diff --git a/DESCRIPTION b/DESCRIPTION
index a712865..6ee6db2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: hbGIS
 Title: Process GIS Data for Human Behaviour Research
 Description: Processes GIS data merge with hbGPS pre-processed data of wearable GPS and accelerometation sensors.
 Version: 0.0.1
-Date: 2023-11-09
+Date: 2023-12-20
 Authors@R: 
     c(person(given = "Vincent",
            family = "van Hees",
diff --git a/NAMESPACE b/NAMESPACE
index 78f74cf..2e381d1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,9 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export(build_days)
-export(build_hbGIS)
 export(build_multimodal)
 export(build_trajectories)
+export(build_whenwhatwhere)
 export(check_and_clean_palms_data)
 export(check_missing_id)
 export(hbGIS)
diff --git a/R/build_days.R b/R/build_days.R
index 29c96a5..2c95c77 100644
--- a/R/build_days.R
+++ b/R/build_days.R
@@ -1,25 +1,16 @@
 
-#' Calculate day-level summaries from the palmsplus dataset
+#' Calculate day-level summaries from the whenwhat dataset
 #'
-#' @description Build a days dataset by summarising \code{palmsplus}
-#' by day and person (\code{identifier}). Not all variables in \code{palmsplus}
-#' are summarised, only those specified using \code{\link{palms_add_field}} with
-#' the argument \code{domain_field = TRUE}. By default, a \code{duration} field
-#' is added (e.g., the total minutes per day).
+#' @description Build a days dataset by summarising \code{whenwhat}
+#' by day and person (\code{identifier}). 
 #'
-#' All data are summarised by default. However, additional aggragation \emph{domains}
-#' can be specified using \code{\link{palms_add_domain}} before building days.
-#' Domains are a subset of data, such as during school time. All \code{domain_field}
-#' variables will be summarised for each \emph{domain} seperatly.
-#'
-#' @param data The palmsplus data obtained from \code{\link{palms_build_palmsplus}}.
+#' @param data The whenwhat data obtained from \code{\link{build_whenwhatwhere}}.
 #' @param verbose Print progress to console. Default is \code{TRUE}.
-#' @param palmsplus_domains ...
-#' @param palmsplus_fields ...
+#' @param where_field ...
+#' @param whenwhat_field ...
 #' @param loca Nested list with location information
 #' @param participant_basis participant_basis
-#'
-#'
+#'#'
 #' @return A table summarised by day.
 #'
 #' @import dplyr
@@ -30,8 +21,8 @@
 #' @export
 # Code modified from https://thets.github.io/palmsplusr/
 build_days <- function(data = NULL, verbose = TRUE, 
-                       palmsplus_domains = NULL,
-                       palmsplus_fields = NULL,
+                       where_field = NULL,
+                       whenwhat_field = NULL,
                        loca = NULL,
                        participant_basis = NULL) {
   # Note:
@@ -47,38 +38,37 @@ build_days <- function(data = NULL, verbose = TRUE,
     }
   }
   
-  duration = datetime = name = domain_field = NULL
-  
-  domain_fields <- palmsplus_domains %>% filter(domain_field == TRUE)
-  domain_names <- domain_fields %>% pull(name)
+  duration = datetime = name = is_where_field = NULL
+  where_field <- where_field %>% filter(is_where_field == TRUE)
+  where_names <- where_field %>% pull(name)
   
-  if (is.null(domain_names)) {
-    domain_names <- "total"
+  if (is.null(where_names)) {
+    where_names <- "total"
   } else {
-    domain_names <- c("total", domain_names)
+    where_names <- c("total", where_names)
   }
-  domain_args <- setNames("1", "total") %>% lapply(parse_expr)
-  domain_args <- c(domain_args, setNames(domain_fields[[2]], domain_fields[[1]]) %>%
+  where_args <- setNames("1", "total") %>% lapply(parse_expr)
+  where_args <- c(where_args, setNames(where_field[[2]], where_field[[1]]) %>%
                      lapply(parse_expr))
   data <- data %>%
-    mutate(!!! domain_args) %>%
+    mutate(!!! where_args) %>%
     mutate_if(is.logical, as.integer)
   
-  fields <- palmsplus_fields %>% filter(domain_field == TRUE) %>% pull(name)
+  fields <- whenwhat_field %>% filter(is_where_field == TRUE) %>% pull(name)
 
   data <- data %>%
     st_set_geometry(NULL) %>%
-    dplyr::select(identifier, datetime, any_of(domain_names), all_of(fields)) %>%
+    dplyr::select(identifier, datetime, any_of(where_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) {
+  for (i in where_names) {
     x[[i]] <- data %>%
       filter(!!(as.name(i)) > 0) %>%
-      dplyr::select(-any_of(domain_names), duration) %>%
+      dplyr::select(-any_of(where_names), duration) %>%
       summarise_all(~ sum(.)) %>%
       ungroup() %>%
       rename_at(vars(-identifier, -date), ~ paste0(i, "_", .))
@@ -87,13 +77,13 @@ 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
+  # Count the number of segments per where 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) {
+  for (dom in where_names) {
     if (dom != "total") {
       result[, dom] <- NA
       for (id in unique(result$identifier)) {
diff --git a/R/build_multimodal.R b/R/build_multimodal.R
index cfd6df8..520a68a 100644
--- a/R/build_multimodal.R
+++ b/R/build_multimodal.R
@@ -6,7 +6,7 @@
 #' @param data The trajectories object built with \code{palms_calc_trajectories}.
 #' @param spatial_threshold Spatial threshold in meters
 #' @param temporal_threshold Temporal threshold in minutes
-#' @param palmsplus The dataset build by \code{build_hbGIS}
+#' @param whenwhat The dataset build by \code{build_hbGIS}
 #' @param verbose Print progress after each step. Default is \code{TRUE}.
 #' @param multimodal_fields ...
 #' @param trajectory_locations ...
@@ -40,7 +40,7 @@
 build_multimodal <- function(data = NULL,
                                  spatial_threshold,
                                  temporal_threshold,
-                                 palmsplus = NULL,
+                                 whenwhat = NULL,
                                  verbose = TRUE,
                                  multimodal_fields = NULL,
                                  trajectory_locations = NULL) {
@@ -127,8 +127,8 @@ build_multimodal <- function(data = NULL,
                       trajectory_locations$end_criteria))
     
