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Changes
Lyndon Estes
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v2.0.1

Improvements

  • Added (back) ability to select a subset of crops, based on target values passed into targets, via tradeoff_mod, tradeoff_batch, and pareto. Switch is made in input_handler.
  • Reordered arguments in tradeoff_mod.
  • Added save for batch parameters to tradeoff_batch.
  • Added more plot flexibility (N crops plotted, colors) to imp_plot.
  • Added heat to create raster showing frequency of conversions.
  • tradeoff_batch passes out the bcode now
  • pareto uses bcode passed from tradeoff_batch, and saves optitab to batch directory.
  • tradeoff_batch impact tables now come out as data.frames from both todisk TRUE and FALSE cases. Changes to batch_param made to accomodate (table rather than list). From the todisk=FALSE case, the output conversion tables are served as a list that is the second element of the output list.
  • Added imp_sorter function for selecting subsets of conversion maps and ordering them to correctly match names of selected impact tables.
  • Added new measures to impact for calculating total travel hours (impact_mod2), and total biodiversity cost (impact_mod3).

Bugs

  • Removed hard-coded input_key ("ZA") in tradeoff_batch call to tradeoff_mod.
  • Fixed .tif append to impacts_tab.rda output from tradeoff_batch.
  • Fixed tradeoff_batch so that impacts_tab.rda is a data.frame not a list.
  • Conversion tables from tradeoff_batch were being re-ordered because of random numbers/time-stamp structure in run_code. The run/batch/name is simplified and fixed, with corresponding changes to tradeoff_batch, tradeoff_mod, pareto.

v2.0

Summary of improvements

  1. Current production becomes non-spatial, adjusted with coefficient

    • Notes:

      • currprod.rda is main file to read

    • Status: Done

  2. Fraction available cropland needs to be incorporated

    • Status:
      • Done in convert
      • Done in impacts

  3. New biodiversity impact metric incorporated

    • Status: Mostly - still need to change the biodiversity metric so that impact can be weighted evenly on protected weighted rarity and intactness

Changes

  • fetch_inputs

    • including altering carbon-names.rda, dumping cropnames.rda entirely
    • Updated fetch_inputs to read in convertible fraction data.table, and to find spatial metadata.
    • Put in logic to check for equality of row number in input data.tables, and to call a halt if there are NAs in any of the inputs.
    • removed datasets in R data folder, because they should be installed as part of library, and therefore not called with a specific path by this function. To allow users to generate their own data.
      • All inputs now live under external/data/[ID], and are read in directly from there. These changes are designed to separate model from R package structure.

  • input_handler

    • yield_mod
      • Name changed from yield_mod_dt
      • fixed to remove pp_curr from list of modified rasters
      • noticed potential standardization issue
      • renamed to just yield_mod
      • moved yield standardization to input_handler
    • added yield standardization here
    • switched off one potential yield modification option
    • all data.tables, including mask, reduced down to location with >0 farmable areas.
    • key set on index of reduced mask
    • cost/yield is performed on those areas only
    • rearranged order of inputs to properly deal with recyled input list
    • disabled yield modification function for now, on the assumption that this becomes an offline process for the time being. If ybeta_update is set to 1, model will halt.

  • targets

    • name changed from targets_dt
    • replaced scheme for modifying current production with simple modification vector, which draws on vector of current production, with argument named currprodmod.
    • yield_mod argument removed.

  • constraints

    • name changed from contraints_dt
    • allocation logic checked
    • j loop in inner allocation loop replaced with data.table-centric code

  • convert

    • Name changed from convert_dt
    • Replaced j for loop with data.table syntax

  • impact

    • Name changed from impact_dt
    • Modularized - impact metrics now calculated in sub-modules, except for total area converted.
      • Revised metrics for cost - mean cost and cost/yield calculated also - these will be more appropriate than total cost
      • New metrics for biodiversity, based on rarity. Several flavors to choose from - mean vegetation type rarity of converted pixels (0-1); rarity + protectedness (priority, 0 - 1); average intactness (0 - 1); mean of intactness and priority (the measure currently used by constraints); ha of forest reserves lost
      • Added additional biodiversityChanged biodiversity impact to be based on both intactness and rarity - i.e. run it on the cons prioritization layer.
    • Reduced number of input arguments to 2 (il and conv).

  • tradeoff_mod

    • Updated to incorporate changes to 4 primary sub-modules.

  • tradeoff_batch

    • Simplified (yield_mod disabled) and parallelized with foreach and doMC.
    • Output saving options altered. Conversion tables written out without xy coordinates, to save disk space and write times.
    • Outputs now write into external/output

  • pareto

    • Modularized
      • pareto_step function created, removing this portion of code from inside main function
      • batch_params combines parameter permutations into matrix used by pareto and tradeoff_batch
      • batch_stat calculates summarizes impact metrics of interest from a batch run, which are fed to non-dominator.
      • non-dominator Separate function created for code that removes non-dominated solutions from output table of impacts
      • Function engine is tradeoff_batch.
    • parameter returned with optimization table in output list