat[-collect_na, ]
+          locationNames = locationNames[-collect_na]
+          loca = loca[-collect_na]
+        }
+      }
     }
   }
+  Nlocations = length(locationNames)
   
-  # Force id numbers to be character(
   locationNames = names(loca)
+  # Force id numbers to be character to standardise format:
   for (i in 1:length(loca)) {
     if (!is.null(loca[[i]][3][[1]])) { # only consider locations with data
       for (j in 1:2) {
@@ -100,7 +137,6 @@ hbGIS <- function(gisdir = "",
       }
     }
   }
-
   #===============================================
   # hbGPS output (PALMS output)
   #===============================================
@@ -180,7 +216,6 @@ hbGIS <- function(gisdir = "",
   write.csv(palms_reduced_cleaned, PALMS_reduced_file, row.names = FALSE)
   palms = palmsplusr::read_palms(PALMS_reduced_file, verbose = FALSE)
   palms$datetime = as.POSIXct(palms$datetime, format = "%d/%m/%Y %H:%M:%S", tz = "")
-  
   #===============================================
   # Load linkage file and identify which PALMS ids and home/school
   # ids are missing, but allow for publiclocations that are not linked
@@ -237,6 +272,8 @@ hbGIS <- function(gisdir = "",
   #=====================================================
   # Expand CONF with standard location based fields
   #=====================================================
+  if (verbose) cat("\n<<< expand CONF...\n")
+  
   # palmsplus_domain:
   #-------------------
   # ignore stored definition as we no longer use this
@@ -254,11 +291,15 @@ hbGIS <- function(gisdir = "",
                                     paste0("!", paste0("at_", locationNames_nbh, "_nbh", collapse = " & !"))),
                              TRUE, NA, "", "")
   