     
-    # Rather than recalculating geometry, just lookup in palmsplus
-    lookup <- palmsplus %>%
+    # Rather than recalculating geometry, just lookup in whenwhat
+    lookup <- whenwhat %>%
       filter(tripnumber > 0 & triptype %in% c(1, 4)) %>%
       as.data.frame() %>%
       dplyr::select(all_of(c("identifier", "tripnumber", "triptype", names)))
diff --git a/R/build_hbGIS.R b/R/build_whenwhatwhere.R
similarity index 74%
rename from R/build_hbGIS.R
rename to R/build_whenwhatwhere.R
index 21a4794..9fdd459 100644
--- a/R/build_hbGIS.R
+++ b/R/build_whenwhatwhere.R
@@ -1,12 +1,11 @@
-
-#' Build the hbGIS dataset
+#' build_whenwhatwhere
 #'
-#' @description Build the \code{hbGIS} dataset by adding additional columns to the hbGPS output data.
-#' The additional columns are specified using \code{\link{palms_add_field}}.
+#' @description Build the whenwhat dataset by adding additional columns to the
+#'  hbGPS output data based on whenwhat_field.
 #'
 #' @param data The hbGPS data obtained using \code{read_palms} from palmplusr.
 #' @param verbose Print progress to console after each iteration. Default is \code{TRUE}.
-#' @param palmsplus_fields palmsplus_fields defined in hbGIS
+#' @param whenwhat_field whenwhat_field defined in hbGIS
 #' @param loca Nested list with location information
 #' @param participant_basis participant_basis
 #'
@@ -21,13 +20,13 @@
 #' @export
 #' 
 # Code modified from https://thets.github.io/palmsplusr/
-build_hbGIS <- function(data = NULL, verbose = TRUE, palmsplus_fields = NULL,
+build_whenwhatwhere <- function(data = NULL, verbose = TRUE, whenwhat_field = 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
-  # So, now we need to create those objects from object loca
+  # So, create those objects from object loca
   identifier = NULL
   Nlocations = length(loca)
   for (i in 1:Nlocations) {
@@ -37,8 +36,7 @@ build_hbGIS <- function(data = NULL, verbose = TRUE, palmsplus_fields = NULL,
     }
   }
   
-
-  field_args <- setNames(palmsplus_fields$formula, palmsplus_fields$name) %>%
+  field_args <- setNames(whenwhat_field$formula, whenwhat_field$name) %>%
     lapply(parse_expr)
   
   x <- list()
diff --git a/R/check_and_clean_palms_data.R b/R/check_and_clean_palms_data.R
index b258b1b..eb2ef99 100644
--- a/R/check_and_clean_palms_data.R
+++ b/R/check_and_clean_palms_data.R
@@ -41,8 +41,9 @@ check_and_clean_palms_data <- function(palms_to_clean, country_name, outputdir =
   
   # Saving the new 'clean'  dataset  - %>% ---------------------------------------
   # write_csv(palms, str_replace(link_to_csv, pattern = '.csv', '_cleaned.csv'), na = "") 
-  data.table::fwrite(error_list, paste(outputdir, country_name,"error_list.csv", sep = "_"))
-  
+  if (nrow(error_list) > 0) {
+    data.table::fwrite(error_list, paste(outputdir, country_name,"error_list.csv", sep = "_"))
+  }
   return(palms_to_clean_lower)
 }
 
diff --git a/R/hbGIS.R b/R/hbGIS.R
index d3d007e..4d72be9 100644
--- a/R/hbGIS.R
+++ b/R/hbGIS.R
@@ -1,4 +1,4 @@
-#' palmsplusr_shiny
+#' hbGIS
 #'
 #' @param gisdir Path to directory with GIS files
 #' @param palmsdir Path to hbGPS output directory
@@ -7,6 +7,11 @@
 #' @param dataset_name Name of dataset
 #' @param configfile Configuration file
 #' @param verbose verbose Boolean
+#' @param baselocation character, to specify reference location for individuals, e.g. home
+#' @param groupinglocation character, to specify reference location location for groups, e.g. school
+#' @param write_shp boolean, to indicate whether shape file should be written
+#' @param split_GIS boolean, to indicate whether sublocation inside GIS files are to be split
+#' @param sublocationID character, GIS column name to be used as identifier for sublocations
 #' @return palms_to_clean_lower object
 #' @importFrom stats end start formula as.formula
 #' @importFrom tidyr pivot_wider
@@ -22,18 +27,68 @@ hbGIS <- function(gisdir = "",
                   gislinkfile = "",
                   outputdir = "",
                   dataset_name = "",
-                  configfile = "",
-                  verbose = TRUE) {
-  # Hard code arguments that may need to become function arguments to give control to user
-  groupinglocation = "school"
-  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
-  
+                  configfile = NULL,
+                  verbose = TRUE,
+                  baselocation = NULL,
+                  groupinglocation = NULL,
+                  write_shp = NULL,
+                  split_GIS = NULL,
+                  sublocationID = NULL) {
   
+  #===============================================
+  # Load configuration and define field tables
+  #===============================================
+  if (length(configfile) > 0) {
+    # check for missing parameters, such that hbGIS can fall back on defaults
+    # here the config_pamsplusr file inside the package is assumed to hold all the defaults.
+    config_def  = system.file("testfiles_hbGIS/config_hbGIS.csv", package = "hbGIS")[1]
+    
+    params_def = load_params(file = config_def)
+    params_def$id = rownames(params_def)
+    params = load_params(file = configfile)
+    params$id = rownames(params)
+    missingPar = which(params_def$id %in% params$id == FALSE)
+    if (length(missingPar) > 0) {
+      # update the configfile as provide by the user
+      params = rbind(params, params_def[missingPar,])
+      params = params[, -which(colnames(params) == "id")]
+      update_params(new_params = params, file = configfile)
+    }
+    rm(params_def)
+    config <- configfile
+  } else {
+    # If no configfile is provided fall back on default
+    config <- system.file("testfiles_hbGIS/config_hbGIS.csv", package = "hbGIS")[1]
+  }
+  # adding fields
+  CONF = read.csv(config, sep = ",")
+  CONF$start_criteria = ""
+  CONF$end_criteria = ""
+
+  # Extract general parameters from config file if not provided as input arguments
+  if (is.null(groupinglocation)) {
+    groupinglocation =  CONF$formula[which(CONF$name == "groupinglocation")]
+  }
+  if (is.null(baselocation)) {
+    baselocation = CONF$formula[which(CONF$name == "baselocation")]
+  }
+  if (is.null(write_shp)) {
+    write_shp = CONF$formula[which(CONF$name == "write_shp")] # whether to wrist a shape file
+  }
+  if (is.null(split_GIS)) {
+    split_GIS = CONF$formula[which(CONF$name == "split_GIS")] # whether to split sublocations (TRUE) or union them
+  }
+  if (is.null(sublocationID)) {
+    sublocationID = CONF$formula[which(CONF$name == "sublocationID")]  # column name in GIS file to identify sublocation id
+  }
+  CONF = CONF[-which(CONF$context == "general"),]
+
   #------------------------------------------------------------
   lon = identifier = palms = NULL # . = was also included, but probably wrong
   
