Merge branch '0.2.0-beta1'

.gitignore

@@ -35,4 +35,6 @@ network.xml.gz
 analysis_berlin10/
 kelheim/
 test/
+dashboard_test/
 .sentinel*
+inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: matsim
 Type: Package
 Title: R library for interfacing with MATSim agent-based microsimulation model
-Version: 0.1.9
+Version: 0.2.0
 Authors@R: c(
   person("Billy", "Charlton", email = "[email protected]", role=c("aut","cre")),
   person("Oleksandr", "Soboliev", role="aut"))
@@ -11,10 +11,10 @@ Description: MATSim support package for R
     of the Python matsim-tools package, and thus supports reading standard 
     MATSim networks and soon, plans and events as well. 
  .
-           Developed with support from the Technische Universität Berlin's
+              Developed with support from the Technische Universität Berlin's
     VSP Transport Planning and Transport Telematics department. 
  .
-           This project is under ongoing development and submissions are welcome!
+              This project is under ongoing development and submissions are welcome!
 License: GPL (>= 3)
 Encoding: UTF-8
 Imports: 
@@ -42,5 +42,8 @@ URL: https://github.com/matsim-vsp/matsim-r
 BugReports: https://github.com/matsim-vsp/matsim-r/issues
 RoxygenNote: 7.2.3
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+VignetteBuilder: knitr

Makefile

@@ -29,4 +29,5 @@ docs: .sentinel-make-docs
 clean:
 > rm -rf docs
 > rm -rf man
+> rm .sentinel*
 .PHONY: clean

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(appendDistanceCategory)
 export(boxplotScoreDifferences)
 export(compareAverageTravelWait)
 export(compareBasePolicyOutput)
@@ -11,7 +12,6 @@ export(deriveODMatrix)
 export(filterByRegion)
 export(generateXYHexagonYaml)
 export(getCrsFromConfig)
-export(loadNetwork)
 export(mergeCountsAndLinks)
 export(plotActivityEndTimes)
 export(plotArrivalTimesPerTripPurpose)
@@ -29,33 +29,68 @@ export(plotTripCountByDepTime)
 export(plotTripDistanceByMode)
 export(plotTripDistancedByType)
 export(plotTripTypesPieChart)
+export(plot_arrtime_by_act)
+export(plot_compare_count_by_spatialcat_barchart)
+export(plot_compare_distcat_by_mainmode_barchart)
+export(plot_compare_mainmode_barchart)
+export(plot_compare_mainmode_sankey)
+export(plot_compare_score_boxplot)
+export(plot_compare_travelwaittime_by_mainmode)
+export(plot_compare_travelwaittime_by_mainmode_barchart)
+export(plot_deptime_by_act)
+export(plot_distance_by_mainmode_barchart)
+export(plot_distance_by_spatialcat_barchart)
+export(plot_distcat_by_mainmode_barchart)
+export(plot_mainmode_barchart)
+export(plot_mainmode_piechart)
+export(plot_map_trips)
+export(plot_map_trips_by_spatialcat)
+export(plot_spatialtype_by_shape_piechart)
+export(plot_travelwaittime_mean_barchart)
+export(plot_trips_count_by_deptime_and_mainmode_linechart)
 export(prepareComparisonSimwrapperDashboardFromTable)
 export(prepareSimwrapperDashboardFromFolder)
 export(prepareSimwrapperDashboardFromTable)
 export(processDtvEstimationQuality)
 export(processLinkStatsDtvDistribution)
+export(process_append_distcat)
+export(process_append_spatialcat)
+export(process_convert_table_to_sf)
+export(process_convert_time)
+export(process_filter_by_shape)
+export(process_get_crs_from_config)
+export(process_get_mainmode_distribution)
+export(process_get_od_matrix)
+export(process_get_travdistance_distribution)
+export(process_get_travelwaittime_by_mainmode)
+export(process_rename_category)
+export(process_rename_mainmodes)
 export(readCounts)
 export(readLinkStats)
 export(readPersonsTable)
 export(readTripsTable)
+export(read_config)
+export(read_network)
+export(read_output_persons)
+export(read_output_trips)
 export(symlog_trans)
 export(transformToSf)
 import(dplyr)
 import(forcats)
 import(geomtextpath)
 import(ggalluvial)
-import(ggplot2)
+import(ggplot2, except = last_plot)
 import(ggrepel)
 import(htmltools)
 import(leaflet)
 import(lubridate)
 import(plotly)
 import(purrr)
 import(readr)
-import(reshape)
-import(scales)
+import(reshape, except = c(stamp,rename,expand))
+import(scales, except = c(discard, col_factor))
 import(sf)
-import(tidyr)
+import(tidyr, except = expand)
 import(tidyverse)
 import(xml2)
 import(yaml)