+  cnt = nrow(CONF)
+  CONF[cnt + Nlocations,] = NA
+  cnt = cnt + 1
+
   for (i in 1:Nlocations) {
     # palmsplus_domain:
     #-------------------
     if (locationNames[i] %in% locationNames_table) {
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+      CONF[cnt, ] = c("palmsplus_domain",
                                  locationNames[i],
                                  paste0("at_", locationNames[i]), 
                                  TRUE,
@@ -266,72 +307,80 @@ hbGIS <- function(gisdir = "",
     } else if (locationNames[i] %in% locationNames_nbh) {
       # condition that only needs to be used if table element is present
       at_table = ifelse(test = locationNames[i] %in% locationNames_table == TRUE, yes = paste0("!at_", locationNames[i], " &"), no = "")
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+      CONF[cnt, ] = c("palmsplus_domain",
                                  paste0(locationNames[i], "_nbh"),
                                  paste0(at_table, " at_", locationNames[i], "_nbh", 
                                         " & (!vehicle)"), # removed !pedestrian & !bicycle &  because unclear why these are not possible in a neighbourhood, e.g. park
                                  TRUE,
                                  NA, "", "")
     }
-    
+    cnt = cnt + 1
     # palmsplus_field:
     #-------------------
     if (!is.null(loca[[i]][[1]])) {
       # only do this if there is table data (meaning that location is linked to participant basis file)
       if (locationNames[i] == "home") {
-        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+        CONF[cnt, ] = c("palmsplus_field",
                                    paste0("at_", locationNames[i]), 
                                    paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
                                           locationNames[i],", identifier == i), identifier)"),
                                    NA, "", "", "")
-        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+        cnt = cnt + 1
+        CONF[cnt, ] = c("palmsplus_field",
                                    paste0("at_", locationNames[i], "_nbh"), 
                                    paste0("palms_in_polygon(datai, polygons = dplyr::filter(",
                                           locationNames[i], "_nbh, identifier == i), identifier)"),
                                    NA, "", "", "")
+        cnt = cnt + 1
       } else {
-        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+        CONF[cnt, ] = c("palmsplus_field",
                                    paste0("at_", locationNames[i]), 
                                    paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
                                           locationNames[i],",", locationNames[i],
                                           "_id == participant_basis %>% filter(identifier == i) %>% pull(",
                                           locationNames[i], "_id)))"),
                                    NA, "", "", "")
-        CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+        cnt = cnt + 1
+        CONF[cnt, ] = c("palmsplus_field",
                                    paste0("at_", locationNames[i], "_nbh"), 
                                    paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
                                           locationNames[i], "_nbh,", locationNames[i],
                                           "_id == participant_basis %>% filter(identifier == i) %>% pull(",
                                           locationNames[i], "_id)))"),
                                    NA, "", "", "")
+        cnt = cnt + 1
       }
     } else {
-      # palmsplus_domain:
-      #-------------------
       # locations not in linkagefile
-      # Note palms_in_polygon allows for aggregating polygons based by variable
-      CONF[nrow(CONF) + 1, ] = c("palmsplus_field",
+      # note that colSums will ensure that sublocation are combined
+      CONF[cnt, ] = c("palmsplus_field",
                                  paste0("at_", locationNames[i], "_nbh"), 
                                  paste0("suppressMessages(colSums(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
                                  NA, "", "", "")
+      cnt = cnt + 1
     }
     reference_location = ifelse("home" %in% locationNames, yes = "home", no = locationNames[1])
     for (j in 1:Nlocations) {
-      #add nbh if table is missing
-      element1 = ifelse(test = is.null(loca[[i]][[1]]), yes = "_nbh", no = "")
-      element2 = ifelse(test = is.null(loca[[j]][[1]]), yes = "_nbh", no = "")
-      element4 = ifelse(test = is.null(loca[[reference_location]][[1]]), yes = "_nbh", no = "")
-      # trajectory_location:
-      #-------------------
-      CONF[nrow(CONF) + 1, ] = c("trajectory_location",
-                                 paste0(locationNames[i], element1, "_", locationNames[j], element2),
-                                 paste0("at_", locationNames[i]), NA,
-                                 paste0("at_", reference_location, element4),
-                                 paste0("at_", locationNames[i], element1),
-                                 paste0("at_", locationNames[j], element2))
+      # Do not derive trajectories for sublocation combinations
+      if (all(locationNames[c(i, j)] %in% ignore4trajectories == FALSE)) {
+        #add nbh if table is missing
+        element1 = ifelse(test = is.null(loca[[i]][[1]]), yes = "_nbh", no = "")
+        element2 = ifelse(test = is.null(loca[[j]][[1]]), yes = "_nbh", no = "")
+        element4 = ifelse(test = is.null(loca[[reference_location]][[1]]), yes = "_nbh", no = "")
+        # trajectory_location:
+        #-------------------
+        CONF[cnt, ] = c("trajectory_location",
+                        paste0(locationNames[i], element1, "_", locationNames[j], element2),
+                        paste0("at_", locationNames[i]), NA,
+                        paste0("at_", reference_location, element4),
+                        paste0("at_", locationNames[i], element1),
+                        paste0("at_", locationNames[j], element2))
+        cnt = cnt + 1
+      }
     }
     CONF = CONF[!duplicated(CONF),]
   }
+  if (verbose) cat(">>>\n\n")
   palmsplusr_field_rows = which(CONF$context == "palmsplus_field")
   palmsplus_fields = tibble(name = CONF$name[palmsplusr_field_rows],
                             formula = CONF$formula[palmsplusr_field_rows],
@@ -367,7 +416,6 @@ hbGIS <- function(gisdir = "",
   for (fn in fns) {
     if (file.exists(fn)) file.remove(fn)
   }
-  
   Nlocation_objects = NULL
   for (i in 1:Nlocations) {
     Nlocation_objects = c(Nlocation_objects, length(loca[[i]][[2]])) # at least a nbh object is expected #length(loca[[i]][[1]]), 
@@ -413,11 +461,20 @@ hbGIS <- function(gisdir = "",
     trajectories <- build_trajectories(data = palmsplus,
                                        trajectory_fields = trajectory_fields,
                                        trajectory_locations = trajectory_locations)
+    
+    
+    # library(mapview)
+    # mapview(list(trajectories, loca$green$green_nbh), col.regions=list("red","blue"), col = list("red", "blue"),
+    #         layer.name = c("trajectories", "green spaces"))
+
+    # browser()
     if (length(trajectories) > 0) {
       write_csv(trajectories,  file = fns[3])
       shp_file = paste0(palmsplus_folder, "/", dataset_name, "_trajectories.shp")
-      if (file.exists(shp_file)) file.remove(shp_file) # remove because st_write does not know how to overwrite
-      sf::st_write(obj = trajectories, dsn = shp_file)
+      if (writeshp == TRUE) {
+        if (file.exists(shp_file)) file.remove(shp_file) # remove because st_write does not know how to overwrite
+        sf::st_write(obj = trajectories, dsn = shp_file)
+      }
       if (verbose) cat(paste0("  N rows in trajectories object: ", nrow(trajectories)))
     } else {
       if (verbose) cat(paste0("  WARNING: no trajectories object produced."))
@@ -439,8 +496,10 @@ hbGIS <- function(gisdir = "",
     if (length(multimodal) > 0) {
       write_csv(multimodal, file = fns[4])
       shp_file = paste0(palmsplus_folder, "/", dataset_name, "_multimodal.shp")
-      if (file.exists(shp_file)) file.remove(shp_file) # remove because st_write does not know how to overwrite
-      sf::st_write(obj = multimodal, dsn = shp_file)
+      if (writeshp == TRUE) {
+        if (file.exists(shp_file)) file.remove(shp_file) # remove because st_write does not know how to overwrite
+        sf::st_write(obj = multimodal, dsn = shp_file)
+      }
       if (verbose) cat(paste0("  N rows in multimodal object: ", nrow(multimodal)))
     } else {
       if (verbose) cat(paste0("  WARNING: no multimodal object produced."))