+  
+  
+  
   #===============================================
   # GIS files
   #===============================================
@@ -100,19 +155,18 @@ 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 (publiclocation == TRUE) {
+      if (publiclocation == TRUE & verbose == 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) {
+      if (nshp > 1 & split_GIS == TRUE & sublocationID %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]))
+          objectname = as.character(sf::st_drop_geometry(shp_dat[gi, sublocationID]))
           if (objectname == "NA") collect_na = c(collect_na, gi)
           loca[[gi2]][[2]] = shp_dat[gi, ]
           loca[[gi2]][[4]] = fn_4
@@ -150,55 +204,22 @@ hbGIS <- function(gisdir = "",
   #===============================================
   # hbGPS output (PALMS output)
   #===============================================
-  palmsplus_folder = paste0(outputdir, "/hbGIS_output")
-  if (!dir.exists(palmsplus_folder)) {
+  outputFolder = paste0(outputdir, "/hbGIS_output")
+  if (!dir.exists(outputFolder)) {
     if (verbose) cat("\nCreating hbGIS output directory\n")
-    dir.create(palmsplus_folder)
+    dir.create(outputFolder)
   }
   sf::sf_use_s2(FALSE)
   # identify palms csv output files in palmsdir:
-  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 (!is.null(palmsdir)) {
+    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)
+  } else {
+    palms_country_files = NULL
+  }
   if (length(palms_country_files) == 0) {
-    # Simulate hbGPS output (only for code developement purposes)
-    Nmin = 500
-    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)
-    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)
-    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)
-    tripMOT = rep(0, Nmin)
-    tripType[which(diff(tripNumber) > 0) + 1] = 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)
+    stop("\nno data found")
   }
   
   # read and combine palms csv output files 
@@ -221,80 +242,34 @@ hbGIS <- function(gisdir = "",
   PALMS_reduced$dateTime = as.POSIXct(PALMS_reduced$dateTime, format = "%d/%m/%Y %H:%M:%S", tz = "")
   
   # 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_${dataset_name}_reduced.csv")))
+  # if (substring(text = outputFolder, first = 1, last = 1) == ".") {
+  #   print("convert")
+  #   print(outputFolder)
+  #   outputFolder = gsub(pattern = "[.]", replacement = getwd(), x = outputFolder)
+  #   print(outputFolder)
+  # }
+  PALMS_reduced_file = suppressWarnings(normalizePath(paste0(outputFolder, "/", stringr::str_interp("PALMS_${dataset_name}_reduced.csv"))))
   # if (verbose) cat(paste0("\nCheck PALMS_reduced_file: ", PALMS_reduced_file))
   write.csv(palms_reduced_cleaned, PALMS_reduced_file, 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
-  #===============================================
-  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 = ""
-  }
   
-  #===============================================
-  # Load configuration and define field tables
-  #===============================================
-  if (length(configfile) > 0) {
-    # check for missing parameters, such that hbGIS can fall back on defaults
-    # here the config_pamsplusr file inside the package is assumed to hold all the defaults.
-    config_def  = system.file("testfiles_hbGIS/config_hbGIS.csv", package = "hbGIS")[1]
-    params_def = load_params(file = config_def)
-    params_def$id = rownames(params_def)
-    params = load_params(file = configfile)
-    params$id = rownames(params)
-    missingPar = which(params_def$id %in% params$id == FALSE)
-    if (length(missingPar) > 0) {
-      # update the configfile as provide by the user
-      params = rbind(params, params_def[missingPar,])
-      params = params[, -which(colnames(params) == "id")]
-      update_params(new_params = params, file = configfile)
-    }
-    rm(params_def)
-    config <- configfile
-  } else {
-    # If no configfile is provided fall back on default
-    config <- system.file("testfiles_hbGIS/config_hbGIS.csv", package = "hbGIS")[1]
-  }
   
-  # adding fields
-  CONF = read.csv(config, sep = ",")
-  CONF$start_criteria = ""
-  CONF$end_criteria = ""
   #=====================================================
   # Expand CONF with standard location based fields
   #=====================================================
   if (verbose) cat("\n<<< expand CONF...\n")
   
-  # palmsplus_domain:
+  # where_field:
   #-------------------
-  # ignore stored definition as we no longer use this
-  
-  CONF = CONF[which(CONF[,1] != "palmsplus_domain"), ] 
+  # # ignore stored definition as we no longer use this
+  # CONF = CONF[which(CONF[,1] != "where_field"), ] 
   element3 = ifelse(length(locationNames_table) > 0, yes = paste0("!", paste0("at_", locationNames_table, collapse = " & !"), " & "), no = "")
-  CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+  CONF[nrow(CONF) + 1, ] = c("where_field",
                              "transport",
                              paste0(element3, "(pedestrian | bicycle | vehicle)"),
                              TRUE, NA, "", "")
-  CONF[nrow(CONF) + 1, ] = c("palmsplus_domain",
+  CONF[nrow(CONF) + 1, ] = c("where_field",
                              "other",
                              paste0(element3, "(!pedestrian & !bicycle & !vehicle)", # removed because theorectically possible
                                     ifelse(test = length(locationNames_nbh) > 0, yes = " & ", no = ""),
@@ -306,10 +281,10 @@ hbGIS <- function(gisdir = "",
   cnt = cnt + 1
   
   for (i in 1:Nlocations) {
-    # palmsplus_domain:
+    # where_field:
     #-------------------
     if (locationNames[i] %in% locationNames_table) {
-      CONF[cnt, ] = c("palmsplus_domain",
+      CONF[cnt, ] = c("where_field",
                       locationNames[i],
                       paste0("at_", locationNames[i]), 
                       TRUE,
@@ -317,7 +292,7 @@ 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[cnt, ] = c("palmsplus_domain",
+      CONF[cnt, ] = c("where_field",
                       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
@@ -325,25 +300,25 @@ hbGIS <- function(gisdir = "",
                       NA, "", "")
     }
     cnt = cnt + 1
-    # palmsplus_field:
+    # whenwhat_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[cnt, ] = c("palmsplus_field",
+        CONF[cnt, ] = c("whenwhat_field",
                         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",
+        CONF[cnt, ] = c("whenwhat_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[cnt, ] = c("palmsplus_field",
+        CONF[cnt, ] = c("whenwhat_field",
                         paste0("at_", locationNames[i]), 
                         paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
                                locationNames[i],",", locationNames[i],
@@ -351,7 +326,7 @@ hbGIS <- function(gisdir = "",
                                locationNames[i], "_id)))"),
                         NA, "", "", "")
         cnt = cnt + 1
-        CONF[cnt, ] = c("palmsplus_field",
+        CONF[cnt, ] = c("whenwhat_field",
                         paste0("at_", locationNames[i], "_nbh"), 
                         paste0("palms_in_polygon(datai, polygons = dplyr::filter(", 
                                locationNames[i], "_nbh,", locationNames[i],
@@ -363,9 +338,9 @@ hbGIS <- function(gisdir = "",
     } else {
       # locations not in linkagefile
       # note that colSums will ensure that sublocation are combined
-      CONF[cnt, ] = c("palmsplus_field",
+      CONF[cnt, ] = c("whenwhat_field",
                       paste0("at_", locationNames[i], "_nbh"), 
-                      paste0("suppressMessages(colSums(st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
+                      paste0("suppressMessages(colSums(sf::st_contains(", locationNames[i], "_nbh, datai, sparse = FALSE)))"),
                       NA, "", "", "")
       cnt = cnt + 1
     }
@@ -391,15 +366,15 @@ hbGIS <- function(gisdir = "",
     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$formula[palmsplusr_field_rows],
-                            domain_field = CONF$domain_field[palmsplusr_field_rows])
+  whenwhat_field_rows = which(CONF$context == "whenwhat_field")
+  whenwhat_field = tibble(name = CONF$name[whenwhat_field_rows],
+                            formula = CONF$formula[whenwhat_field_rows],
+                            is_where_field = CONF$is_where_field[whenwhat_field_rows])
   
