In dymium-org/dymiumModules: A utility package for `dymium` module management

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
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knitr::opts_knit$set(root.dir = normalizePath(rprojroot::find_rstudio_root_file()))
library(dymiumCore)

MATSim module documentation

This module provides the following functionalities:

• runControl.R: run MATSim using a MATSim config file.
• createVISTADemand.R: assign daily activity patterns to a population and write it as a MATSim plan_v4 file.
• helpers.R: reader and edit matsim's config, create a MATSim network_v2 file from shpfiles, assign random geographical locations to activities.

Release note

Version 0.1.2

• runControler has new requirements in model. It can now set the path to a matsim.jar file and the maximum amount of memory for MATSim to use using matsim_path_to_jar and matsim_max_memory, respectively. matsim_config_params accepts a named list which will be used to modify a given matsim_config. See its documentation section for more details.

Version 0.1.1

• add use_rJava argument to runControler this allows the event to be configured how it should run MATSim's controler.

Version 0.1.0

• Allows basic calls to MATSim APIs from R.
• Adds functions for preparing MATSim inputs.

Requiements

R packages

• R CRAN packages: data.table, modules, StatMatch, checkmate, here, rJava, xml2, sf, glue, furrr, fs
• R github packages: dymium-org/dymiumCore,

MATSim

• You will need to install Java. It is recommended to use Java 8 to run MATSim (see related issues here: https://github.com/matsim-org/matsim-code-examples/issues/176, https://github.com/matsim-org/matsim-code-examples/issues/16).

• The matsim module doesn't shipped with a MATSim java executable file that is required to make this module works. The user must download MATSim from MATSim website. I recommend to use the latest stable release (version 0.10.0 as of r Sys.Date()) with this module. Once, you have downloaded MATSim you must extract the matsim zip file into your matsim module folder (usually under the root folder of your active R project modules/matsim). Then rename the extracted file as 'matsim'. Then you are good to go! :)

Events

Run controler

Description

Run MATSim using a MATSim config file.

dymium always makes a copy of the original MATSim config file and saves the copy in the same location with a suffix -dymium, incase it needs to modify some settings. If you are using dymium's scenario, your matsim output will be automatically saved inside the outputs folder of your active scenario.

Usage

event_matsim_runcontroler <- modules::use(here::here("modules/matsim/runControler.R"))

event_matsim_runcontroler

Parameters

• world: a World object.
• model: a named list that contains path to a MATSim config file.
• matsim_config: a path to a matsim config file
• matsim_config_params: a named list that is used to modify the given matsim_config. From the example below, controler is a module name and firstIteration and lastIteration are param names that belong to the controler module. We set firstIteration to 0 and lastIteration to 10. To learn more about what parameters can be set please see a MATSim documentation.
• matsim_path_to_jar: (optional, with a default value of "here::here('modules/matsim/matsim/matsim-0.10.1.jar')") path to a MATSim.jar file.
• matsim_max_memory: (optional, with a default value of "-Xmx1024m" which is 1GB) max amount of RAM for MATSim to use.

model <- list(
  matsim_config = "path/to/config.xml",
  matsim_config_params = list(
    controler = list(
      firstIteration = 0,
      lastIteration = 10
  )),
  matsim_path_to_jar = "path/to/matsim.jar",
  matsim_max_memory = "-Xmx1024m" # 1024mbs or 1gb which is also the default value.
)

• target: NULL
• time_steps: a integer vector that contains the time steps in which this event should be run.
• use_rJava: a logical value default as TRUE, this determine the method that the function uses to run MATSim. By default, the function will attempt to use rJava to start MATSim's controler. If FALSE, then it will call MATSim using a commandline command. Note that, calling MATSim from the commandline only possible on a UNIX machine if you are running this through a Windows machine then you must use rJava to call MATSim. An error will be raised if this is set to FALSE on a Windows machine.

Example

The following example runs an example MATSim scenario for five iterations.

event_matsim_runcontroler <-
  modules::use(here::here('modules/matsim/runControler.R'))

create_toy_world()

for (i in 1:1) {
  world$start_iter(time_step = i, unit = 'year') %>%
    event_matsim_runcontroler$run(model = list(
      matsim_config = here::here("modules/matsim/matsim/examples/equil/config.xml"),
      matsim_config_params = list(controler = list(
        firstIteration = 0,
        lastIteration = 5
      ))
    ))
}

Create a MATSim plan

Description

This event function assigns daily travel activity patterns to Dymium individuals using a statistical matching technique. It uses a travel survey in this case the 2009 VISTA household travel survey of Victoria state, Australia (link). It then parses the fused travel activities to an xml file that follows the format of MATSim's population_V6 and save it to your matsim input folder.

Note

The implementation of this function is very specific to the 2009 VISTA data hence it's most likely not going to work if you replace the vista data with other data. However, this can be used as a template for implementing other travel surveys or can be replaced this step entirely with a proper activity-based model if available.

Usage

event_matsim_createVISTADemand <- modules::use('modules/matsim/createVISTADemand.R')

event_matsim_createVISTADemand

Parameters

• world: a World object.
• model: a named list.
• vista_persons: a data.frame that contains a vista person file
• vista_trips: a data.frame that contains a vista trip file

model <- list(vista_persons = data.frame(),
              vista_trips = data.frame())

• target: NULL
• time_steps: a integer vector that contains the time steps in which this event should be run.

Helper functions

• MatsimConfig: an R6 class that can modify a MATSim config file
• create_population_v6: create a population xml file that complies with MATSim's Population V6.
• assign_location: assign a random locations within a shapefile
• shp2xml: convert a network shapfile to a MATSim compatible xml network file

See the helpers.R script for more details.

Additionally, there are some functions for binding MATSim's histogram plots into a single animated histogram by iteration number in plots.R

Known issues

MATSim

The MATSim melbourne scenario has the following unresolved issues

• strategy setting 'SubtourModeChoice' doesn't work. If this setting is used, the error will be raised about modeParam 'pt' and 'walk' not being valid.

MATSim works best with Java 8. If you are running newer versions of Java there is a high chance that some dependencies might be missing one of which is the JAXB libraries as discussed here.

Setup Java

(2020-01-12) Java JDK 11.0.1 must be installed in order for the rJava pacakge to work. This issue has been discussed here and here. This is only required if you would like to run the MATSim module using rJava as implemented in .run_matsim_rjava function inside runControler.R. Otherwise, you can use .run_matsim_system() which basically invoke your matsim.jar from the OS command, this option requires you to make sure that Java8+ is installed and is callable using the OS command.

To install the required version of Java click on this link and download Java SE Development Kit 11.0.1 that works on your machine.

You will need to run R CMD javareconf on terminal to make sure R detects your new java installation. Make sure that all R sessions are close before running this command.

rJava failed to load! Ughhhhh!

If you get the following error..

> library(rJava)
# Error: package or namespace load failed for 'rJava':
#  .onLoad failed in loadNamespace() for 'rJava', details:
#   call: dyn.load(file, DLLpath = DLLpath, ...)
#   error: unable to load shared object '/Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so':
#   dlopen(/Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
#   Referenced from: /Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so
#   Reason: image not found

It may be a good idea to run the following command in your Terminal.

R CMD javareconf

Then quit RStudio and launch it again to try library(rJava). If the error still persist then Google search is your best friend!

dymium-org/dymiumModules documentation built on May 23, 2020, 10:30 a.m.