From 341584a8d782b17ee299b8e1129ec72e23ebca69 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 18:04:40 +0100
Subject: [PATCH 10/14] replace hyphen trip number values as it is interpretted
 by Excel as a date

---
 R/build_multimodal.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/build_multimodal.R b/R/build_multimodal.R
index 17566eb..cfd6df8 100644
--- a/R/build_multimodal.R
+++ b/R/build_multimodal.R
@@ -152,9 +152,9 @@ build_multimodal <- function(data = NULL,
       group_by(identifier, mmt_number) %>%
       summarise(start_trip = first(tripnumber),
                 end_trip = last(tripnumber),
-                trip_numbers = paste0(tripnumber, collapse = "-"),
+                trip_numbers = paste0(tripnumber, collapse = ">"),
                 n_segments = n(),
-                mot_order = paste0(mot, collapse = "-"),
+                mot_order = paste0(mot, collapse = ">"),
                 start = first(start),
                 end = last(end),
                 do_union = FALSE, .groups = 'keep') %>%

From d758827e1275ff7ab1abdb4310852dda7c77265c Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 18:05:05 +0100
Subject: [PATCH 11/14] move candidate new arguments to top of function #1

---
 R/hbGIS.R | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 23f8bf2..1c92e6a 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -24,9 +24,14 @@ hbGIS <- function(gisdir = "",
                   dataset_name = "",
                   configfile = "",
                   verbose = TRUE) {
+  # Hard code arguments that may need to become function arguments to give control to user
   groupinglocation = "school"
-  writeshp = FALSE
-  splitGIS = TRUE
+  writeshp = FALSE # whether to wrist a shape file
+  splitGIS = TRUE # whether to split sublocations (TRUE) or union them
+  sublocid = "OBJECTID" # column name in GIS file to identify sublocation id
+  
+  
+  #------------------------------------------------------------
   lon = identifier = palms = NULL # . = was also included, but probably wrong
   