-  palmsplusr_domain_rows = which(CONF$context == "palmsplus_domain")
-  palmsplus_domains = tibble(name = CONF$name[palmsplusr_domain_rows],
-                             formula = CONF$formula[palmsplusr_domain_rows],
-                             domain_field = CONF$domain_field[palmsplusr_domain_rows])
+  where_field_rows = which(CONF$context == "where_field")
+  where_field = tibble(name = CONF$name[where_field_rows],
+                             formula = CONF$formula[where_field_rows],
+                             is_where_field = CONF$is_where_field[where_field_rows])
   #=============================
   # trajectory_fields
   trajectory_field_rows = which(CONF$context == "trajectory_field")
@@ -417,12 +392,37 @@ hbGIS <- function(gisdir = "",
   trajectory_locations = tibble(name = CONF$name[trajectory_location_rows],
                                 start_criteria = CONF$start_criteria[trajectory_location_rows],
                                 end_criteria = CONF$end_criteria[trajectory_location_rows])
+  write.csv(x = CONF[order(CONF$context), ], file = paste0(outputFolder, "/formula_log.csv"), row.names = FALSE)
+  #===============================================
+  # Load linkage file and identify which PALMS ids and home/school
+  # ids are missing, but allow for publiclocations that are not linked
+  # to an ID
+  #===============================================
+  if (length(gislinkfile) > 0) {
+    participant_basis = read_csv(gislinkfile, show_col_types = FALSE)
+    
+    
+    # Check for missing IDs -------------------------------------------------------------------------
+    withoutMissingId = check_missing_id(participant_basis, outputFolder, dataset_name, palms,
+                                        loca, groupinglocation = groupinglocation,
+                                        verbose = verbose)
+    palms = withoutMissingId$palms
+    participant_basis = withoutMissingId$participant_basis
+    loca = withoutMissingId$loca
+    write.csv(participant_basis, paste0(outputFolder, "/", 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 = ""
+  }
+  
   
   # Run palmsplusr ----------------------------------------------------------
-  fns = c(paste0(palmsplus_folder, "/", dataset_name, "_palmsplus.csv"),
-          paste0(palmsplus_folder, "/", dataset_name, "_days.csv"),
-          paste0(palmsplus_folder, "/", dataset_name, "_trajectories.csv"),
-          paste0(palmsplus_folder, "/", dataset_name, "_multimodal.csv"))
+  fns = c(paste0(outputFolder, "/", dataset_name, "_whenwhatwhere.csv"),
+          paste0(outputFolder, "/", dataset_name, "_days.csv"),
+          paste0(outputFolder, "/", dataset_name, "_trajectories.csv"),
+          paste0(outputFolder, "/", dataset_name, "_multimodal.csv"))
   for (fn in fns) {
     if (file.exists(fn)) file.remove(fn)
   }
@@ -430,26 +430,26 @@ 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) &
+  if (verbose) cat("\n<<< building whenwhatwhere...\n")
+  if (length(palms) > 0 & length(whenwhat_field) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {
     
-    palmsplus <- build_hbGIS(data = palms, 
-                             palmsplus_fields = palmsplus_fields,
+    whenwhat <- build_whenwhatwhere(data = palms, 
+                             whenwhat_field = whenwhat_field,
                              loca = loca,
                              participant_basis = participant_basis,
                              verbose = verbose)
-    write_csv(palmsplus, file = fns[1])
+    write_csv(whenwhat, file = fns[1])
     if (verbose) cat(">>>\n")
   } 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) &
+  if (length(whenwhat) > 0 & length(where_field) > 0 & length(whenwhat_field) &
       all(Nlocation_objects > 0) & length(participant_basis) > 0) {
-    days <- build_days(data = palmsplus,
-                       palmsplus_domains = palmsplus_domains,
-                       palmsplus_fields = palmsplus_fields,
+    days <- build_days(data = whenwhat,
+                       where_field = where_field,
+                       whenwhat_field = whenwhat_field,
                        loca = loca,
                        participant_basis = participant_basis,
                        verbose = verbose)
@@ -466,8 +466,8 @@ 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,
+  if (length(whenwhat) > 0 & length(trajectory_fields) > 0) {
+    trajectories <- build_trajectories(data = whenwhat,
                                        trajectory_fields = trajectory_fields,
                                        trajectory_locations = trajectory_locations)
     
@@ -478,8 +478,8 @@ hbGIS <- function(gisdir = "",
     # browser()
     if (length(trajectories) > 0) {
       write_csv(trajectories,  file = fns[3])
-      shp_file = paste0(palmsplus_folder, "/", dataset_name, "_trajectories.shp")
-      if (writeshp == TRUE) {
+      shp_file = paste0(outputFolder, "/", dataset_name, "_trajectories.shp")
+      if (write_shp == 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)
       }
@@ -492,18 +492,18 @@ hbGIS <- function(gisdir = "",
     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) {
+  if (length(whenwhat) > 0 & length(multimodal_fields) > 0 & length(trajectory_locations) > 0) {
     multimodal <- build_multimodal(data = trajectories,
                                    spatial_threshold = 200,
                                    temporal_threshold = 10,
-                                   palmsplus = palmsplus,
+                                   whenwhat = whenwhat,
                                    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")
-      if (writeshp == TRUE) {
+      shp_file = paste0(outputFolder, "/", dataset_name, "_multimodal.shp")
+      if (write_shp == 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)
       }
diff --git a/R/load_params.R b/R/load_params.R
index 3338276..53ffe8b 100644
--- a/R/load_params.R
+++ b/R/load_params.R
@@ -26,7 +26,7 @@ load_params = function(file=c()) {
   colnames(params_merged)[which(colnames(params_merged) == "formula")] = "value"
   # colnames(params_merged)[which(colnames(params_merged) == "id")] = "field"
   colnames(params_merged)[which(colnames(params_merged) == "name")] = "subfield"
-  expected_tsv_columns = c(expected_tsv_columns, "domain_field", "after_conversion")
+  expected_tsv_columns = c(expected_tsv_columns, "is_where_field", "after_conversion")
   params = params_merged[, expected_tsv_columns]
   params = params[,-which(colnames(params) %in% c("subfield", "id", "field"))]
   
diff --git a/README.md b/README.md
index e245635..e5d620f 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,58 @@
 ![GitHub Actions R-CMD-check](https://github.com/habitus-eu/hbGIS/workflows/R-CMD-check-full/badge.svg)
 
