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Workshop (Monday 13th July 2015)

Combining computational methods and experimental data

The workshop will be led by Jon Yearsley and Dave Goodrich.

The venue will be Room ALO232 in Science North on the main UCD campus (see below).

The workshop will largely be a hands-on introduction to computer models and fitting relatively complex models to experimental data. We will largely work with the KINEROS2 runoff and erosion model as a specific example of a command line dynamical computer model. We will look at running this model and approaches of fitting this model to experimental data.

The skills learned during the day will be broadly applicable to many scenarios; KINEROS2 typifies many command line computer models and the model fitting procedures will be generic approaches.

You will need a laptop for the workshop.
Contact fesp5@ucd.ie if you will not be able to have a laptop with you.

You will also need to install some software (explained at the bottom of the page)

Venue

The workshop will be held in room ALE232 (Science Centre North, UCD campus). This room is not easy to find. We will meet at 09:15 outside the Moore auditorium of the main O'Brien Centre for Science building.

Workshop Schedule

DayTimeTopic
Monday
13th July
09:15 Meet in O'Brien Centre for Science outside Moore auditorium
09:30 Workshop Introduction (Room ALE 232 Science Centre North)
09:30-10:30 Introduction to uses and types of computer model
10:30 Coffee/Tea
11:30-12:30 Using a runoff and erosion computer model (KINEROS2)
12:30-13:30Lunch
13:30-15:00Fitting a model to data
15:00Coffee/Tea
15:30-17:00More fitting of a model to data
17:00Workshop Closing Comments

Software to install before the workshop

The workshop will be using KINEROS2 software for numerical simulations. This software will be available for download at the workshop.

To visualise and analyse the results from the KINEROS2 simulations we will use spreadsheets (e.g. Excel) and the R statistical software.

Please install two programs: R and RStudio

To install R

The homepage for downloading the latest R software is http://cran.r-project.org/. On 8th July 2015 the latest R software is version 3.2.1.

Below we provide shortcuts directly to the installer files for Windows, Mac and Linux operating systems. If the downloads are slow you can select your nearest mirror site from this list

R for Windows

The installer for the latest version of R for Windows can be downloaded from http://cran.r-project.org/bin/windows/base/. The latest version will runon Windows XP and later (including 64-bit versions of Windows).

R for Mac

The installer package for the latest version of R for Macs can be downloaded from http://cran.r-project.org/bin/macosx/. For Mac OS X 10.9 (Mavericks) and higher use the R-3.2.1.pkg link.

R for Linux

To install on a Linux machine go to http://cran.r-project.org/bin/linux/ and select your distribution of linux from the list. Installation instructions for each Linux ditribution can be found in a README file.

To install RStudio

Rstudio is a user interface for R that has a free open source version available for Windows, Mac and Linux operating systems.

To install RStudio go to https://www.rstudio.com/products/rstudio/download/ and select the installer for your operating system under the "Installers for Supported Platforms" section. To complete the installation, save and open the installer and follow the installer's instructions.

To install ggplot2 for R

To visualise the simulations in R we will use a graphics package called ggplot2.

There are two ways to install ggplot2.

Method using RStudio

Follow steps 1-4 (see image below)

  1. Open RStudio, click on the Packages tab in the bottom right panel
  2. click on the install icon
  3. type "ggplot2" in the dialogue box underneath "Packages (separate multiple with space or comma)"
  4. click the install button

Method using just R

Open R and in the command window type

install.packages("ggplot2")