   #===============================================
@@ -101,7 +106,7 @@ hbGIS <- function(gisdir = "",
           fn_4 = as.character(unlist(loca[[jj]][4]))
           gi2 = Nlocations + gi
           loca[[gi2]] = vector("list", 4)
-          objectname = as.character(st_drop_geometry(shp_dat[gi, "OBJECTID"]))
+          objectname = as.character(st_drop_geometry(shp_dat[gi, sublocid]))
           if (objectname == "NA") collect_na = c(collect_na, gi)
           loca[[gi2]][[2]] = shp_dat[gi, ]
           loca[[gi2]][[4]] = fn_4
@@ -492,7 +497,6 @@ hbGIS <- function(gisdir = "",
                                    multimodal_fields = multimodal_fields,
                                    trajectory_locations = trajectory_locations,
                                    verbose = verbose)
-    
     if (length(multimodal) > 0) {
       write_csv(multimodal, file = fns[4])
       shp_file = paste0(palmsplus_folder, "/", dataset_name, "_multimodal.shp")

From 39136341d9ab2c6a5a7c69adaf921e239b2f28ec Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 18:27:22 +0100
Subject: [PATCH 12/14] Update r_new.yml

---
 .github/workflows/r_new.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/r_new.yml b/.github/workflows/r_new.yml
index 5c7a488..63a8f4a 100644
--- a/.github/workflows/r_new.yml
+++ b/.github/workflows/r_new.yml
@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check-new
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,10 +29,9 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
- 
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-tinytex@v2
       - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
@@ -41,7 +40,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::XML
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

From 1349b76aafda8c0b1b8bd4c16832c1b81f6cd648 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Tue, 19 Dec 2023 18:27:29 +0100
Subject: [PATCH 13/14] Update NEWS.Rd

---
 inst/NEWS.Rd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 881aac6..e1938be 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,8 +1,9 @@
 \name{NEWS}
 \title{News for Package \pkg{HabitusGUI}}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
-\section{Changes in version 0.0.1 (GitHub-only-release date: 09-11-2023)}{
+\section{Changes in version 0.0.1 (GitHub-only-release date: 20-12-2023)}{
   \itemize{
     \item First release, based on code from the HabitusGUI and palmsplusr libraries
+    \item Expansion with ability to handle public locations not tight to an individual
   }
 }

From 394bfc0e7fb06639b8ee7e7a4406427e47a17db7 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 20 Dec 2023 08:40:09 +0100
Subject: [PATCH 14/14] fix broken functionality for datasets without public
 spaces

---
 R/hbGIS.R | 97 ++++++++++++++++++++++++++++---------------------------
 1 file changed, 50 insertions(+), 47 deletions(-)