-... documentation to follow
\ No newline at end of file
+
+# hbGIS
+
+R package to analyse relationships between when, where and what behaviour takes place, by combining the output from package hbGPS (or old software library palms) and GIS files.
+The code in this packages is an adaptation of the code in the R package palmsplusr.
+In particular it has been modified to:
+- Be build as a CRAN package
+- Be used inside the Shiny app HabitusGUI
+- Be used based on a configuration file
+- Be used as a generic tool
+
+
+## Installation
+
+```
+install.packages("remotes")
+remotes::install_github("habitus-eu/hbGIS")
+```
+
+## Usage
+
+The code below shows an example of how use hbGIS.
+
+
+```
+library(hbGIS)
+hbGIS(gisdir = "D:/myproject/GIS", # path to GIS file
+      palmsdir = "D:/myproject/hbGPSoutput", # path to palms or hbGPS output folder
+      gislinkfile = "D:/myproject/Tables/participant_basis.csv", # same as palmsplusr
+      outputdir = "D:/myproject/", # path to output folder
+      dataset_name = "myproject", # dataset name 
+      configfile = "D:/myproject/config_hbGIS.csv", # hbGIS config file (see note below)
+      baselocation = "home", # base for individuals (leave empty if not available)
+      groupinglocation = "school",  # grouping for individuals (leave empty if not available)
+      write_shp = FALSE, # whether to store shape files as output
+      split_GIS = TRUE, # whether to split GIS files in sublocations (only for public places)
+      sublocationID = "ID_NR") # column name in GIS file to identify sublocation
+
+```
+
+Note:
+- GIS filenames are used as location names and at the moment the code can only handle names that are shorter than 6 characters.
+- Example config file can be found [here](https://github.com/habitus-eu/hbGIS/blob/main/inst/testfiles_hbGIS/config_hbGIS.csv)
+
+## Output
+
+hbGIS will create four output files:
+
+Name                        | Content
+----------------------------|----------------
+$datasetname_whenwhatwhere.csv | Time series with information about when what where happened
+$datasetname_days.csv           | Day level summaries
+$datasetname_trajectories.csv   | Trajectory based summaries
+$datasetname_multimodal.csv     | Breakdown of trajectories by mode of transport
+
+
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index e1938be..3feb7fa 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -5,5 +5,7 @@
   \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
+    \item Revise terminology from domains and fields to when, what, and where
+    \item Export formula log to clarify to user what formulas where used
   }
 }
diff --git a/inst/dev_code_hbGIS.R b/inst/dev_code_hbGIS.R
index ead1284..e53130f 100644
--- a/inst/dev_code_hbGIS.R
+++ b/inst/dev_code_hbGIS.R
@@ -23,24 +23,22 @@ library(lwgeom)
 #       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
+#       configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_hbGIS.csv")
 # 
 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
+                 configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010/config_hbGIS.csv")
 
