Merge branch 'dev'

Author: gertjanssenswillen

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: processmapR
 Type: Package
 Title: Construct Process Maps Using Event Data
-Version: 0.5.5
+Version: 0.5.7
 Authors@R: c(person("Gert","Janssenswillen",email = "gert.janssenswillen@uhasselt.be", role = c("aut","cre")),
  person("Gerard","van Hulzen", email = "gerard.vanhulzen@uhasselt.be", role = c("ctb")),
  person("Benoît","Depaire",email = "benoit.depaire@uhasselt.be", role = c("ctb")),
@@ -39,7 +39,7 @@ Imports:
     lifecycle,
     htmlwidgets
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -69,6 +69,7 @@ importFrom(data.table,data.table)
 importFrom(data.table,dcast.data.table)
 importFrom(data.table,setnames)
 importFrom(data.table,setorder)
+importFrom(dplyr,"%>%")
 importFrom(glue,glue)
 importFrom(hms,as_hms)
 importFrom(lifecycle,deprecated)

R/precedence_matrix.plot.R

@@ -26,7 +26,7 @@ plot.process_matrix <- function(x, ...) {
 
 			x %>%
 				ggplot(aes(antecedent, consequent)) +
-				geom_raster(aes(fill = n)) +
+				geom_tile(aes(fill = n)) +
 				geom_text(aes(label = n), color = "white", fontface = "bold")  +
 				scale_fill_continuous_bupaR(name = "Absolute Frequency") +
 				coord_flip() +
@@ -39,7 +39,7 @@ plot.process_matrix <- function(x, ...) {
 		} else if(type == "relative") {
 			x %>%
 				ggplot(aes(antecedent, consequent)) +
-				geom_raster(aes(fill = rel_n)) +
+				geom_tile(aes(fill = rel_n)) +
 				geom_text(aes(label = round(rel_n*100, 2)), color = "white", fontface = "bold") +
 				scale_fill_continuous_bupaR(name = "Relative Frequency") +
 				theme_light() +
@@ -107,7 +107,7 @@ plot.process_matrix <- function(x, ...) {
 		x %>%
 			filter(antecedent != "Start", consequent != "End") %>%
 			ggplot(aes(antecedent, consequent)) +
-			geom_raster(aes(fill = flow_time)) +
+			geom_tile(aes(fill = flow_time)) +
 			geom_text(aes(label =round(flow_time, 2)), color = "white", fontface = "bold") +
 			scale_fill_continuous_bupaR(name = paste0("Flow time in ", attr(type, "units")), palette = "orange") +
 			theme_light() +

R/process_map.R

@@ -162,29 +162,37 @@ process_map.eventlog <- function(log,
 			as.data.frame() -> base_log
 	}
 
-	#create end points for graph
-
-	base_log %>%
-		group_by(CASE_CLASSIFIER_) %>%
-		arrange(start_time, min_order) -> points_temp
-
-	points_temp %>%
-		slice(1) %>%
-		mutate(ACTIVITY_CLASSIFIER_ = "ARTIFICIAL_START",
-			   end_time = start_time,
-			   min_order = -Inf) -> end_points_start
-	points_temp %>%
-		slice(n()) %>%
-		mutate(ACTIVITY_CLASSIFIER_ = "ARTIFICIAL_END",
-			   start_time = end_time,
-			   min_order = Inf) -> end_points_end
+	#create end points for graph using data.table slicing
+	dt <- as.data.table(base_log)
+	#set correct ordering within groups
+	data.table::setorder(dt, CASE_CLASSIFIER_, start_time, min_order, na.last=TRUE)
+	#specifying order of columns to reorder end_points_start and end_points_end 
+	colorder <- c('ACTIVITY_CLASSIFIER_', 'ACTIVITY_INSTANCE_CLASSIFIER_', 'CASE_CLASSIFIER_', 'start_time', 'end_time', 'min_order')
+	
+	end_points_start <- dt[, .SD[1], by = CASE_CLASSIFIER_]
+	end_points_start[, min_order := as.numeric(min_order)] #prevents warning when setting value to -Inf
+	end_points_start[, `:=`(ACTIVITY_CLASSIFIER_ = "ARTIFICIAL_START",
+							end_time = start_time,
+							min_order = -Inf)]
+	data.table::setcolorder(end_points_start, colorder)
+
+	end_points_end <- dt[, .SD[.N], by = CASE_CLASSIFIER_]
+	end_points_end[, min_order := as.numeric(min_order)] #prevents warning when setting value to Inf
+	end_points_end[, `:=`(ACTIVITY_CLASSIFIER_ = "ARTIFICIAL_END",
+						  start_time = end_time,
+						  min_order = Inf)]
+	data.table::setcolorder(end_points_end, colorder)
 