diff --git a/R/hbGIS.R b/R/hbGIS.R
index 1c92e6a..d3d007e 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -74,7 +74,8 @@ hbGIS <- function(gisdir = "",
     # files with _table at the end of their name indicate that it is
     # a location for which entries exist in the GIS-Person linkage file
     findfile3 = find_file(path = gisdir, namelowercase = paste0(locationNames[jj], "_table.shp"))
-    if (!is.null(findfile3)) {
+    publiclocation = ifelse(test = is.null(findfile3), yes = TRUE, no = FALSE)
+    if (publiclocation == FALSE) {
       loca[[jj]][3] = findfile3
       loca[[jj]][[1]] = sf::read_sf(loca[[jj]][3]) #e.g. school or home
       locationNames_table = c(locationNames_table, locationNames[jj])
@@ -99,22 +100,27 @@ hbGIS <- function(gisdir = "",
       # Check whether there are multiple polygons in the shapefile:
       nshp = nrow(shp_dat)
       loca[[jj]][[2]] = shp_dat # look at all sublocations combined either way
-      if (nshp > 1 & splitGIS == TRUE) {
+      if (publiclocation == TRUE) {
+        cat(paste0("\n", basename(as.character(unlist(loca[[jj]][4]))),
+                   " => ", paste0(names(shp_dat), collapse = ", "), " (", nshp, " geoms)"))
+      }
+      if (nshp > 1 & splitGIS == TRUE & sublocid %in% names(shp_dat) & publiclocation) {
         collect_na = NULL
         # Treat each polygon as a separate location
         for (gi in 1:nshp) {
           fn_4 = as.character(unlist(loca[[jj]][4]))
           gi2 = Nlocations + gi
           loca[[gi2]] = vector("list", 4)
+          
           objectname = as.character(st_drop_geometry(shp_dat[gi, sublocid]))
           if (objectname == "NA") collect_na = c(collect_na, gi)
           loca[[gi2]][[2]] = shp_dat[gi, ]
           loca[[gi2]][[4]] = fn_4
           newname = paste0(locationNames[jj], objectname)
           names(loca[[gi2]]) =  c(newname,
-                                 paste0(newname, "_nbh"), 
-                                 paste0(newname, "_tablefile"),
-                                 paste0(newname, "_locbufferfile"))
+                                  paste0(newname, "_nbh"), 
+                                  paste0(newname, "_tablefile"),
+                                  paste0(newname, "_locbufferfile"))
           locationNames = c(locationNames, newname)
           names(loca)[[gi2]] = newname
           locationNames_nbh = c(locationNames_nbh, newname)
@@ -129,7 +135,6 @@ hbGIS <- function(gisdir = "",
     }
   }
   Nlocations = length(locationNames)
-  
   locationNames = names(loca)
   # Force id numbers to be character to standardise format:
   for (i in 1:length(loca)) {
@@ -195,7 +200,7 @@ hbGIS <- function(gisdir = "",
     palms_country_files = paste0(palmsdir, "/combined.csv")
     write.csv(hbGPSout, file = palms_country_files, row.names = FALSE)
   }
-
+  
   # read and combine palms csv output files 
   csv_palms <- lapply(palms_country_files, FUN = readr::read_csv, col_types = list(
     identifier = readr::col_character(),
@@ -287,7 +292,7 @@ hbGIS <- function(gisdir = "",
   element3 = ifelse(length(locationNames_table) > 0, yes = paste0("!", paste0("at_", locationNames_table, collapse = " & !"), " & "), no = "")
   CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
                              "transport",
-                            paste0(element3, "(pedestrian | bicycle | vehicle)"),
+                             paste0(element3, "(pedestrian | bicycle | vehicle)"),
                              TRUE, NA, "", "")
   CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
                              "other",
@@ -299,25 +304,25 @@ hbGIS <- function(gisdir = "",
   cnt = nrow(CONF)
   CONF[cnt + Nlocations,] = NA
   cnt = cnt + 1
-
+  
   for (i in 1:Nlocations) {
     # palmsplus_domain:
     #-------------------
     if (locationNames[i] %in% locationNames_table) {
       CONF[cnt, ] = c("palmsplus_domain",
-                                 locationNames[i],
-                                 paste0("at_", locationNames[i]), 
-                                 TRUE,
-                                 NA, "", "")
+                      locationNames[i],
+                      paste0("at_", locationNames[i]), 
+                      TRUE,
+                      NA, "", "")
     } else if (locationNames[i] %in% locationNames_nbh) {
       # condition that only needs to be used if table element is present
       at_table = ifelse(test = locationNames[i] %in% locationNames_table == TRUE, yes = paste0("!at_", locationNames[i], " &"), no = "")
       CONF[cnt, ] = c("palmsplus_domain",
-                                 paste0(locationNames[i], "_nbh"),
-                                 paste0(at_table, " at_", locationNames[i], "_nbh", 
-                                        " & (!vehicle)"), # removed !pedestrian & !bicycle &  because unclear why these are not possible in a neighbourhood, e.g. park
-                                 TRUE,
-                                 NA, "", "")
+                      paste0(locationNames[i], "_nbh"),
+                      paste0(at_table, " at_", locationNames[i], "_nbh", 
+                             " & (!vehicle)"), # removed !pedestrian & !bicycle &  because unclear why these are not possible in a neighbourhood, e.g. park
+                      TRUE,
+                      NA, "", "")
     }
     cnt = cnt + 1
     # palmsplus_field:
@@ -326,42 +331,42 @@ hbGIS <- function(gisdir = "",