 # 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_hbGIS.csv")
 jkjj
 # hbGIS(gisdir = "/media/vincent/projects/Habitus/palmsplusr/testdata/GIS",
 #                  palmsdir = "/media/vincent/projects/Habitus/palmsplusr/testdata/PALMS_output/",
diff --git a/inst/testfiles_hbGIS/config_hbGIS.csv b/inst/testfiles_hbGIS/config_hbGIS.csv
index 32a1d04..b114d55 100644
--- a/inst/testfiles_hbGIS/config_hbGIS.csv
+++ b/inst/testfiles_hbGIS/config_hbGIS.csv
@@ -1,47 +1,46 @@
-"context","name","formula","domain_field","after_conversion"
-"palmsplus_field","weekday","dow < 6",FALSE,NA
-"palmsplus_field","weekend","dow > 5",FALSE,NA
-"palmsplus_field","indoors","iov == 3",FALSE,NA
-"palmsplus_field","outdoors","iov == 1",FALSE,NA
-"palmsplus_field","in_vehicle","iov == 2",FALSE,NA
-"palmsplus_field","inserted","fixtypecode == 6",FALSE,NA
-"palmsplus_field","pedestrian","tripmot == 1",FALSE,NA
-"palmsplus_field","bicycle","tripmot == 2",FALSE,NA
-"palmsplus_field","vehicle","tripmot == 3",FALSE,NA
-"palmsplus_field","nonwear","activityintensity < 0",TRUE,NA
-"palmsplus_field","wear","activityintensity >= 0",TRUE,NA
-"palmsplus_field","sedentary","activityintensity == 0",TRUE,NA
-"palmsplus_field","light","activityintensity == 1",TRUE,NA
-"palmsplus_field","moderate","activityintensity == 2",TRUE,NA
-"palmsplus_field","vigorous","activityintensity == 3",TRUE,NA
-"palmsplus_field","mvpa","moderate + vigorous",TRUE,NA
-"trajectory_field","mot","first(tripmot)",NA,FALSE
-"trajectory_field","date","first(as.Date(datetime))",NA,FALSE
-"trajectory_field","start","datetime[triptype==1]",NA,FALSE
-"trajectory_field","end","datetime[triptype==4]",NA,FALSE
-"trajectory_field","duration","as.numeric(difftime(end, start, units = ""secs"") + 30)",NA,FALSE
-"trajectory_field","nonwear","sum(activityintensity < 0) * 15",NA,FALSE
-"trajectory_field","wear","sum(activityintensity >= 0) * 15",NA,FALSE
-"trajectory_field","sedentary","sum(activityintensity == 1) * 15",NA,FALSE
-"trajectory_field","light","sum(activityintensity == 1) * 15",NA,FALSE
-"trajectory_field","moderate","sum(activityintensity == 2) * 15",NA,FALSE
-"trajectory_field","vigorous","sum(activityintensity == 3) * 15",NA,FALSE
-"trajectory_field","mvpa","moderate + vigorous",NA,FALSE
-"trajectory_field","length","as.numeric(st_length(geometry))",NA,TRUE
-"trajectory_field","speed","(length / duration) * 3.6",NA,TRUE
-"multimodal_field","duration","sum",NA,NA
-"multimodal_field","nonwear","sum",NA,NA
-"multimodal_field","wear","sum",NA,NA
-"multimodal_field","sedentary","sum",NA,NA
-"multimodal_field","light","sum",NA,NA
-"multimodal_field","moderate","sum",NA,NA
-"multimodal_field","vigorous","sum",NA,NA
-"multimodal_field","mvpa","sum",NA,NA
-"multimodal_field","length","sum",NA,NA
-"multimodal_field","speed","mean",NA,NA
-"palmsplus_domain","home","at_home",TRUE,NA
-"palmsplus_domain","school","(!at_home & at_school)",TRUE,NA
-"palmsplus_domain","transport","!at_home & !(at_school) & (pedestrian | bicycle | vehicle)",TRUE,NA
-"palmsplus_domain","home_nbh","!at_home & !(at_school) & (!pedestrian & !bicycle & !vehicle) & at_home_nbh",TRUE,NA
-"palmsplus_domain","school_nbh","!at_home & !(at_school) & (!pedestrian & !bicycle & !vehicle) &  !(at_home_nbh) & at_school_nbh",TRUE,NA
-"palmsplus_domain","other","!at_home & !(at_school) & (!pedestrian & !bicycle & !vehicle) & !(at_home_nbh) & !(at_school_nbh)",TRUE,NA
+context,name,formula,is_where_field,after_conversion
+whenwhat_field,weekday,dow < 6,FALSE,NA
+whenwhat_field,weekend,dow > 5,FALSE,NA
+whenwhat_field,indoors,iov == 3,FALSE,NA
+whenwhat_field,outdoors,iov == 1,FALSE,NA
+whenwhat_field,in_vehicle,iov == 2,FALSE,NA
+whenwhat_field,inserted,fixtypecode == 6,FALSE,NA
+whenwhat_field,pedestrian,tripmot == 1,FALSE,NA
+whenwhat_field,bicycle,tripmot == 2,FALSE,NA
+whenwhat_field,vehicle,tripmot == 3,FALSE,NA
+whenwhat_field,nonwear,activityintensity < 0,TRUE,NA
+whenwhat_field,wear,activityintensity >= 0,TRUE,NA
+whenwhat_field,sedentary,activityintensity == 0,TRUE,NA
+whenwhat_field,light,activityintensity == 1,TRUE,NA
+whenwhat_field,moderate,activityintensity == 2,TRUE,NA
+whenwhat_field,vigorous,activityintensity == 3,TRUE,NA
+whenwhat_field,mvpa,moderate + vigorous,TRUE,NA
+trajectory_field,mot,first(tripmot),NA,FALSE
+trajectory_field,date,first(as.Date(datetime)),NA,FALSE
+trajectory_field,start,datetime[triptype==1],NA,FALSE
+trajectory_field,end,datetime[triptype==4],NA,FALSE
+trajectory_field,duration,"as.numeric(difftime(end, start, units = ""secs"") + 30)",NA,FALSE
+trajectory_field,nonwear,sum(activityintensity < 0) * 15,NA,FALSE
+trajectory_field,wear,sum(activityintensity >= 0) * 15,NA,FALSE
+trajectory_field,sedentary,sum(activityintensity == 1) * 15,NA,FALSE
+trajectory_field,light,sum(activityintensity == 1) * 15,NA,FALSE
+trajectory_field,moderate,sum(activityintensity == 2) * 15,NA,FALSE
+trajectory_field,vigorous,sum(activityintensity == 3) * 15,NA,FALSE
+trajectory_field,mvpa,moderate + vigorous,NA,FALSE
+trajectory_field,length,as.numeric(st_length(geometry)),NA,TRUE
+trajectory_field,speed,(length / duration) * 3.6,NA,TRUE
+multimodal_field,duration,sum,NA,NA
+multimodal_field,nonwear,sum,NA,NA
+multimodal_field,wear,sum,NA,NA
+multimodal_field,sedentary,sum,NA,NA
+multimodal_field,light,sum,NA,NA
+multimodal_field,moderate,sum,NA,NA
+multimodal_field,vigorous,sum,NA,NA
+multimodal_field,mvpa,sum,NA,NA
+multimodal_field,length,sum,NA,NA
+multimodal_field,speed,mean,NA,NA
+general,groupinglocation,school,NA,NA
+general,baselocation,home,NA,NA
+general,write_shp,FALSE,NA,NA
+general,split_GIS,TRUE,NA,NA
+general,sublocationID,OBJECTID,NA,NA
diff --git a/inst/testfiles_hbGIS/loc_park.CPG b/inst/testfiles_hbGIS/loc_park.CPG
new file mode 100644
index 0000000..3ad133c
--- /dev/null
+++ b/inst/testfiles_hbGIS/loc_park.CPG
@@ -0,0 +1 @@
+UTF-8
\ No newline at end of file
diff --git a/inst/testfiles_hbGIS/loc_park.dbf b/inst/testfiles_hbGIS/loc_park.dbf
new file mode 100644
index 0000000..13dfe5b
Binary files /dev/null and b/inst/testfiles_hbGIS/loc_park.dbf differ
diff --git a/inst/testfiles_hbGIS/loc_park.prj b/inst/testfiles_hbGIS/loc_park.prj
new file mode 100644
index 0000000..f45cbad
--- /dev/null
+++ b/inst/testfiles_hbGIS/loc_park.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
\ No newline at end of file
diff --git a/inst/testfiles_hbGIS/loc_park.sbn b/inst/testfiles_hbGIS/loc_park.sbn
new file mode 100644
index 0000000..22ad9f3
Binary files /dev/null and b/inst/testfiles_hbGIS/loc_park.sbn differ
diff --git a/inst/testfiles_hbGIS/loc_park.sbx b/inst/testfiles_hbGIS/loc_park.sbx
new file mode 100644
index 0000000..28c40df
Binary files /dev/null and b/inst/testfiles_hbGIS/loc_park.sbx differ
diff --git a/inst/testfiles_hbGIS/loc_park.shp b/inst/testfiles_hbGIS/loc_park.shp
new file mode 100644
index 0000000..b9a4cd1
Binary files /dev/null and b/inst/testfiles_hbGIS/loc_park.shp differ
diff --git a/inst/testfiles_hbGIS/loc_park.shx b/inst/testfiles_hbGIS/loc_park.shx
new file mode 100644
index 0000000..0f98733
Binary files /dev/null and b/inst/testfiles_hbGIS/loc_park.shx differ
diff --git a/inst/testfiles_hbGIS/params_description_hbGIS.tsv b/inst/testfiles_hbGIS/params_description_hbGIS.tsv
index 73f1211..eac75b2 100644
--- a/inst/testfiles_hbGIS/params_description_hbGIS.tsv
+++ b/inst/testfiles_hbGIS/params_description_hbGIS.tsv
@@ -1,24 +1,24 @@
 parameter	field	subfield	display	class	minimum	maximum	set	priority	description
-weekday	palmsplus_field		TRUE	formula				0	description missing
-weekend	palmsplus_field		TRUE	formula				0	description missing
-indoors	palmsplus_field		TRUE	formula				0	description missing
-outdoors	palmsplus_field		TRUE	formula				0	description missing
-in_vehicle	palmsplus_field		TRUE	formula				0	description missing
-inserted	palmsplus_field		TRUE	formula				0	description missing
-pedestrian	palmsplus_field		TRUE	formula				0	description missing
-bicycle	palmsplus_field		TRUE	formula				0	description missing
-vehicle	palmsplus_field		TRUE	formula				0	description missing
-nonwear	palmsplus_field		TRUE	formula				0	description missing
-wear	palmsplus_field		TRUE	formula				0	description missing
-sedentary	palmsplus_field		TRUE	formula				0	description missing
-light	palmsplus_field		TRUE	formula				0	description missing
-moderate	palmsplus_field		TRUE	formula				0	description missing
-vigorous	palmsplus_field		TRUE	formula				0	description missing
-mvpa	palmsplus_field		TRUE	formula				0	description missing
-at_home	palmsplus_field		TRUE	formula				0	description missing
-at_school	palmsplus_field		TRUE	formula				0	description missing
-at_home_nbh	palmsplus_field		TRUE	formula				0	description missing
-at_school_nbh	palmsplus_field		TRUE	formula				0	description missing
+weekday	whenwhat_field		TRUE	formula				0	description missing
+weekend	whenwhat_field		TRUE	formula				0	description missing
+indoors	whenwhat_field		TRUE	formula				0	description missing
+outdoors	whenwhat_field		TRUE	formula				0	description missing
+in_vehicle	whenwhat_field		TRUE	formula				0	description missing
+inserted	whenwhat_field		TRUE	formula				0	description missing
+pedestrian	whenwhat_field		TRUE	formula				0	description missing
+bicycle	whenwhat_field		TRUE	formula				0	description missing
+vehicle	whenwhat_field		TRUE	formula				0	description missing
+nonwear	whenwhat_field		TRUE	formula				0	description missing
+wear	whenwhat_field		TRUE	formula				0	description missing
+sedentary	whenwhat_field		TRUE	formula				0	description missing
+light	whenwhat_field		TRUE	formula				0	description missing
+moderate	whenwhat_field		TRUE	formula				0	description missing
+vigorous	whenwhat_field		TRUE	formula				0	description missing
+mvpa	whenwhat_field		TRUE	formula				0	description missing
+at_home	whenwhat_field		TRUE	formula				0	description missing
+at_school	whenwhat_field		TRUE	formula				0	description missing
+at_home_nbh	whenwhat_field		TRUE	formula				0	description missing
+at_school_nbh	whenwhat_field		TRUE	formula				0	description missing
 mot	trajectory_field		TRUE	formula				0	description missing
 date	trajectory_field		TRUE	formula				0	description missing
 start	trajectory_field		TRUE	formula				0	description missing
@@ -47,9 +47,8 @@ vigorous	multimodal_field		TRUE	formula				0	description missing
 mvpa	multimodal_field		TRUE	formula				0	description missing
 length	multimodal_field		TRUE	formula				0	description missing
 speed	multimodal_field		TRUE	formula				0	description missing
-home	palmsplus_domain		TRUE	formula				0	description missing
-school	palmsplus_domain		TRUE	formula				0	description missing
-transport	palmsplus_domain		TRUE	formula				0	description missing
-home_nbh	palmsplus_domain		TRUE	formula				0	description missing
-school_nbh	palmsplus_domain		TRUE	formula				0	description missing
-other	palmsplus_domain		TRUE	formula				0	description missing
+groupinglocation	general		TRUE	character				0	description missing
+baselocation	general		TRUE	character				0	description missing
+write_shp	general		TRUE	set			TRUE;FALSE	0	description missing
+split_GIS	general		TRUE	set			TRUE;FALSE	0	description missing
+sublocationID	general		TRUE	character				0	description missing
diff --git a/man/build_days.Rd b/man/build_days.Rd
index d977381..d71ef80 100644
--- a/man/build_days.Rd
+++ b/man/build_days.Rd
@@ -2,42 +2,35 @@
 % Please edit documentation in R/build_days.R
 \name{build_days}
 \alias{build_days}
-\title{Calculate day-level summaries from the palmsplus dataset}
+\title{Calculate day-level summaries from the whenwhat dataset}
 \usage{
 build_days(
   data = NULL,
   verbose = TRUE,
-  palmsplus_domains = NULL,
-  palmsplus_fields = NULL,
+  where_field = NULL,
+  whenwhat_field = NULL,
   loca = NULL,
   participant_basis = NULL
 )
 }
 \arguments{
-\item{data}{The palmsplus data obtained from \code{\link{palms_build_palmsplus}}.}
+\item{data}{The whenwhat data obtained from \code{\link{build_whenwhatwhere}}.}
 
