Merge pull request #9 from habitus-eu/issue3_prepare_first_release

Prepare first release

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",

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)

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)) {

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)))

R/build_hbGIS.R → 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()

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)
 }