 	#add endpoints to base log
 
 	suppressWarnings(
 		bind_rows(end_points_start, end_points_end, base_log) %>%
 			ungroup() -> base_log
 	)
+	
+	#converting ACTIVITY_CLASSIFIER_ to character to keep `base_log` identical to the previous dplyr method
+	base_log <- base_log %>%
+				mutate(ACTIVITY_CLASSIFIER_ = as.character(ACTIVITY_CLASSIFIER_))
 
 	#create base nodes list
 

R/processmapR.R

@@ -2,7 +2,7 @@
 #'
 #' @description This package provides several useful techniques process visualization.
 #'
-#' @docType package
+# @docType package
 #' @name processmapR
 #'
 #' @import dplyr

R/trace_explorer.R

@@ -2,8 +2,8 @@
 #'
 #' @description
 #' Different activity sequences in the `log` can be visualized with [`trace_explorer()`]. With the `type` argument,
-#' it can be used to explore frequent as well as infrequent traces. The `coverage` argument specificies how much of the
-#' `log` you want to explore. By default it is set at `0.2`, meaning that it will show the most (in)frequency traces
+#' it can be used to explore frequent as well as infrequent traces. The `coverage` argument specifies how much of the
+#' `log` you want to explore. By default it is set at `0.2`, meaning that it will show the most (in)frequent traces
 #' covering 20% of the `log`.
 #'
 #' @param log [`log`][`bupaR::log`]: Object of class [`log`][`bupaR::log`] or derivatives ([`eventlog`][`bupaR::eventlog`]
@@ -89,7 +89,7 @@ trace_explorer.eventlog <- function(log,
                   "x" = "You supplied a {.cls {class(coverage)}}: {.val {coverage}}"))
   } else if(is.null(coverage)) {
     if(n_traces <= 0 || !is_integerish(n_traces, n = 1))
-      cli_abort(c("{.arg n_traces} must be an interger-like {.cls numeric} larger than {.val {0}}.",
+      cli_abort(c("{.arg n_traces} must be an integer-like {.cls numeric} larger than {.val {0}}.",
                   "x" = "You supplied a {.cls {class(n_traces)}}: {.val {n_traces}}"))
   }
 

README.Rmd

@@ -19,7 +19,7 @@ options(tibble.print_min = 5, tibble.print_max = 5)
 
 <!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/processmapR)](https://CRAN.R-project.org/package=processmapR)
-[![GitHub version](https://img.shields.io/badge/GitHub-0.5.4-blue)](https://github.com/bupaverse/processmapR)
+[![GitHub version](https://img.shields.io/badge/GitHub-0.5.7-blue)](https://github.com/bupaverse/processmapR)
 [![R-CMD-check](https://github.com/bupaverse/processmapR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bupaverse/processmapR/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/bupaverse/processmapR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bupaverse/processmapR?branch=master)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

README.md

@@ -8,7 +8,7 @@
 [![CRAN
 status](https://www.r-pkg.org/badges/version/processmapR)](https://CRAN.R-project.org/package=processmapR)
 [![GitHub
-version](https://img.shields.io/badge/GitHub-0.5.4-blue)](https://github.com/bupaverse/processmapR)
+version](https://img.shields.io/badge/GitHub-0.5.7-blue)](https://github.com/bupaverse/processmapR)
 [![R-CMD-check](https://github.com/bupaverse/processmapR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bupaverse/processmapR/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/bupaverse/processmapR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bupaverse/processmapR?branch=master)
 [![Lifecycle:
@@ -63,7 +63,6 @@ library(bupaR)
 # Process map
 patients %>%
   process_map()
-#> PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
 ```
 
 <figure>