 \item{verbose}{Print progress to console. Default is \code{TRUE}.}
 
-\item{palmsplus_domains}{...}
+\item{where_field}{...}
 
-\item{palmsplus_fields}{...}
+\item{whenwhat_field}{...}
 
 \item{loca}{Nested list with location information}
 
-\item{participant_basis}{participant_basis}
+\item{participant_basis}{participant_basis
+#'}
 }
 \value{
 A table summarised by day.
 }
 \description{
-Build a days dataset by summarising \code{palmsplus}
-by day and person (\code{identifier}). Not all variables in \code{palmsplus}
-are summarised, only those specified using \code{\link{palms_add_field}} with
-the argument \code{domain_field = TRUE}. By default, a \code{duration} field
-is added (e.g., the total minutes per day).
-
-All data are summarised by default. However, additional aggragation \emph{domains}
-can be specified using \code{\link{palms_add_domain}} before building days.
-Domains are a subset of data, such as during school time. All \code{domain_field}
-variables will be summarised for each \emph{domain} seperatly.
+Build a days dataset by summarising \code{whenwhat}
+by day and person (\code{identifier}).
 }
diff --git a/man/build_multimodal.Rd b/man/build_multimodal.Rd
index cfc362c..2afee10 100644
--- a/man/build_multimodal.Rd
+++ b/man/build_multimodal.Rd
@@ -8,7 +8,7 @@ build_multimodal(
   data = NULL,
   spatial_threshold,
   temporal_threshold,
-  palmsplus = NULL,
+  whenwhat = NULL,
   verbose = TRUE,
   multimodal_fields = NULL,
   trajectory_locations = NULL
@@ -21,7 +21,7 @@ build_multimodal(
 
 \item{temporal_threshold}{Temporal threshold in minutes}
 
-\item{palmsplus}{The dataset build by \code{build_hbGIS}}
+\item{whenwhat}{The dataset build by \code{build_hbGIS}}
 
 \item{verbose}{Print progress after each step. Default is \code{TRUE}.}
 
diff --git a/man/build_hbGIS.Rd b/man/build_whenwhatwhere.Rd
similarity index 53%
rename from man/build_hbGIS.Rd
rename to man/build_whenwhatwhere.Rd
index 7863652..f997f1b 100644
--- a/man/build_hbGIS.Rd
+++ b/man/build_whenwhatwhere.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/build_hbGIS.R
-\name{build_hbGIS}
-\alias{build_hbGIS}
-\title{Build the hbGIS dataset}
+% Please edit documentation in R/build_whenwhatwhere.R
+\name{build_whenwhatwhere}
+\alias{build_whenwhatwhere}
+\title{build_whenwhatwhere}
 \usage{
-build_hbGIS(
+build_whenwhatwhere(
   data = NULL,
   verbose = TRUE,
-  palmsplus_fields = NULL,
+  whenwhat_field = NULL,
   loca = NULL,
   participant_basis = NULL
 )
@@ -17,13 +17,13 @@ build_hbGIS(
 
