Monday, November 7, 2016

Read NetLogo BehaviorSpace data in R

I recently started to use the NetLogo, a platform for agent-based modelling. As I am a truly R lover, I miss the direct connection between importing the data produced from NetLogo BehaviorSpace to R platform to facilitate data analysis and plotting.

Even really helpful, I found R Marries NetLogo: Introduction to the RNetLogo Package (Jan C. Thiele, 2014, little too complicated for the beginners in R and NetLogo alone.

A complete beginners guide how to read and use NetLogo BehaviorSpace data in R

Firstly, we need to export a data in table output from NetLogo BehaviorSpace.

NetLogo BehviorSpace Run options spreadsheet table output

Sure, you can keep the Spreadsheet format as well, but in R, the Table output is more suitable.

First, have a look of the structure of the BehaviorSpace Table output data. Data consist of information about the executed NetLogo experiment and applied model (description....), and of the true table: consisted of table header (column names) and reporter values (data values). The columns represent reporters' values over simulation run.

  NetLogo BehaviorSpace final table ouput structure

Now, we are ready to read NetLogo BehaviorSpace Data in R.

Firstly, we need to identify the working directory,  where your NetLogo table is stored

      # set working directory 

Now, we need to load the table (read.table()), skip the "description data" part of table (thus skip first 6 rows), and read table correctly by defining the columns by sep and quote.

      # --------------------------------------------------------
      # import .csv files by names
      # skip the first columns but keep names of columns

      my.df<-read.table("Fire experiment-table.csv", 
                        header = T,   # set columns names true
                        sep = ",",    # define the separator between       columns
                        skip = 6,     # skip first 6 rows 
                        quote = "\"", # correct the column separator
                        fill = TRUE ) # add blank fields if rows           have unequal length

Check if table has been read correctly


Plot the data as boxplot

      boxplot(burned.trees ~ density, 
              data = my.df, 
              col = "lightgray",
              main = "",
              xlab = "density",
              ylab = "burned trees")
Tadaaa !!!