       # only do this if there is table data (meaning that location is linked to participant basis file)
       if (locationNames[i] == "home") {
         CONF[cnt, ] = c("palmsplus_field",
-                                   paste0("at_", locationNames[i]), 
-                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                          locationNames[i],", identifier == i), identifier)"),
-                                   NA, "", "", "")
+                        paste0("at_", locationNames[i]), 
+                        paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                               locationNames[i],", identifier == i), identifier)"),
+                        NA, "", "", "")
         cnt = cnt + 1
         CONF[cnt, ] = c("palmsplus_field",
-                                   paste0("at_", locationNames[i], "_nbh"), 
-                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(",
-                                          locationNames[i], "_nbh, identifier == i), identifier)"),
-                                   NA, "", "", "")
+                        paste0("at_", locationNames[i], "_nbh"), 
+                        paste0("palms_in_polygon(datai, polygons = dplyr::filter(",
+                               locationNames[i], "_nbh, identifier == i), identifier)"),
+                        NA, "", "", "")
         cnt = cnt + 1
       } else {
         CONF[cnt, ] = c("palmsplus_field",
-                                   paste0("at_", locationNames[i]), 
-                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                          locationNames[i],",", locationNames[i],
-                                          "_id == participant_basis %>% filter(identifier == i) %>% pull(",
-                                          locationNames[i], "_id)))"),
-                                   NA, "", "", "")
+                        paste0("at_", locationNames[i]), 
+                        paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                               locationNames[i],",", locationNames[i],
+                               "_id == participant_basis %>% filter(identifier == i) %>% pull(",
+                               locationNames[i], "_id)))"),
+                        NA, "", "", "")
         cnt = cnt + 1
         CONF[cnt, ] = c("palmsplus_field",
-                                   paste0("at_", locationNames[i], "_nbh"), 
-                                   paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
-                                          locationNames[i], "_nbh,", locationNames[i],
-                                          "_id == participant_basis %>% filter(identifier == i) %>% pull(",
-                                          locationNames[i], "_id)))"),
-                                   NA, "", "", "")
+                        paste0("at_", locationNames[i], "_nbh"), 
+                        paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
+                               locationNames[i], "_nbh,", locationNames[i],
+                               "_id == participant_basis %>% filter(identifier == i) %>% pull(",
+                               locationNames[i], "_id)))"),
+                        NA, "", "", "")
         cnt = cnt + 1
       }
     } else {
       # locations not in linkagefile
       # note that colSums will ensure that sublocation are combined
       CONF[cnt, ] = c("palmsplus_field",
-                                 paste0("at_", locationNames[i], "_nbh"), 
-                                 paste0("suppressMessages(colSums(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
-                                 NA, "", "", "")
+                      paste0("at_", locationNames[i], "_nbh"), 
+                      paste0("suppressMessages(colSums(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
+                      NA, "", "", "")
       cnt = cnt + 1
     }
     reference_location = ifelse("home" %in% locationNames, yes = "home", no = locationNames[1])
@@ -448,30 +453,28 @@ hbGIS <- function(gisdir = "",
                        loca = loca,
                        participant_basis = participant_basis,
                        verbose = verbose)
-    
     if (length(days) > 0) {
-      if (verbose) cat(paste0("  N rows in days object: ", nrow(days)))
+      if (verbose) cat(paste0("\n  N rows in days object: ", nrow(days)))
       write_csv(x = days, file = fns[2])
     } else {
-      if (verbose) cat(paste0("  WARNING: no days object produced."))
+      if (verbose) cat(paste0("\n  WARNING: no days object produced."))
     }
   } else {
     if (verbose) cat("skipped because insufficient input data>>>\n")
   }
   if (verbose) cat(">>>\n")
-  
   trajectory_locations = trajectory_locations[order(trajectory_locations$name),]
+  
   if (verbose) cat("\n<<< building trajectories...\n")
   if (length(palmsplus) > 0 & length(trajectory_fields) > 0) {
     trajectories <- build_trajectories(data = palmsplus,
                                        trajectory_fields = trajectory_fields,
                                        trajectory_locations = trajectory_locations)
     
-    
     # library(mapview)
     # mapview(list(trajectories, loca$green$green_nbh), col.regions=list("red","blue"), col = list("red", "blue"),
     #         layer.name = c("trajectories", "green spaces"))
-
+    
     # browser()
     if (length(trajectories) > 0) {
       write_csv(trajectories,  file = fns[3])