 \item{verbose}{Print progress to console after each iteration. Default is \code{TRUE}.}
 
-\item{palmsplus_fields}{palmsplus_fields defined in hbGIS}
+\item{whenwhat_field}{whenwhat_field defined in hbGIS}
 
 \item{loca}{Nested list with location information}
 
 \item{participant_basis}{participant_basis}
 }
 \description{
-Build the \code{hbGIS} dataset by adding additional columns to the hbGPS output data.
-The additional columns are specified using \code{\link{palms_add_field}}.
+Build the whenwhat dataset by adding additional columns to the
+hbGPS output data based on whenwhat_field.
 }
diff --git a/man/hbGIS.Rd b/man/hbGIS.Rd
index 5fa9459..b9eee7b 100644
--- a/man/hbGIS.Rd
+++ b/man/hbGIS.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/hbGIS.R
 \name{hbGIS}
 \alias{hbGIS}
-\title{palmsplusr_shiny}
+\title{hbGIS}
 \usage{
 hbGIS(
   gisdir = "",
@@ -10,8 +10,13 @@ hbGIS(
   gislinkfile = "",
   outputdir = "",
   dataset_name = "",
-  configfile = "",
-  verbose = TRUE
+  configfile = NULL,
+  verbose = TRUE,
+  baselocation = NULL,
+  groupinglocation = NULL,
+  write_shp = NULL,
+  split_GIS = NULL,
+  sublocationID = NULL
 )
 }
 \arguments{
@@ -28,10 +33,20 @@ hbGIS(
 \item{configfile}{Configuration file}
 
 \item{verbose}{verbose Boolean}
+
+\item{baselocation}{character, to specify reference location for individuals, e.g. home}
+
+\item{groupinglocation}{character, to specify reference location location for groups, e.g. school}
+
+\item{write_shp}{boolean, to indicate whether shape file should be written}
+
+\item{split_GIS}{boolean, to indicate whether sublocation inside GIS files are to be split}
+
+\item{sublocationID}{character, GIS column name to be used as identifier for sublocations}
 }
 \value{
 palms_to_clean_lower object
 }
 \description{
-palmsplusr_shiny
+hbGIS
 }
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..a7f999e
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,3 @@
+library("testthat")
+library("hbGIS")
+test_check("hbGIS")
\ No newline at end of file
diff --git a/tests/testthat/test_hbGIS.R b/tests/testthat/test_hbGIS.R
new file mode 100644
index 0000000..3a2b105
--- /dev/null
+++ b/tests/testthat/test_hbGIS.R
@@ -0,0 +1,81 @@
+library(hbGIS)
+context("hbGIS pipeline")
+test_that("hbGIS pipeline process file", {
+  # 
+  # # Prepare input data
+  # GIS_files  = dir(system.file("testfiles_hbGIS", package = "hbGIS"), full.names = TRUE, pattern = "loc_")
+  # dn1 = "./GIS"
+  # if (!dir.exists(dn1)) {
+  #   dir.create(dn1, recursive = TRUE)
+  # }
+  # for (fn in GIS_files) file.copy(from = fn, to = dn1)
+  # 
+  # hbGPSoutput_file  = system.file("testfiles_hbGIS/hbGPS_out.csv", package = "hbGIS")
+  # dn2 = "./hbGPSoutput"
+  # if (!dir.exists(paths = dn2)) {
+  #   dir.create(path = dn2)
+  # }
+  # file.copy(from = hbGPSoutput_file, to = dn2)
+  # 
+  # # Prepare output folder
+  # outdir = "./output"
+  # if (!dir.exists(outdir)) {
+  #   dir.create(outdir, recursive = TRUE)
+  # }
+  # 
+  # # Run pipeline
+  # hbGIS(gisdir = "./GIS",
+  #       palmsdir = dn2, # note: function will simulat palms data if palmsdir not provided
+  #       gislinkfile = NULL,
+  #       outputdir = outdir,
+  #       dataset_name = "test",
+  #       verbose = FALSE,
+  #       sublocationID = "ignore")
+  # 
+  # # Check days
+  # file = paste0(outdir, "/hbGIS_output/test_days.csv")
+  # expect_true(file.exists(file))
+  # test_days = read.csv(file)
+  # expect_equal(length(test_days), 37)
+  # expect_equal(sum(test_days[, 3:ncol(test_days)], na.rm = TRUE), 24573.25)
+  # 
+  # # Check whenwhatwhere
+  # file = paste0(outdir, "/hbGIS_output/test_whenwhatwhere.csv")
+  # expect_true(file.exists(file))
+  # test_whenwhatwhere = read.csv(file)
+  # expect_equal(nrow(test_whenwhatwhere), 21523)
+  # expect_equal(ncol(test_whenwhatwhere), 30)
+  # expect_equal(sum(test_whenwhatwhere[, 3:(ncol(test_whenwhatwhere) - 1)]), 558765.2)
+  # 
+  # # Check trajectories
+  # file = paste0(outdir, "/hbGIS_output/test_trajectories.csv")
+  # expect_true(file.exists(file))
+  # test_trajectories = read.csv(file)
+  # expect_equal(nrow(test_trajectories), 50)
+  # expect_equal(ncol(test_trajectories), 18)
+  # expect_equal(sum(test_trajectories$length), 21993.49, tol = 0.1)
+  # expect_equal(sum(test_trajectories$speed), 212.9411, tol = 0.001)
+  # 
+  # 
+  # # Check multimodal
+  # file = paste0(outdir, "/hbGIS_output/test_multimodal.csv")
+  # expect_true(file.exists(file))
+  # test_multimodal = read.csv(file)
+  # expect_equal(nrow(test_multimodal), 2)
+  # expect_equal(ncol(test_multimodal), 31)
+  # expect_equal(test_multimodal$trip_numbers, c(1, 2))
+  # expect_equal(test_multimodal$start, c("2023-11-30T13:50:00Z", "2023-11-30T14:25:00Z"))
+  # expect_equal(test_multimodal$end, c("2023-11-30T13:54:00Z", "2023-11-30T14:29:00Z"))
+  # 
+  # # Check formula_log
+  # file = paste0(outdir, "/hbGIS_output/formula_log.csv")
+  # expect_true(file.exists(file))
+  # test_formula_log = read.csv(file)
+  # expect_equal(nrow(test_formula_log), 45)
+  # expect_equal(ncol(test_formula_log), 7)
+  # 
+  # # Clean up
+  # if (dir.exists(dn))  unlink(dn, recursive = TRUE)
+  # if (dir.exists(outdir))  unlink(outdir, recursive = TRUE)
+  # if (file.exists("./output_test_error_list.csv")) file.remove("./output_test_error_list.csv")
+})