R/config.R

@@ -0,0 +1,42 @@
+#' Load MATSIM config file into Memory
+#'
+#' Loads a MATSim xml config from file or archive,
+#' creating a list with parameters as in xml file
+#'
+#' @param input_path character string, path to matsim output directory or http link to the file.
+#' @param n_max integer, maximum number of lines to read within output_trips
+#' @return tibble of trips_output
+#'
+#' @export
+read_config <- function(input_path = ".", n_max = Inf) {
+
+  result_tibble <- tibble(module = character(),
+                          param = character(),
+                          value = character())
+
+  config_xml<-read_xml(input_path)
+
+  module_nodeset<-xml_children(config_xml)
+
+  result_list <- list()
+
+  for(i in 1:length(module_nodeset)){
+    module_name = xml_attr(module_nodeset[[i]],"name")
+
+    param_nodeset = xml_children(module_nodeset[[i]])
+    for(j in 1:length(param_nodeset)){
+      param_name<-xml_attr(param_nodeset[[j]],"name")
+      value_name<-xml_attr(param_nodeset[[j]],"value")
+      #print(param_name,value_name)
+
+      result_list[[module_name]][[param_name]] <- value_name
+
+
+    }
+
+  }
+
+  return(result_list)
+
+
+}

R/counts.R

@@ -1,5 +1,5 @@
 #'@import tidyverse
-#'@import scales
+#' @rawNamespace import(scales, except = c(discard, col_factor))
 #'@import xml2
 #'@import geomtextpath
 #'@import readr
@@ -8,12 +8,12 @@
 #'
 #'@title Load a MATSim Counts file into memory
 #'
-#'@description Loads a MATSim Counts XML-File as tibble into memory
+#'@description Loads a MATSim Counts XML-file as tibble into memory
 #'
 #'
 #'@param file File to load. Must be an .xml file
 #'
-#'@return tibble containing with MATSim Link id as "loc_id" as key
+#'@return tibble with MATSim link id ("loc_id") as key
 #'
 #'@export
 readCounts <- function(file){
@@ -51,11 +51,11 @@ readCounts <- function(file){
   result
 }
 
-#' Load linkstats as tibble into memory
+#' Load a MATSim linkstats file into memory
 #'
-#' Reads Linkstats as .tsv created from LinkStats.class
-#' as dataframe into memory.
-#' Counts can be provided in any time bins.
+#' Loads a linkstats tsv file created from the LinkStats class
+#' as a dataframe into memory.
+#' Counts can be provided in any time bin.
 #' Counts can be provided for any qsim mode. The argument networkModes is used to
 #' select and filter the columns.
 #'
@@ -107,30 +107,30 @@ readLinkStats <- function(runId, file, sampleSize = 0.25){
 }
 
 
-#' Load Counts, a limited number of Linkstats and Network links as joined tibble into memory
+#' Join counts and linkstats to the network, creating a tibble into memory
 #'
-#'Function to join counts, network links and several matsim link stats. Data can be aggregated
-#'and filtered by time or network mode.
+#'Function to join counts, linkstats and network links. Data can be aggregated
+#'and filtered by time or mode.
 #'
 #'
 #'@param counts Tibble with counts data
 #'
 #'@param network Tibble with network nodes and links
 #'
-#'@param linkStats List with link stats tibbles
+#'@param linkStats List with linkstats tibbles
 #'
-#'@param networkModes a vector with network modes, which are needed for analysis
+#'@param networkModes Vector with network modes that will be analyzed, default is "car".
 #'
-#'@param aggr_to Determinates if data should be aggregated to hour values or DTV, can either be "day" or "hour"
+#'@param aggr_to Determines if data should be aggregated into hourly bins or as daily traffic volume, can either be "day" or "hour"
 #'
-#'@param earliest Lower limit to filter link stats by time, default is 0
+#'@param earliest Integer. Lower limit to filter link stats by time, default = 0.
 #'
-#'@param latest Upper limit to filter link stats by time, default is 86400 (midnight)
-#'
-#'@return Long-format tibble with MATSim link id as key ("loc_id"), traffic volume from MATSim runs and link type
+#'@param latest Integer. Upper limit to filter link stats by time, default = 86400 (midnight).
 #'
+#'@return Long-format tibble with MATSim link id as key ("loc_id"), traffic volumes from MATSim runs and link type
 #'
 #'@export
+
 mergeCountsAndLinks <- function(counts, network, linkStats, networkModes = c("car"), aggr_to = c("day", "hour"), earliest = 0, latest = 86400){
 
   if(!is.list(linkStats)){
@@ -242,7 +242,7 @@ mergeCountsAndLinks <- function(counts, network, linkStats, networkModes = c("ca
   join.long
 }
 
