CRAFTYOutput

Scripts to analyse output from the CRAFTY Brazil ABM simulation model

The individual analysis scripts described below produce numerous model output analysis files. Many scripts have dependencies on files produced by other scripts. The number prefixing a filename (e.g. 1_summarise...) indicates the order in which files should be excuted.

To ease use however, the A_allOutputAnalysis.r script combines several of these scripts (2,3,4,7a,7b,8) into a single script in the correct order. Note that this combined file assumes output from a model run in which CRAFTY and STELLA are linked. When STELLA is not used, the final section of the script will fail (i.e. code from 8_analyseProduction.r); in this case 8a_analyseProduction_solo.r on completion of the combined script.

To use any of the files for analysing output from a given model run, the following values must be set (all as character strings):

• scenario: the scenario CRAFTY parameter (set in Scenario.xml) used to name the run (e.g. "Testing_2018-08-12")
• runID: the CRAFTY ID of current run (runNumber-randomSeed) (e.g. "0-0")
• cl: the land cover classification used in model data (from MapBiomas data; e.g. "PastureB")

Other items that can be specified include:

• yrs: a list of integers indicating the years for which the model was run (e.g. seq(2000, 2015, 1))
• calib_yrs: a list of integers indicating the years calibration analysis; ususally this will be a selection of yrs (e.g. c(2005, 2010, 2015))
• sim_yrs: a list of integers indicating the years to include in any video made (will usually be identical to yrs above)
• fig_yrs: a list of integers indicating the years for which figures should be output (often the same as calib_yrs)
• pdfprint: a boolean indicating whether pdf files should be output (usually this should be TRUE
• video_output: a boolean indicating whether video files should be made (can be slow so often set to FALSE)

The data_dir variable can also be changed, but this is currently set to assume output scenario directory is copied to CRAFTY_testing/CRAFTYOutput/Data/. Files assumed to be in this directoy are the CRAFTY cell values csv files for each year (e.g. Testing_2018-08-12-0-0-Cell-2001.csv) and the region.csv that was used to initialise the run. Other files assumed to exist are:

• sim10_BRmunis_latlon_5km_2018-04-27.asc (currently) in a directory named ObservedLCmaps (in the Data directory
• summary tables (produced by 1_summarise_LCmaps_5LCs.r) in a directory named SummaryTables

Individual analysis scripts

• 1_summarise_LCmaps_5LCs.r: needed only once to produce SummaryTables, but prior to other CRAFTYOutput scripts. Takes the MapBiomas input maps (currently version 2.3) and converts them to tables of summary data by municipality
• 2_CRAFTYsummary_5LCs.r: takes CRAFTY cell values csv files for each year and combines them with region.csv to summarise data to municipality level. Two summary files are produced:

• summary of Services and Capitals (ending CRAFTYmunisServCap.csv)
• summary of Land Cover (ending CRAFTYmunisLC.csv)

• 3_LCcalibrationAnalysis_5LCs.r: comparison analysis of modelled vs observed land cover; reads a file created by 2_CRAFTYsummary_5LCs.r and creates a pdf file (name ending _LCcomparisonAnalysis.pdf)
• 4_LCcalibrationMaps_5LCs.r: creates comparison analysis maps of modelled vs observed land cover; reads a file created by 2_CRAFTYsummary_5LCs.r and creates a pdf file (name ending _LCcomparisonMaps.pdf)
• 5_LCcalibrationShiny_5LCs.r: creates interactive Shiny maps for comparison of modelled vs observed land cover (possibly currently incomplete, needs checking)
• 6_LCcalibrationAnalysis_singleMuni_5LCs.r: analysis as for 3_LCcalibrationAnalysis_5LCs.r but for a single municipality (specified by target_muni variable)
• 7a_outputRasterAnalysis.r: produces figures (images) and (optionally) videos of land cover, Services and Capitals for raster (cell-by-cell) data. Also outputs comparison matrices for pairs of model output raster maps (as .pdf files). Requires files from multiple other individual analysis scripts.
• 7b_outputVectorMaps.r produces figures (images) and (optionally) videos of land cover, Services and Capitals for vector (Municipality). Requires files from multiple other individual analysis scripts.
• 8_analyseProduction.r: analyses production data, reading values from FromMaestro####.csv files from StellaData directory
• 8a_analyseProduction_solo.r: version of 8_analyseProduction.r script but using Services calculated from the CRAFTY cell values csv file. Used with data from runs that do not use STELLA (i.e. no FromMaestro####.csv files created)