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Changelog

Source: NEWS.md

arrR 2.0.0

  • Split arrR into several sup-packages

arrR 1.5.2

  • Update rcpp_get_adjacencies

arrR 1.5.1

  • Fix bug in detritus pool consumption if pool was very low
  • Remove codemeta.json

arrR 1.5

  • Remove terra dependency
  • Remove RcppDist dependency

arrR 1.4.3

  • Allow to write results into a text file
  • Renamed get_stable_values to get_req_nutrients and changes to function
  • Renamed all *_var parameters to *_sd

arrR 1.4.2.1

arrR 1.4.2

  • Update to “behav” movement
  • Renamed pop_thres_reserves_lo/pop_thres_reserves_hi to pop_thres_reserves_mean/pop_thres_reserves_var
  • Using rcpp_rnorm() for random reserves threshold value

arrR 1.4.1

  • Move some pre-process code from R to Rcpp and use internal functions
  • Improve documentation

arrR 1.4

  • Use terra instead of raster
  • Rename nutr_input to nutrients_input
  • Rename nutrients_output to nutrients_loss
  • Rename detritus_output to detritus_loss
  • Run all seagrass/water column processes on same temporal scale
  • Better global variables handling

arrR 1.3.1

  • Changes to get_stable_values

arrR 1.3

  • Adding pkgdown homepage
  • Add detritus_output to rcpp_nutr_output
  • Streamlined code for summarize_mdlrn and plot.mdl_rn
  • Adding get_production and plot_production function
  • Adding reset argument to filter_mdlrn

arrR 1.2

  • Return pop_reserves_thres in final mdl_rn object
  • Fix bug in get_density if not max_i was selected as timestep
  • Return max_dist in run_simulation
  • Minor bugfix in run_simulation if fishpop with 0 indiv was provided

arrR 1.1

  • Fix bug in run_simulation and return of nutr_input
  • Export R and Rcpp interfaces of core functions
  • Renamed starting_values and parameters
  • Renamed extent to dimensions

arrR 1.0

  • Renamed rcpp_run_simulation to rcpp_sim_processes
  • Adding all needed references
  • Nested loop to diffuse values in rcpp_diffuse_values
  • Improvment of get_neighbors using modular division

arrR 0.5.1

  • Main simulation loop completely in Rcpp rcpp_run_simulation
  • Better tracking of fish consumption and excretion
  • Age counter in iterations
  • Better name for pop_reserves_* parameters
  • Renamed setup_seafloor_mdlrn to mdlrn_to_raster

arrR 0.5.0

  • Simpler allocation rule based on curves.
  • Adding new movement behaviors code based on reserve
  • Minor bugfixing and rename of many functions
  • New plot_threshold function.
  • Fix bug in movement and specify maximum movement distance based on 95% of distribution
  • Remove rlognorm again…lol
  • Remove extract_result again
  • Adding rcpp_shuffle
  • Remove reef_dist
  • Adding rcpp_update_coords
  • Adding rcpp_allocation_ratio and smoother sigmoid function
  • Adding get_stable_values function
  • Calling all rcpp_ functions directly if possible in run_simulation
  • Renamed detritus_ratio to seagrass_slough
  • Renamed detritus_fish_ratio to detritus_fish_decomp
  • Remove pop_want_reserves parameter. Fish always try to fill up reserves

arrR 0.4.0

  • Add simulate_input and simulate_output
  • Rename simulate_fishpop_growth to simulate_growth

arrR 0.3.1

  • Add rlognorm for better code structure

arrR 0.3.0

  • Update authors list
  • Re-implement movement of fish individuals in Rcpp mainly
  • Rename dead detritus to fish detritus (and all corresponding parameters)

arrR 0.2.9

  • Fix bug that not all starting values are included in mdl_rn object
  • Print progress each timestep because why not?
    • Change to GPL3 license
  • Fix bug in rcpp_calc_seagrass_growth.cpp with allocation rules

arrR 0.2.8

  • Add hexlogo
  • Add extract_result function and extract argument to run_simulation
  • Add bg_gamma and ag_gamma to parameters. Was hard-coded previously
  • Better checking if object is mdl_rn
  • Renamed master branch to main

arrR 0.2.7

  • Add default parameters and starting values as data
  • Add structure for vignettes
  • Use absolute iterations for burn-in
  • Add return_burnin argument to run_simulation

arrR 0.2.6

  • Renamed all pop_*grunt parameters to only pop*
    • Adding burn-in option to run_simulation
  • Track production, slough, nutrient uptake cumulative for each cell
  • summarize_mdlrn returns burn_in column

arrR 0.2.5

  • Renamed filter_result to filter_mdlrn
  • Slight changes to print.mdl_rn
  • Rename summarize_result to summarize_mdlrn and allow to select summary fun

arrR 0.2.4

  • Better memory usage by using mainly Rcpp for core functions
  • Removed pop_max_size and replace with pop_linf_grunt

arrR 0.2.3

  • Add GitHub actions
  • Resulting object contains parameters and starting values
  • get_limits can return limits over time period
  • plot.mdl_rn also takes limits if summarize = TRUE for seafloor

arrR 0.2.2

  • Better plotting labels
  • Renamed parameters$detritus_decomposition to parameter$detritus_mineralization

arrR 0.2.1

  • Reworked seagrass growth
  • Rename package to arrR
  • Add pkgdown homepage

arrR 0.2.0

  • Speed and RAM improvements of many function
  • Including Rcpp

arrR 0.1.0

  • First re-implementation of model code