-#' Categorize DTV and calculate DTV distribution
+#' Categorize daily traffic volume (DTV) and calculate DTV for different link types.
 #'
 #' Takes a tibble from mergeCountsAndLinks. DTV is categorized into bins. Finally
 #' data is aggregated to calculate DTV distribution in each link type category,
@@ -252,13 +252,13 @@ mergeCountsAndLinks <- function(counts, network, linkStats, networkModes = c("ca
 #'
 #' @param joinedFrame A tibble from mergeCountsAndLinks
 #'
-#' @param from Lower limit for count bin
+#' @param from Integer. Lower limit for count bin, default = 0.
 #'
-#' @param to Upper limit for count bins
+#' @param to Integer. Upper limit for count bins, default = 40000.
 #'
-#' @param by Size of each count bin
+#' @param by Integer. Size of each count bin, default = 5000.
 #'
-#' @return A long-format tibble which contains share of DTV Categories
+#' @return A long-format tibble which contains share of DTV for link types
 #'
 #' @export
 processLinkStatsDtvDistribution <- function(joinedFrame, from = 0, to = 40000, by = 5000){
@@ -311,17 +311,16 @@ processLinkStatsDtvDistribution <- function(joinedFrame, from = 0, to = 40000, b
 #' Categorize DTV deviation and aggregate data
 #'
 #' Takes a tibble from mergeCountsAndLinks.
-#' Deviation between count volumes and Linkstats is calculated
-#' (e.g. deviation of 1.2 means 20 percent more DTV in MATSim than in counts) and
-#' categorized.
+#' Deviation between count volumes and Linkstats is calculated and
+#' categorized (i.e. deviation of 1.2 means 20 percent more DTV in MATSim than in counts).
 #' If parameter 'aggr' is set to TRUE, data will be aggregated for each run and link type.
 #' Can be used to visualize model quality by link type and to compare several runs.
 #'
-#' Estimation quality is determinated by the 'cut' function, limits for the label
-#' 'exact' can be adjusted by tuning the parameter 'll' and 'ul'
+#' Estimation quality is determined by the 'cut' function, limits for the label
+#' 'exact' can be adjusted by tuning the parameters 'll' (lower limit) and 'ul' (upper limit)
 #'
 #' @param joinedFrame A tibble from mergeCountsAndLinks
-#' @param aggr Boolean, if categorized data should returned aggregated
+#' @param aggr Boolean, if categorized data should returned aggregated, default is TRUE.
 #' @param ll Formula to calculate lower limit of the quality label 'exact', default = 0.8*x - 200
 #' @param ul Formula to calculate lower limit of the quality label 'exact', default = 1.2*x + 200
 #'
@@ -341,8 +340,8 @@ processDtvEstimationQuality <- function(joinedFrame, aggr = TRUE, ll =  ~ x *0.8
   join.1 <- joinedFrame %>%
     mutate(ll = ifelse(ll < 0, 0, ll),
            estimation = ifelse(volume < ll, "less",
-                            ifelse(volume > ul, "more",
-                                   "exact")),
+                               ifelse(volume > ul, "more",
+                                      "exact")),
            estimation = factor(estimation, levels = c("less", "exact", "more")))
 
   if(aggr){
@@ -361,12 +360,12 @@ processDtvEstimationQuality <- function(joinedFrame, aggr = TRUE, ll =  ~ x *0.8
 #' Creates a Via-Style scatterplot for each run
 #'
 #' Takes a tibble from mergeCountsAndLinks.
-#' A scatterplot with counts on the x axis and matsim dtv on the y axis is created and colored
+#' A scatterplot with counts on the x axis and MATSim dtv on the y axis is created and colored
 #' by the road type.
-#' Lower and upper Limits define the section which is considered as an 'exact' estimation. Limits
+#' Lower and upper limits define the section which is considered an 'exact' estimation. Limits
 #' are defined by custom formulas.
 #'
-#' The function calls the matsim-r function processDtvEstimationQuality which is handeling the limits.
+#' The function calls the matsim-r function processDtvEstimationQuality which is handling the limits.
 #'
 #' @param joinedFrame A tibble from mergeCountsAndLinks
 #' @param ll Formula to calculate lower limit of the quality label 'exact', default = 0.8*x - 200